Thermo

Compound Discoverer
User Guide for LC Studies
Software Version 3.3 SP2

B51001313 Revision A March 2023

© 2023 Thermo Fisher Scientific Inc. All rights reserved.

Compound Discoverer, Exactive, Foundation, FreeStyle, Mass Frontier, Metabolika, mzCloud, mzVault,
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Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
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The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.

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Release history: Revision A March 2023

Software version: Compound Discoverer 3.3.2

For Research Use Only. Not for use in diagnostic procedures.

 C

Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20
Access the documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
View the user guides and tutorials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Download the user documentation for any Thermo Scientific product . . . . . 22
System requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Check the computer specifications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Check the format setting for region and language . . . . . . . . . . . . . . . . . . . . . 25
Installation instructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Install the Compound Discoverer application . . . . . . . . . . . . . . . . . . . . . . . . 26
Install the mzCloud offline libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Install the mzVault 2.3 SP1 application. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
NIST libraries for GC EI Orbitrap data . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
NIST 2020 MSMS library for LC/MS/MS data . . . . . . . . . . . . . . . . . . . . . . 29
Special notices. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Create and submit a bug report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Contact us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Chapter 1 Introduction to Compound Discoverer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31

New features and enhancements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Enhancements in the Compound Discoverer 3.3 SP2 release . . . . . . . . . . . . 32
Enhancements in the Compound Discoverer 3.3 SP1 release . . . . . . . . . . . . 33
Enhancements common to both study types in the Compound
Discoverer SP1 release . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Enhancements for LC studies only in the Compound Discoverer SP1
release. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
New features in Compound Discoverer 3.3 for LC studies . . . . . . . . . . . . . . 34
Enhancements in Compound Discoverer 3.3 . . . . . . . . . . . . . . . . . . . . . . . . 36
Obsolete (n/a) Detect Compounds node in legacy processing workflows . . . . . 37
Terminology used in the Compound Discoverer application. . . . . . . . . . . . . . . 38
LC studies overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Start the Compound Discoverer application . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

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The Compound Discoverer window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Compound Discoverer menu bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Compound Discoverer toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Change the size of the toolbar icons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Manage the recently used files lists on the Start Page . . . . . . . . . . . . . . . . . . . 53
Auto-Hide the Start Page, the Chromatograms view, and the Mass
Spectrum view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Show, hide, and rearrange the tabbed pages of the application. . . . . . . . . . . . . . 54
Tabbed pages list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Open a hidden tabbed page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Tab groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Shortcut menu commands that control the layout of the tabbed pages . . . . . 57
Rearrange the tabbed pages and graphical views. . . . . . . . . . . . . . . . . . . . . . . 58
Supported file formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

Chapter 2 Functional description of the data-processing features . . . . . . . . . . . . . . . . . . . .62

Chromatographic peak detection, alignment, and identification for LC
Studies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Chromatographic peak rating filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Peak quality factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
FWHM2Base quality factor. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Jaggedness quality factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Modality quality factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Zig-Zag Quality Factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Online compound databases and metabolism pathways. . . . . . . . . . . . . . . . . . . 70
Local spectral databases, mass lists, and metabolism pathways . . . . . . . . . . . . . . 71
Best scans for composition prediction and spectral matching. . . . . . . . . . . . . . . 71
Best MS1 scan for isotope pattern matching . . . . . . . . . . . . . . . . . . . . . . . . . 71
Best MS2 scan for fragments matching and spectral comparison . . . . . . . . . . 72
Using mzLogic to score candidates for unknown compounds . . . . . . . . . . . . . . 72
Running an untargeted analysis that includes the mzLogic node . . . . . . . . . . 73
Running an mzLogic analysis from the mzLogic Analysis view . . . . . . . . . . . 74
Confidence score for an mzCloud hit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Factors that affect the Confidence score. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
How to use the Confidence score . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
FISh scoring for proposed structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Mass defect types and visualization techniques . . . . . . . . . . . . . . . . . . . . . . . . . 79
Neutral loss detection and visualization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Using quality control samples to compensate for batch effects . . . . . . . . . . . . . . 84
Batch normalization for single sequence runs. . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Batch normalization for multiple sequence runs (LC studies) . . . . . . . . . . . . . . 85
Stable isotope labeling experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
PFAS identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
PFAS processing workflow template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Review the results of a PFAS analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

Thermo Scientific Compound Discoverer User Guide for LC Studies 4

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Methods for imputing values for missing chromatographic peaks across a

set of input files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Random Forest imputation method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Median + Small Value imputation method . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Gap filling method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96

Chapter 3 Create a new study and an analysis by using the wizard . . . . . . . . . . . . . . . . . . .97
Available sample types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Directory structure for Compound Discoverer studies. . . . . . . . . . . . . . . . . . . . 98
Create a study template file that contains all the study information . . . . . . . . . 100
Manually create a template that includes all the study information . . . . . . . 100
Edit a spreadsheet for use as a study template . . . . . . . . . . . . . . . . . . . . . . . 101
Start the New Study and Analysis Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Define the study type, name the study, and optionally select a study
template and a processing workflow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Select the study type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Name the new study, select the top-level studies folder, and optionally
select a study template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Select a processing workflow for the analysis . . . . . . . . . . . . . . . . . . . . . . . . 106
Add input files to the new study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Characterize the new input files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Select the delimiters for parsing the file names. . . . . . . . . . . . . . . . . . . . . . . 111
Add or edit the study factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Add categorical study factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Add numeric study factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Add biological replicate study factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Delete study factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Duplicate study factors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Edit study factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Automatically assign the study factor values. . . . . . . . . . . . . . . . . . . . . . . . . 116
Manually select the study factor values . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Reset the sample assignments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Select the sample types. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Extract study factor values from the file names of the input files . . . . . . . . . . . 120
Set up the sample groups and ratios for a new analysis. . . . . . . . . . . . . . . . . . . 127
Set up the sample groups for an analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
Select the study variables for the sample groups . . . . . . . . . . . . . . . . . . . . 128
Review the generated sample groups and fix any assignment errors. . . . . . 129
Change the hierarchy of the study variables . . . . . . . . . . . . . . . . . . . . . . . 130
Change the sort order of the study variables . . . . . . . . . . . . . . . . . . . . . . . 131
Set up the group ratios. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
Set up the group ratios individually . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Set up the group ratios by using the bulk ratio generator . . . . . . . . . . . . . 133
Prepare to submit the analysis to the job queue . . . . . . . . . . . . . . . . . . . . . . . . 135

Thermo Scientific Compound Discoverer User Guide for LC Studies 5

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Chapter 4 Set up, run, and reprocess analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .136

Set up a new analysis from within an existing study. . . . . . . . . . . . . . . . . . . . . 136
Start a new analysis from within an existing study . . . . . . . . . . . . . . . . . . . . 137
Select a workflow template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Customize the processing workflow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Select the input files for the new analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
Edit the file name for the result file to be generated by the analysis . . . . . . . 141
Select the study variables and set up the group ratios for a
comparison analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
Troubleshoot common analysis errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
Submit an analysis to the job queue and fix any validation issues. . . . . . . . . . . 144
Submit an analysis to the job queue. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Common validation issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Control the Job Queue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Open the Job Queue page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Cancel a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Promote a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
Remove completed or failed jobs from the Job Queue . . . . . . . . . . . . . . . . . 148
Refresh the Job Queue list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
Open a result file from the Job Queue page. . . . . . . . . . . . . . . . . . . . . . . . . 148
Display verbose messages on the Job Queue page . . . . . . . . . . . . . . . . . . . . 148
View the processing steps for a job. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
Filter the Job Queue list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
Job Queue page parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
Review or reprocess an analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Analysis Results page parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Review an analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Reprocess an analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
Reprocess a legacy analysis result from an untargeted analysis . . . . . . . . . . . 156
Analysis view parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
Set up individual isotope patterns by using the Isotope Ratio
Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
Open the Isotope Ratio Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
Define an isotope pattern from an elemental composition . . . . . . . . . . . . . . 160
Copy an elemental composition from the Expected Compounds library . . . 161
Set up a custom isotope pattern . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
Export a mass spectrum from a raw file to the Clipboard. . . . . . . . . . . . . . . 162
Isotope Ratio Editor parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Create an isotope patterns list by using the Pattern List Editor . . . . . . . . . . . . 166
Extract analog and PDA traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
Extract analog traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
Extract PDA traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169

Thermo Scientific Compound Discoverer User Guide for LC Studies 6

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Chapter 5 Edit existing studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .170

Study files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
Open an existing study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Study page commands and tabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Edit the study description and the study factors. . . . . . . . . . . . . . . . . . . . . . . . 174
Add input files to an existing study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
Remove input files or update their location . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
Display the location of the input files for a study. . . . . . . . . . . . . . . . . . . . . 177
Remove input files from a study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
Resolve the location of the input files in a study . . . . . . . . . . . . . . . . . . . . . 178
Input Files page parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
Edit the sample type and study factor values . . . . . . . . . . . . . . . . . . . . . . . . . . 182
Edit the sample identifier on the Samples page . . . . . . . . . . . . . . . . . . . . . . 182
Edit the sample types on the Samples page . . . . . . . . . . . . . . . . . . . . . . . . . 183
Edit the study factor values on the Samples page . . . . . . . . . . . . . . . . . . . . . 183
View the file information on the Samples page . . . . . . . . . . . . . . . . . . . . . . 183
Samples page parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
Save the study file if you turned off the auto-save feature. . . . . . . . . . . . . . . . . 185

Chapter 6 Create and edit processing workflows. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .186

Processing workflow templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Workflows page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Open the Workflows page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Workflows page command bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
Workflows page shortcut menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
Edit an existing processing workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Fix a workflow node that has a caution symbol . . . . . . . . . . . . . . . . . . . . . . 191
Fix a workflow node that has an exclamation mark . . . . . . . . . . . . . . . . . . . 192
Add a workflow node to a processing workflow . . . . . . . . . . . . . . . . . . . . . . 193
Delete a workflow node from a processing workflow . . . . . . . . . . . . . . . . . . 193
Edit the parameter settings for a workflow node . . . . . . . . . . . . . . . . . . . . . 194
Defined processing workflow templates for LC studies . . . . . . . . . . . . . . . . . . 194
Targeted processing workflows for expected compounds . . . . . . . . . . . . . . . 194
Untargeted processing workflows for identifying unknown compounds . . . 203
Nomenclature for the provided processing workflow templates . . . . . . . . . . 208
Defined processing workflow templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210
Create a completely new processing workflow for LC studies . . . . . . . . . . . . . 212
Connect the workflow nodes for an LC study . . . . . . . . . . . . . . . . . . . . . . . . . 216
Manually connect the workflow nodes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
Peak area refinement node connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
Input and output nodes for the workflow nodes . . . . . . . . . . . . . . . . . . . . . 220
Save a custom processing workflow as a template. . . . . . . . . . . . . . . . . . . . . . . 224

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Chapter 7 Workflow nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .225

Input and Output nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226
Export Spectra node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226
Input Files node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
Spectrum Processing nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
Align Retention Times node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228
Align Retention Times (ChromAlign) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
Filter By Mass Defect node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
Filter By Scan Event node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
Filter Centroids node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
Select Spectra node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
Trace Creation nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
Create Analog Trace node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246
Create FISh Trace node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248
Create Mass Trace node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250
Create Pattern Trace node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
Expected Compounds nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
FISh Scoring node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
Find Expected Compounds node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
Find Expected Compounds (Legacy) node . . . . . . . . . . . . . . . . . . . . . . . . . 258
Generate Expected Compounds node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
Group Expected Compounds node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266
Merge Features node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269
Compound Detection nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269
Analyze Labeled Compounds node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
Detect Compounds (Legacy) node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
Detect Compounds node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276
Fill Gaps node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
Group Compounds node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 282
Peak Area Refinement nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
Apply Missing Value Imputation node . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
Apply QC Correction node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286
Apply SERRF QC Correction node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288
Mark Background Compounds node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
Normalize Areas node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 292
Scale Areas node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 293
Compound Identification nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 294
Assign Compound Annotations node (LC studies) . . . . . . . . . . . . . . . . . . . 295
Predict Compositions node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297
Search ChemSpider node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301
Search Mass Lists node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 302
Search mzCloud node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 304
Search mzVault node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309

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Pathway Mapping nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313

Map to BioCyc Pathways node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313
Map to KEGG Pathways node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 314
Map to Metabolika Pathways node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315
Compound Scoring nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317
Apply Spectral Distance node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 318
Apply mzLogic node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 319
Calculate Mass Defect node. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 320
Compound Class Scoring node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321
Generate Molecular Networks node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322
Pattern Scoring node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 326
Search Neutral Losses node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327
Post-Processing nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327
Descriptive Statistics node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328
Differential Analysis node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328
Export Xcalibur Inclusion or Exclusion List node . . . . . . . . . . . . . . . . . . . . 330
Result Exporter node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331
Scripting Node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331

Chapter 8 Review the analysis results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .333

Open, close, and update result files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 334
Open result files created in the current version of the application . . . . . . . . 334
Open result files created in previous versions of the application. . . . . . . . . . 335
Update modes for legacy result files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336
Close a result file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
Factory default layout for a result page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
Modify the result page layout for ease of use . . . . . . . . . . . . . . . . . . . . . . . . . . 339
Float a result page view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339
Enlarge a result page view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340
Use the collapsible pane options for filtering, grouping, coloring, and
discriminating by . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340
Filter the result data by the study variable values . . . . . . . . . . . . . . . . . . . 343
Filter the result data by input file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343
Group the result data by the study variables or by individual files. . . . . . . 343
Show or hide result tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 344
Custom color-coded tags for result table entries. . . . . . . . . . . . . . . . . . . . . . . . 345
Define custom tags by using the Custom Tags Editor . . . . . . . . . . . . . . . . . 345
Add or remove custom tags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 348
Filter a result table by the custom tags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350
Import or export custom tags. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352

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Save, restore, and manage layouts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353

Save the current layout of a result file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353
Reset the layout to the factory defaults. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353
Create a custom layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 354
Apply a layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 354
Manage the layouts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 355
Edit compound annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 355
Add or delete proposed structures for a compound . . . . . . . . . . . . . . . . . . . . . 358
Add structure proposals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 358
Delete structure proposals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 358
Replace an annotation with a structure proposal . . . . . . . . . . . . . . . . . . . . . . . 359
Apply FISh scoring . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359
Apply FISh scoring by using a shortcut menu command . . . . . . . . . . . . . . . 359
Apply FISh Scoring from the Compound Annotation Editor dialog box . . . 360
Specify the FISh scoring parameter settings . . . . . . . . . . . . . . . . . . . . . . . . . 361
Filter the data for data reduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 362
Components of a result table filter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 363
Set up, apply, and save filter sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 364
Create a result filter with an AND logical conjunction . . . . . . . . . . . . . . . . 367
Create a result filter with an OR logical conjunction . . . . . . . . . . . . . . . . . . 368
Create a result filter with both of the logical conjunctions . . . . . . . . . . . . . . 368
Load a saved filter set. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 370
Result Filters view parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 370
View the result summaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371
Workflow summary. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 372
Processing Messages summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 372
Filter summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373
Study summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373
Grouping & Ratios summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373
Shortcut menu commands for the result tables . . . . . . . . . . . . . . . . . . . . . . . . 374
Export the tabular data in a result file to an external file . . . . . . . . . . . . . . . . . 379
Export the result table contents to a spreadsheet . . . . . . . . . . . . . . . . . . . . . 379
Export the result table contents to a text file . . . . . . . . . . . . . . . . . . . . . . . . 381
Export an Xcalibur inclusion or exclusion list from a compounds table . . . . . .
381
Export the contents of the Compounds table to TraceFinder . . . . . . . . . . . 385
Export spectral data to a new or existing mzVault library. . . . . . . . . . . . . . . . . 385
Add a compound to an existing mzVault library . . . . . . . . . . . . . . . . . . . . . 386
Create a new mzVault library. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 387
Export compounds to a new or existing mass list . . . . . . . . . . . . . . . . . . . . . . . 388
Export compounds from the Compounds table to a new mass list . . . . . . . 388
Export compounds from the Compounds table to an existing mass list . . . . 389
Copy or save graphical views for publication . . . . . . . . . . . . . . . . . . . . . . . . . . 390
Copy structures to the Clipboard for use in other applications . . . . . . . . . . . . 391

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Chapter 9 Graphical views for a result file. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .393

Chromatograms view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 394
View a chromatogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 394
Add a chromatogram plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 398
Overlay multiple chromatogram plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 399
Change the grouping in the collapsible pane of an opened result file . . . . . . 399
Hide the traces for a study variable value . . . . . . . . . . . . . . . . . . . . . . . . . . . 399
Update all the chromatogram plots simultaneously . . . . . . . . . . . . . . . . . . . 399
Manually integrate chromatographic peaks . . . . . . . . . . . . . . . . . . . . . . . . . 400
Chromatograms view shortcut menu commands . . . . . . . . . . . . . . . . . . . . . 401
Mass Spectrum view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 406
Display a mass spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 407
Change the zoom level of the Mass Spectrum view . . . . . . . . . . . . . . . . . . . 407
View annotated fragment structures for targeted compounds. . . . . . . . . . . . 408
View annotated fragment structures for untargeted compounds . . . . . . . . . 409
Create a mirror plot. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 410
Search the mzCloud database for a matching fragmentation spectrum. . . . . 410
Spectral tree pane of the Mass Spectrum view . . . . . . . . . . . . . . . . . . . . . . . 411
Isotope pattern matching for compounds with formulas. . . . . . . . . . . . . . . 412
Mass Spectrum view shortcut menu commands. . . . . . . . . . . . . . . . . . . . . . 414
Result Charts view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 416
Open the Result Charts view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 416
Use the copy, export, and zoom commands for the Result Charts
view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 417
Display and pin the Options Pane for the Result Charts view . . . . . . . . . . . 417
Histogram charts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 418
Bar charts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 423
Pie charts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 426
Scatter plots. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 430
Set up a scatter plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 430
Use a filter set to filter the scatter plot . . . . . . . . . . . . . . . . . . . . . . . . . . . 431
Customize the appearance of a scatter plot . . . . . . . . . . . . . . . . . . . . . . . . 431
Customization options for a scatter chart plot . . . . . . . . . . . . . . . . . . . . . 432
Scatter Chart page parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 433
Scatter Chart page shortcut menu commands. . . . . . . . . . . . . . . . . . . . . . 434
Trend Chart view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 435
Open the Trend Chart view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 437
Define the sample groups to compare . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 437
Compare the peak areas for a single compound by sample group. . . . . . . . . 438
Change the sort order of the defined groups . . . . . . . . . . . . . . . . . . . . . . . . 438
Compare the peak areas for multiple compounds by group . . . . . . . . . . . . . 439
Change the hierarchy of the variables used for grouping . . . . . . . . . . . . . . . 440
Show the error bars in a trendline chart . . . . . . . . . . . . . . . . . . . . . . . . . . . . 440
Trend Chart view parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 442
Isotopologues Distribution Chart view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 442

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Mass Defect Plot view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 445

Principal Component Analysis view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 446
Set up a principal component analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 447
Interpret the scores plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 448
Interpret the loadings plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 449
Work interactively with the loadings plot . . . . . . . . . . . . . . . . . . . . . . . . . . 450
Interpret the variance plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451
Principal Component Analysis view parameters. . . . . . . . . . . . . . . . . . . . . . 453
Descriptive Statistics view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 453
Differential Analysis view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457
Review the initial differential analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457
Change the analysis settings for a differential analysis . . . . . . . . . . . . . . . . . 458
Run a new differential analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 459
Differential Analysis view parameters and shortcut menu commands . . . . . 461
Partial Least Squares Discriminant Analysis view. . . . . . . . . . . . . . . . . . . . . . . 463
Identify a set of compounds to discriminate groups . . . . . . . . . . . . . . . . . . . 463
Partial Least Squares-Discriminant Analysis view parameters . . . . . . . . . . . . 465
KEGG Pathways view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 465
BioCyc Pathways view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 467
Metabolika Pathways view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 470
Retention Time Corrections view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 470
Compound Area Corrections view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 472
Hierarchical Clustering Analysis view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 476
Set up a hierarchical clustering analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 478
Work interactively with the heat map grid. . . . . . . . . . . . . . . . . . . . . . . . . . 479
Hierarchical Cluster Analysis view parameters . . . . . . . . . . . . . . . . . . . . . . . 480
mzLogic Analysis view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 484
Perform an mzLogic analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 484
Review the results of an mzLogic analysis . . . . . . . . . . . . . . . . . . . . . . . . . . 485
mzLogic Analysis view parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 485
FISh Scoring Queue view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 486

Chapter 10 Descriptive information for the result tables. . . . . . . . . . . . . . . . . . . . . . . . . . . . .488

Common result tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 488
Adducts table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 489
Chromatogram Peaks table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 489
File Alignments table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 491
FISh Trace Fragments table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 492
Input Files table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 493
Manual Peaks table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 494
Merged Features table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 494
Specialized Traces table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 497
Study Information table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 498
Structure Proposals table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 499

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Expected Compounds result tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 500

Expected Compounds table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 500
Expected Compounds per File table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 505
Expected Features per File table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 508
Expected Formulas table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 510
Related Structures table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 512
Transformations table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 513
Compound detection result tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 514
Compounds table (LC studies) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 514
Compounds per File table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 524
Features per File table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 525
Filled Gaps table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 527
Labeled Features table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 529
Labeled Compounds per File table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 530
Similar Compounds Related table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 531
Compound Identification result tables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 533
ChemSpider Results table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 533
Mass List Search Results table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 535
mzCloud Results table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 537
mzCloud Results Hits table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 539
mzVault Results table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 540
mzVault Results Hits table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 542
Predicted Compositions table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 542
Pathway Mapping result tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 544
BioCyc Pathways table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 545
BioCyc Results table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 546
KEGG Pathways table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 547
Metabolika Pathways table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 549
Metabolika Results table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 550
Compound Scoring tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 551
Compound Class Matches table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 551
Matched Patterns table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 553
Neutral Losses table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 554
Statistical Methods table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 556
Differential analysis columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 556
Descriptive statistics columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 560
QC Correction columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 560
Annotations Source column in a compounds table . . . . . . . . . . . . . . . . . . . . . 561
Peak Rating columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 562
Peak quality factor (PQF) columns in the result tables. . . . . . . . . . . . . . . . . . . 563

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Chapter 11 Create and print reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .564

Reporting workflow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 564
Generate a report with an existing report template . . . . . . . . . . . . . . . . . . . . . 566
Report templates provided with the application. . . . . . . . . . . . . . . . . . . . . . 567
Preview and print a report by using an existing report template . . . . . . . . . . 568
Create new report templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 570
Create a new report template by using the Customize Report dialog
box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 570
Add, remove, or modify the color schemes for a report template . . . . . . . . . 574
Customize Report dialog box parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . 576
Edit existing report templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 578
Open a report template for editing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 579
Add a cover page to a report template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 580
Change the logo image for a report template . . . . . . . . . . . . . . . . . . . . . . . . 582
Change the format of the date and time field in a report template . . . . . . . . 582
Add items in the Section Reports pane to a report template. . . . . . . . . . . . . 584
Add a rich text box to a report template. . . . . . . . . . . . . . . . . . . . . . . . . . . . 584
Add main table columns to a report template . . . . . . . . . . . . . . . . . . . . . . . 585
Add data graphs to a report template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 586
Add mzCloud mirror plots to a report template. . . . . . . . . . . . . . . . . . . . . . 587
Add the mirror plots for each mzCloud hit for a compound to a
report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 587
Create a report template for the mzCloud Results table that includes
a mirror plot. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 589
Add related table columns to a report template . . . . . . . . . . . . . . . . . . . . . . 593
Edit the properties of subreport columns in a report template . . . . . . . . . . . 596
Move a subreport column to the main table of a report table. . . . . . . . . . . . 597
Modify the properties of a section report item . . . . . . . . . . . . . . . . . . . . . . . 599
Add page breaks to a report template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 600
Delete a pair of workspace sections on the report template page . . . . . . . . . 600
Resize the sections of a report template . . . . . . . . . . . . . . . . . . . . . . . . . . . . 600
Add, align, and transpose columns in a report template by using the
shortcut menu commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 601
Add a border to an item by using the Format Border command . . . . . . . . . 602
Reference information for the report template page . . . . . . . . . . . . . . . . . . . . . 603
Workspace sections and sizing bar on the report template page . . . . . . . . . . 604
Report template page toolbars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 606
Shortcut menu commands for the report template page. . . . . . . . . . . . . . . . 609
Section report items for a report template . . . . . . . . . . . . . . . . . . . . . . . . . . 610
Property settings for the sections and items in a report template . . . . . . . . . 613
Appearance properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 614
Behavior properties. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 617
Data properties. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 619
Design properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 622
Layout properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 622

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Miscellaneous properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 623

Open the property dialog box for a workspace section or a specific
report item . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 624
Select the paper type, print width, page orientation, and watermark for
a report template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 625
Open the property settings for a report template . . . . . . . . . . . . . . . . . . . . . 626
Add a watermark to a report template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 627
Change the print width of a report template . . . . . . . . . . . . . . . . . . . . . . . . 627
Change the page orientation of a report template . . . . . . . . . . . . . . . . . . . . 627
Change the paper size for the printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 628
Preview and print a report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 628
Preview a report for up to five rows in the main result table. . . . . . . . . . . . . 628
Preview a report for all the visible rows in the main result table . . . . . . . . . . 629
Open the Report Resolution page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 629
Find a text item in a resolved report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 629
Copy a portion of a report to the Clipboard . . . . . . . . . . . . . . . . . . . . . . . . 630
Export the contents of a report to an external document . . . . . . . . . . . . . . . 630
Print a report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631
Report preview toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631
Page thumbnails pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 633

Chapter 12 Manage the lists and libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .634

Lists & Libraries manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 635
Expected Compounds view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 635
Expected Compounds view parameter descriptions . . . . . . . . . . . . . . . . . . . 636
Delete, import, or export expected compounds . . . . . . . . . . . . . . . . . . . . . . 637
Add and edit expected compounds with the Compound Editor . . . . . . . . . 638
Generate an Xcalibur inclusion list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 640
Adducts view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 642
Adducts view parameter descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 643
Delete, import, and export adducts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 643
Add and edit adducts with the Adduct Editor . . . . . . . . . . . . . . . . . . . . . . . 644
Ion Definitions view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 645
Ion Definition view parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 646
Default list of ion definitions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 647
Delete an ion definition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 648
Import ion definitions from an XML file. . . . . . . . . . . . . . . . . . . . . . . . . . . 649
Export the ion definitions list to an XML File . . . . . . . . . . . . . . . . . . . . . . . 649
Add or edit ion definitions with the Ion Definition Editor . . . . . . . . . . . . . 649

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Transformations view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 651

Transformations view parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 652
Delete a transformation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 653
Import a list of transformations from an XML File . . . . . . . . . . . . . . . . . . . 654
Export the transformations list to an XML file . . . . . . . . . . . . . . . . . . . . . . 654
Add or edit transformations with the Transformation Editor. . . . . . . . . . . . 654
Transformation Editor dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 656
Neutral Losses view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 657
Add, edit, delete, import, or export neutral loss entries . . . . . . . . . . . . . . . . 657
Neutral Loss Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 659
Default neutral loss entries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 660
Mass Lists view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 661
Flowchart for creating and editing mass lists . . . . . . . . . . . . . . . . . . . . . . . . 663
Delete or replace mass list files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 665
Import a mass list from a CSV file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 665
Import a mass list from a massList file, an XML file, or an SDF file . . . . . . 666
Export a mass list file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 666
Mass Lists view parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 667
Create and edit mass list files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 668
Add and edit mass list compounds with the Compound Editor. . . . . . . . . . 671
Spectral Libraries view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 672
Metabolika Pathways view. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 674
Metabolika Pathways view parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 674
Delete, import, export, and replace Metabolika pathways . . . . . . . . . . . . . . 675
Edit new and existing Metabolika pathways. . . . . . . . . . . . . . . . . . . . . . . . . . . 676
Create a new Metabolika Pathway file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 676
Edit an existing Metabolika pathway . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 678
Modify the arrows in a Metabolika pathway . . . . . . . . . . . . . . . . . . . . . . . . 678
Shortcut menu for the Metabolika pathway editor. . . . . . . . . . . . . . . . . . . . 680
Add and edit Metabolika pathway structures . . . . . . . . . . . . . . . . . . . . . . . . 681
Compound Classes view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 682
Compound Classes view parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 684
Add new files to the Compound Classes library . . . . . . . . . . . . . . . . . . . . . . 685
Delete, import, and export compound class files . . . . . . . . . . . . . . . . . . . . . 687
Edit compound class files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 687
Edit Compound Class dialog box parameters . . . . . . . . . . . . . . . . . . . . . . . 688
Use the Fragment Editor to define fragment ions . . . . . . . . . . . . . . . . . . . . 689
Load a structure from a structure file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 691
Find a structure in the ChemSpider database. . . . . . . . . . . . . . . . . . . . . . . . . . 691

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Structure drawing tools and commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 693

Toolbar for the structure editors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 693
Shortcut menu commands for the drawing area of the structure editors. . . . 694
Use the structure icons in the toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 695
Create template structures and adding them to a drawing . . . . . . . . . . . . . . 695
Check the validity of a structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 696
Manipulate structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 698
Select atoms and bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 700
Move structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 701
Edit bond properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 701
Edit atom properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 701
Save a structure to a structure file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 703
Copy and paste InChi strings and MOL strings. . . . . . . . . . . . . . . . . . . . . . . . 703

Chapter 13 Use the License Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .704

Open the License Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 704
License Manager command bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 705
Activate the software license . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 705
Enter the product ID and the activation code . . . . . . . . . . . . . . . . . . . . . . . 705
Activate the license on an online computer . . . . . . . . . . . . . . . . . . . . . . . . . 707
Activate the license on an offline computer . . . . . . . . . . . . . . . . . . . . . . . . . 708
Deactivate the software license for transfer to another computer . . . . . . . . . . . 711
Deactivate the software license on an online computer . . . . . . . . . . . . . . . . 711
Deactivate the software license on an offline computer . . . . . . . . . . . . . . . . 712
Install or update a processing workflow node. . . . . . . . . . . . . . . . . . . . . . . . . . 713
Obtain and install the KEGG license. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 714
Contact Pathway Solutions to obtain a KEGG Pathways activation key . . . 714
Install the KEGG license . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 715

Chapter 14 Compound Discoverer configuration options . . . . . . . . . . . . . . . . . . . . . . . . . . . .716

Open the Configuration page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 716
Select the maximum number of parallel processing jobs . . . . . . . . . . . . . . . . . 716
Select where to store temporary data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 717
Turn off the auto-save feature for studies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 718
Hide the workflow node numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 718

Thermo Scientific Compound Discoverer User Guide for LC Studies 17

 Contents

Set up the global color palette . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 719

Open the color schema view of the configuration page . . . . . . . . . . . . . . . . 720
Select a standard color palette . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 720
Create new custom color palettes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 721
Delete custom color palettes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 721
Import custom color palettes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 722
Export custom color palettes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 722
Edit custom color palettes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 722
Add colors to a custom palette . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 723
Insert colors in a custom palette. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 723
Replace a color in a custom palette . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 724
Remove a color from a custom palette . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 725
Select a color in the gradient color chart . . . . . . . . . . . . . . . . . . . . . . . . . . . 725
Specify the default mzCloud mass tolerance settings . . . . . . . . . . . . . . . . . . . . 726
Set up a BioCyc account and optionally purchase a subscription . . . . . . . . . . . 727
Open the BioCyc User Login view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 728
Create a BioCyc user account . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 730
Purchase a subscription or request a free 30-day trial period . . . . . . . . . . . . 730
Enter, test, and save your BioCyc user account information . . . . . . . . . . . . 731
Specify the fragmentation databases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 732

Chapter 15 Common operations for manipulating data tables . . . . . . . . . . . . . . . . . . . . . . . .733

Move table rows up or down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 733
Sort data tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 734
Sort table entries by one or more columns . . . . . . . . . . . . . . . . . . . . . . . . . . 734
Sort table entries by a column with a distribution map . . . . . . . . . . . . . . . . 734
Freeze table rows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 735
Group table rows. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 736
Change the position of table columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 737
Change the column order . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 737
Stack two table columns into one column . . . . . . . . . . . . . . . . . . . . . . . . . . 738
Freeze table columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 739
Show or hide table columns. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 739
Copy table entries to the clipboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 741
Copy the contents of a single table cell to the Clipboard . . . . . . . . . . . . . . . 741
Copy the contents of a single table row to the Clipboard. . . . . . . . . . . . . . . 742
Copy the contents of multiple rows to the Clipboard . . . . . . . . . . . . . . . . . 742
Filter the tables on a study page or a list or library view . . . . . . . . . . . . . . . . . . 742
Set up single-condition filters for the table columns. . . . . . . . . . . . . . . . . . . 743
Set up a single-condition wild card filter . . . . . . . . . . . . . . . . . . . . . . . . . . . 743
Set up a single-condition filter for numeric data . . . . . . . . . . . . . . . . . . . . . 743
Operators and operands for a single-condition table filter . . . . . . . . . . . . . . 744
Set up a custom filter with multiple conditions . . . . . . . . . . . . . . . . . . . . . . . . 749
Custom Filter Selection dialog box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 753

Thermo Scientific Compound Discoverer User Guide for LC Studies 18

 Contents

Chapter 16 Explore compound relations with the molecular networks viewer . . . . . . . . .754
Overview of using the molecular networks feature . . . . . . . . . . . . . . . . . . . . . . 754
How the Generate Molecular Networks node works . . . . . . . . . . . . . . . . . . . . 755
Information displayed in the Similar Compounds table. . . . . . . . . . . . . . . . . . 757
Send compounds to the molecular networks viewer. . . . . . . . . . . . . . . . . . . . . 758
Mark selected compounds in the main compounds table. . . . . . . . . . . . . . . . . 760
Modify the simulation in the molecular networks viewer. . . . . . . . . . . . . . . . . 762
Move, Seek, and Selection modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 763
Move mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 763
Seek mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 763
Selection mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 766
Use the Isolation mode to display specific clusters . . . . . . . . . . . . . . . . . . . . 767
Use the Toggle Backbone tool to display the backbone of a cluster . . . . . . . 767
Color-coded nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 769
Change the node style to display a pie chart or a structure . . . . . . . . . . . . . . 771
Size the nodes by peak area or MW of a compound. . . . . . . . . . . . . . . . . . . 772
Colorize a link by its score, coverage, or number of fragments . . . . . . . . . . . 772
Add directional arrows to the links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 773
Interactive functions performed by using the mouse pointer . . . . . . . . . . . . 774
Molecular networks viewer toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 774
Panes at the left of the molecular networks viewer . . . . . . . . . . . . . . . . . . . . . . 775
Search pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 776
Graph Info pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 776
Isolation pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 777
Filters pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 777
Thresholds pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 778
Clusters pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 779
Node Style pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 780
Link Style pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 781
Pane at the right of the molecular networks viewer . . . . . . . . . . . . . . . . . . . . . 781

Chapter 17 Test communication to the online databases . . . . . . . . . . . . . . . . . . . . . . . . . . . .783

Troubleshoot access to the online databases. . . . . . . . . . . . . . . . . . . . . . . . . . . 783
Run the communication tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 784
Check the URLs for the online databases in your browser . . . . . . . . . . . . . . . . 786
Specify the IP address of the proxy server . . . . . . . . . . . . . . . . . . . . . . . . . . . . 786
Set the correct time and time zone on the processing computer. . . . . . . . . . . . 787

Appendix A Experiment design for comparison statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . .788

Biological versus technical replicates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 788
Non-Nested versus nested experiment designs . . . . . . . . . . . . . . . . . . . . . . . . . 788

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .792

Thermo Scientific Compound Discoverer User Guide for LC Studies 19

 P

Preface
This guide describes how to use the Compound Discoverer™ application to qualitatively
process RAW data files with a targeted or untargeted workflow. A targeted workflow evaluates
the mass spectral data for the presence of specific compounds. An untargeted workflow
evaluates the mass spectral data, predicts the elemental composition of unknown compounds,
and searches mass spectral databases to identify these compounds.

To familiarize yourself with the Compound Discoverer application, follow the tutorials that
are available from the application Help menu.

Contents
• Access the documentation
• System requirements
• Installation instructions
• Special notices
• Create and submit a bug report
• Contact us

Access the documentation

The Compound Discoverer application includes these manuals as PDF files:
• Compound Discoverer User Guide for LC Studies
• Compound Discoverer User Guide for GC Studies
• Compound Discoverer Tutorial for GC CI Workflows
• Compound Discoverer Tutorial for GC EI Workflows
• Compound Discoverer Tutorial for E & L Studies
• Compound Discoverer Metabolism Tutorial
• Compound Discoverer Metabolomics Tutorial

Thermo Scientific Compound Discoverer User Guide for LC Studies 20

 Preface

• Compound Discoverer Stable Isotope Labeling Tutorial

• Compound Discoverer BioCyc Tutorial
• Compound Discoverer Reporting Quick Start Guide

The Compound Discoverer application also includes a context-sensitive Help system, which
means that you can access content-specific Help for each page or dialog box in the user
interface by pressing the F1 key (or equivalent keys) on your computer keyboard. You can also
open the Help system to the Welcome page by choosing Help > Compound Discoverer Help
from the application menu bar.

For information about accessing the manuals, see these topics:

• View the user guides and tutorials
• Download the user documentation for any Thermo Scientific product

View the user guides and tutorials

Y To view the Compound Discoverer manuals

• From the application window, choose Help > Manuals.

–or–
a. Do one of the following:
– From the Microsoft Windows™ 10 taskbar, click the Start button, .
– From the Microsoft™ Windows™ 11 taskbar, click the Start button, , and
click All Apps.
b. Choose Thermo Compound Discoverer 3.3
c. Select a manual (PDF file).
The list of manuals includes two user guides (one for each study type), two tutorials for
GC studies, five tutorials for LC studies by field of study (vertical market), and one quick
start for reporting.

Thermo Scientific Compound Discoverer User Guide for LC Studies 21

 Preface

Download the user documentation for any Thermo Scientific product

You can find user documentation for Thermo Scientific products on the Thermo Scientific
website.

Y To download user documentation from the Thermo Scientific website

1. Go to thermofisher.com.
2. Point to Support, and then click Manuals under Product Documentation on the left.

Link to the Documents & Support page

3. On the Documents & Support page, type the product name in the search box, and then
click the Search icon.
Search box

4. In the results list, click the title to open the document in your web browser, save it, or
print it.

Thermo Scientific Compound Discoverer User Guide for LC Studies 22

 Preface

System requirements
The Compound Discoverer 3.3 application can process data files produced by high-resolution
accurate-mass (HRAM) Thermo Scientific™ mass spectrometers, such as the Orbitrap
Fusion™, Q Exactive™, and Exactive™.

Table 1 lists the hardware and software requirements for the processing computer.
Table 1. Hardware and software requirements for the processing computer
System Minimum requirements
Hardware • 3.4 GHz dual-core processor
• 16 GB RAM
• 500 GB hard drive
• USB port
• Display monitor resolution of 1920 × 1080
Software • Microsoft Windows 10 64-bit operating system or Microsoft
Windows 11 64-bit operating system
• Microsoft .NET Framework 4.8
• Microsoft Office 2013
• PDF reader
System settings • To run processing workflows with online mass spectral database
searches, the computer must have unblocked access to the mass
spectral databases on the Internet.
• The computer must have the correct time and date settings and be
synchronized with Internet time.
• The Region and Language setting for the operating system must
be set to English (United States).

Thermo Scientific Compound Discoverer User Guide for LC Studies 23

 Preface

Table 2 lists the recommended hardware configurations for enhanced performance using the
Compound Discoverer application.
Table 2. Recommended hardware configurations for enhanced performance
System Recommended configurations
Hardware • Dual 8-core processor (for example, 2x Intel™ Xeon™ Gold 6134
CPU @ 3.20 GHz)
• 64 GB RAM
• 1 TB SSD (solid-state disk) hard drive for OS
• 2nd 3 TB (conventional disk) hard drive for data storage
• USB port
• Two 27 in. UHD monitors: Display monitor resolution of
3840 × 2160 pixels

To check the access to the mass spectral databases, the time and date settings, and the Internet
time, see Chapter 17, “Test communication to the online databases.”

To verify that the system meets the minimum requirements, see these topics:
• Check the computer specifications
• Check the format setting for region and language

Check the computer specifications

Y To check the computer specifications

1. From the Windows Explorer directory, right-click OSDisk (Drive:) (the directory for the
hard drive where the operating system is installed) and choose Properties.
The OSDisk (Drive:) Properties dialog box opens. This dialog box lists the file system
(NTFS or FAT) and the free disk drive space.
2. In the Windows search box, type System. Then, click System Information.
The System Information page opens. This page lists the operating system; the processor
type, speed, and number of cores; the installed RAM; and the system type (32-bit or
64-bit).

Thermo Scientific Compound Discoverer User Guide for LC Studies 24

 Preface

Check the format setting for region and language

Table 3 provides instructions for checking the operating system’s region and language setting.
Table 3. Instructions for checking the format setting for region and language
Operating system Steps
Windows 10 or 11 1. In the search box, type Region Settings and press ENTER.
2. On the Region page, under Regional Format, select
Recommended [English (United States)]

Installation instructions
Thermo Compound Discoverer is a licensed application. After you install the application, you
can use it for up to 60 days without activating the software license.

After you order the Compound Discoverer 3.3 application, you will receive a software media
kit that includes a key-shaped USB flash drive with the installation executable. In addition,
you will receive an email from Thermo MS Licensing providing you with the information
that you need to activate the software license.

When you are upgrading the software from a previous version of the application, you can find
the software installer and a license on the LSMS Software Download and Licensing Portal.

IMPORTANT Read the following:

• The installation requires the Windows 10 64-bit operating system. For the
recommended hardware requirements and system settings, see “System requirements.”
• The Compound Discoverer 3.3 SP2 licensing process requires an Internet connection
to validate the software license. You can install the application on a computer without
Internet access and complete the activation process on a computer with Internet
access.
• The Compound Discoverer application is supported for US-English Only locale.

Note The following versions of the Compound Discoverer application can coexist on the
same computer: 1.0, 2.0, 2.1, 3.0, 3.1, 3.2, and 3.3 SP2.

The installation executable includes three installers. The Thermo Compound Discoverer 3.3
installer installs the Compound Discoverer application. The Thermo mzCloud Offline
Library installer installs four mzVault libraries that are July 2021 snapshots of the online
mzCloud mass spectral database, and the Thermo mzVault installer installs the mzVault
application.

Thermo Scientific Compound Discoverer User Guide for LC Studies 25

 Preface

To install the applications and the libraries, see these topics:

• Install the Compound Discoverer application
• Install the mzCloud offline libraries
• Install the mzVault 2.3 SP1 application
• NIST libraries for GC EI Orbitrap data

Install the Compound Discoverer application

Y To install the Compound Discoverer application

1. Do one of the following:

a. Insert the Compound Discoverer USB flash drive into a USB port on your computer.
b. Open Windows Explorer and select the USB drive to view its contents.
c. Locate the executable: XStart_Compound Discoverer.exe.
–or–
a. Go to the following website address:
https://thermo.flexnetoperations.com
b. Log in to your account. If you do not have an account, click Register and create one.
c. On the left side of the Life Sciences Mass Spectrometry Software Download and
Licensing Portal, click Product List under Software and Services.
d. On the Product List page, click the Demo link.
e. On the Product Information page, click the Compound Discoverer 3.3 SP2 link.
f. On the Product Download page, in the File Name column, click the down arrow to
the left of Compound Discoverer 3.3 SP2.zip, click Save As, and then save the
compressed zipped folder to your computer.
g. Extract the contents of the zipped folder, and locate the executable:
XStart_Compound Discoverer.exe.

Note If you are upgrading from the Compound Discoverer 3.0, 3.1, or 3.2
software, which is a free upgrade, you can also find your software license on the
Product Download web page.

2. Double-click XStart_Compound Discoverer.exe.

The installation wizard starts.

Thermo Scientific Compound Discoverer User Guide for LC Studies 26

 Preface

Figure 1. Compound Discoverer installation wizard

© Copyright 2014–2021 Thermo Fisher Scientific Inc.

All rights reserved. This program is protected by copyright
law and international treaties as described in Help About.

3. Click Compound Discoverer 3.3 SP2.

The installation wizard opens to the License Agreement page.
4. Select the I Agree to the License and Trial License Terms and Conditions check box.
5. (Optional) Open the System Requirements page and check whether your system meets
the minimum requirements.
6. Click Install.
7. At the Prompt, click Yes.
The installation starts.
8. (Optional) When the Successfully Installed page appears, click IQ Report to view the
Installation Qualification report.
9. Click Close to close the installation wizard.

Install the mzCloud offline libraries

After you install the mzCloud offline libraries, they appear in the Spectral Libraries view of
the Compound Discoverer application.

Y To install the mzVault libraries

1. If the installer restarted your computer, double-click XStart_Compound Discoverer.exe

to restart the installer.
2. Click mzCloud Offline Library Installer to install the mzVault libraries.

Thermo Scientific Compound Discoverer User Guide for LC Studies 27

 Preface

Install the mzVault 2.3 SP1 application

To create mass spectral libraries from your own data acquired with a high-resolution
accurate-mass (HRAM) Thermo Scientific mass spectrometer, install the mzVault 2.3 SP1
application. The Compound Discover installer includes an installer for the mzVault
application.

Y To install the mzVault application

1. If the Compound Discoverer installer is not open, open it as follows:

a. Locate the XStart_Compound Discoverer executable.
You can find the executable on the USB drive provided in the Compound Discoverer
application media or in the zip folder that you downloaded from the product
download web site.
b. Double-click XStart_Compound Discoverer.exe.
2. Click mzVault 2.3 SPI.
The Thermo mzVault Installshield Wizard opens.

Note If you have an earlier version of the application, follow the instructions to
remove it, and then restart the mzVault 2.3 SP1 installer.

If your computer meets the minimum requirements, the Next button becomes available.
3. Click Next to continue.
4. When the installation is complete, click Finish.

NIST libraries for GC EI Orbitrap data

To process GC EI Orbitrap data with the Compound Discoverer application, Thermo Fisher
Scientific recommends that you install at least one NIST MS Search formatted EI-MS library
on the processing computer. The Compound Discoverer installer does not include any NIST
formatted libraries. You can purchase them from third-party vendors and install them
separately within the NIST MS Search folder.

Customers who purchased an LC/MS system from Thermo Fisher Scientific on or after
January 1, 2018 are eligible for a free copy of the NIST 2020 MSMS library. You can obtain a
compatible version (that has been converted to the mzVault format) for use in the Compound
Discoverer application by sending an email message to Licensing at
[email protected]. Include the Sales Order number or the Purchase
Order number for the instrument in the email.

Customers who purchased the NIST 2020 library elsewhere can obtain the converted version
for use in the Compound Discoverer application by sending a proof of purchase for the library
to Licensing at [email protected].

Thermo Scientific Compound Discoverer User Guide for LC Studies 28

 Preface

NIST 2020 MSMS library for LC/MS/MS data

Customers who purchased an LC/MS system from Thermo Fisher Scientific on or after
January 1, 2018 are eligible for a free copy of the NIST 2020 MSMS library. You can obtain a
compatible version (that has been converted to the mzVault format) for use in the Compound
Discoverer application by sending an email message to Licensing at
[email protected]. Include the Sales Order number or the Purchase
Order number for the instrument in the email.

Customers who purchased the NIST 2020 library elsewhere can obtain the converted version
for use in the Compound Discoverer application by sending a proof of purchase for the library
to Licensing at [email protected].

Special notices
Make sure that you follow the precautionary statements presented in this guide. The special
notices appear in boxes.

Special notices include the following: Important, Note, and Tip.

IMPORTANT Highlights information necessary to prevent damage to software, loss of

data, or invalid test results; or might contain information that is critical for optimal
performance of the system.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

Create and submit a bug report

If you discover a software error in the Compound Discoverer application, report the error to
the Compound Discoverer support team.

Y To report an error in the application

1. From the Compound Discoverer menu bar (on the processing computer where the error
occurred), choose Help > Create Bug Report.
The Thermo Discoverer Bug Reporter dialog box opens.

Thermo Scientific Compound Discoverer User Guide for LC Studies 29

 Preface

2. Click Create Bug Report.

The application creates a report of your computer configuration and stores it as a
Compound Discoverer Bug Report (timestamp).zip on your computer desktop.
3. Send a detailed error description with screenshots and the bug report as an attachment to
the following email address:
[email protected]

Contact us
Contact Email Telephone QR Code

U.S. Technical Support [email protected] (U.S.) 1 (800) 532-4752

U.S. Customer Service [email protected] (U.S.) 1 (800) 532-4752

and Sales

Global support Y To find global contact information or customize your request

1. Go to thermofisher.com.
2. Click Contact Us, select the country, and then select the type of support
you need.
3. At the prompt, type the product name.
4. Use the phone number or complete the online form.

Y To find product support, knowledge bases, and resources

Go to thermofisher.com/us/en/home/technical-resources.

Y To find product information

Go to thermofisher.com/us/en/home/brands/thermo-scientific.

Y For Compound Discoverer customer support questions

Send an email message to [email protected].

Thermo Scientific Compound Discoverer User Guide for LC Studies 30

 1

Introduction to Compound Discoverer

Compound Discoverer is a qualitative data-processing application that uses accurate mass
data, isotope pattern matching, fragment matching, and mass spectral library searches for the
structural identification of small molecules. It can process the accurate-mass spectra from the
entire product line of Thermo Scientific high-resolution mass spectrometers. It can also
display the graphical data acquired from a variety of LC detectors: UV-visible and photodiode
array (PDA) detectors that are controlled by a Thermo Scientific data system and third-party
analog detectors that are connected to the analog input channels of a Thermo Scientific mass
spectrometer (MS).

The Compound Discoverer application is a study-based application—that is, all data

processing takes place from within the study environment. When data processing is complete,
the application automatically stores the result file or files in the study folder. See “Directory
structure for Compound Discoverer studies.”

This introduction describes the features and enhancements in this release and how to set up
the application window, choose the size of the toolbar icons, and manage the recently used file
lists on the Start Page. In addition, the overview topic summarizes the application workflow
from starting the application to reporting the results of an analysis.

For details, see these topics:

• New features and enhancements
• Obsolete (n/a) Detect Compounds node in legacy processing workflows
• Terminology used in the Compound Discoverer application
• LC studies overview
• Start the Compound Discoverer application
• The Compound Discoverer window
• Auto-Hide the Start Page, the Chromatograms view, and the Mass Spectrum view
• Show, hide, and rearrange the tabbed pages of the application
• Supported file formats

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 1 Introduction to Compound Discoverer
New features and enhancements

New features and enhancements

The Compound Discoverer application uses a study format to define the experimental
variables for a set of samples. It uses a customizable node-based processing workflow to
process Xcalibur™ RAW files and create either a single result file with statistical analyses for the
input file set or one result file per input file without any statistical analyses.

Some of the workflow nodes in the processing workflows require input from the customizable
lists and libraries for the application. For LC studies, these lists and libraries include the
structures of known compounds, mass lists, adduct ions, chemical transformations, ion
definitions, neutral losses, Metabolika pathways, compound classes (fragment lists), and mass
spectral libraries.

The result file from data processing includes a set of result tables and graphical views that are
based on the processing workflow. The application provides graphical views for displaying
chromatograms and spectra and statistical views for comparing the detected compounds by
sample file or sample group.

The application comes with defined templates for the processing workflows and reports.

These topics describe the new features and enhancements in the Compound Discoverer 3.3
application and the enhancements in the two service packs (3.3 SP1 and 3.3 SP2):
• Enhancements in the Compound Discoverer 3.3 SP2 release
• Enhancements in the Compound Discoverer 3.3 SP1 release
• New features in Compound Discoverer 3.3 for LC studies
• Enhancements in Compound Discoverer 3.3

Enhancements in the Compound Discoverer 3.3 SP2 release

For LC studies, the Compound Discoverer 3.3 service pack 2 (SP2) application includes the
following enhancements:
• Additional spectral libraries in the Spectral Libraries library
See “Spectral Libraries view.”
• Additional mass lists in the Mass Lists library, including new mass lists for the
identification of compounds in the PFAS family
See “Mass Lists view.”
• New PFAS compound class file in the Compound Classes library
See “Compound Classes view.”

Thermo Scientific Compound Discoverer User Guide for LC Studies 32

 1 Introduction to Compound Discoverer
New features and enhancements

• New processing workflow template for identifying the per- and polyfluoroalkyl
substances (PFAS) family of compounds
See “Defined processing workflow templates,” and “PFAS identification.”
For more information about using the Compound Discoverer application to identify
compounds in the PFAS family, refer to the following document:
http://assets.thermofisher.com/TFS-Assets/CMD/Application-Notes/an-001826-lsms-pf
as-analysis-workflow-compound-discoverer-an001826-na-en.pdf
• Additional transformation reaction, PFAS Chain Shortening, for the PFAS family of
compounds in the Transformations list
See “Transformations view.”
• Increased limit for the number of compounds that you can export to the molecular
networks viewer
The limit is now 3.000 compounds. See “Send compounds to the molecular networks
viewer.”

Enhancements in the Compound Discoverer 3.3 SP1 release

For information about the enhancements in the Compound Discoverer 3.3 SP1 release, see
these topics:
• Enhancements common to both study types in the Compound Discoverer SP1 release
• Enhancements for LC studies only in the Compound Discoverer SP1 release

Enhancements common to both study types in the Compound Discoverer SP1 release
The Compound Discoverer 3.3 SP1 application includes the following enhancements for
both study types (LC and GC):
• The Mass List Editor can now open compound lists with a file size of up to 600 MB.
• The Natural Product Atlas database in the mass lists available from the Lists & Libraries
menu has been updated to version 2021_08. See “Mass Lists view.”
• The performance of the Map to BioCyc Pathways node has been improved to reduce the
run time of the mapping process.

Thermo Scientific Compound Discoverer User Guide for LC Studies 33

 1 Introduction to Compound Discoverer
New features and enhancements

Enhancements for LC studies only in the Compound Discoverer SP1 release

The Compound Discoverer 3.3 SP1 application includes the following enhancements for LC
studies only:
• The Fill Gaps node includes a new parameter that lets you specify a less restrictive
retention time tolerance for filling the gaps for compounds across the input files. For the
Gap Filling node, gaps are missing chromatographic peaks for putative compounds in one
or more of the input files for an analysis. See “Fill Gaps node.”
• Peak ratings are now available for chromatographic peaks that the Fill Gaps node
gap-filled by using a matching ion or a re-detected peak for the missing peak.

New features in Compound Discoverer 3.3 for LC studies

The Compound Discoverer 3.3 application includes the following new features for LC
studies:
• Improved chromatographic peak detection and integration
The Detect Compounds and Find Expected Compounds nodes
– Are significantly faster and more sensitive than the original Detect Compounds
(Legacy) and Find Expected Compounds (Legacy) nodes.
– Provide improved peak integration.
– Include an option to base the mass trace and chromatographic peak area for each
compound on the most intense isotope in the isotopic pattern or all the detected
isotopes. Both options use the specified minimum number of isotopes to validate the
mass traces.
See the Use Most Intense Isotope Only parameter in the Detect Compounds node
and the Find Expected Compounds node.
– Include a baseline integration option.
See the Remove Baseline parameter in the Detect Compounds node and the Find
Expected Compounds node.
– Report the quality of the chromatographic peaks in the result tables.
See Peak quality factor (PQF) columns in the result tables.

Note The Detect Compounds (Legacy) node and the Find Expected Compound
(Legacy) node, with some performance improvements, are still available for
comparisons with existing analysis results.

• Improved chromatographic peak area determination for relative quantitation

The Group Compounds and Group Expected Compounds nodes

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 1 Introduction to Compound Discoverer
New features and enhancements

– Find the most common adduct ion for each compound across all samples for relative
quantitation. Provide the option to base the chromatographic peak area for each
compound on the most common adduct ion or the summed area of all the detected
ions.
See the Area Integration parameter in the Group Compounds node and the Group
Expected Compounds node.

Note By default, the Area Integration parameter is set to Most Common Ion.

– Display the m/z value of the most common adduct ion in the m/z column and its ion
definition in the Reference Ion column of the Compounds and Expected
Compounds tables.
• New peak rating filter in the Group Compounds, Group Expected Compounds, and
Differential Analysis nodes provides peak thresholding based on the quality of the
chromatographic peaks.
This peak rating filter lets you filter out low-quality chromatographic peaks without
setting an overly restrictive minimum peak intensity threshold. To pass the filter,
chromatographic peaks must have a peak rating equal to or greater than the user-specified
threshold and be detected or found in at least the user-specified minimum number of input
files submitted for analysis. See Chromatographic peak rating filter.

Peaks that do not pass the peak rating thresholds in the Detect Compounds and Find
Expected Compounds nodes are removed early in the processing workflow. This data
reduction speeds up processing for the downstream nodes (gap, peak area refinement,
identification, mapping, and scoring) and increases overall performance.
The Differential Analysis node recalculates the peak ratings to capture changes in the
peak areas from the Fill Gaps node and the peak area refinement nodes.
The peak rating values of the chromatographic peaks are based on peak quality factors1,
relative peak area, and the coefficient of variance values (CVs).
• The Search mzCloud and Search mzVault nodes can perform MSn searches against the
library spectra in the mzCloud mass spectral database. The mzCloud search can retrieve
KEGG IDs and compound class information from the online mzCloud mass spectral
database and display these results in the Compounds table of the result file (analysis
result).

Tip The Search MSn parameter in the Search mzCloud and Search mzVault nodes is
set to True in the processing workflow templates provided with the Compound
Discoverer application. When you create your own custom processing workflow
templates, you must set this parameter to True to perform MSn searches. See the
Search MSn parameter in the Search mzCloud node and the Search mzVault node.

1
Chetnik et al, MetaClean: a machine learning-based classifier for reduced false positive peak detection in
untargeted LC-MS metabolomics data, http://www.ncbi.nlm.nih.gov/pmc/articles/pmc7895495/

Thermo Scientific Compound Discoverer User Guide for LC Studies 35

 1 Introduction to Compound Discoverer
New features and enhancements

• The new chromatographic peak alignment node—Align Retention Times (ChromAlign)2

node— is faster and more sensitive than the original alignment node. In addition, you
have the option to align the chromatographic peaks on the compound level in the Group
Compounds and Group Expected Compounds nodes by setting the Align Peaks
parameter to True.

Enhancements in Compound Discoverer 3.3

The Compound Discoverer 3.3 application includes the following enhancements for LC
studies:
• Improvements to the molecular networking feature let you do the following:
– Display chemical structures in the nodes.
– Control the maximum cluster size.
– Show only the backbone of each cluster.
See Panes at the left of the molecular networks viewer.
• Support for data acquisition using multiple mass ranges. See the MS1 Mass Range
parameter in the Select Spectra node.
• Support for data acquisition using multiple FAIMS compensation voltage (CV) values.
See the FAIMS CV parameter in the Select Spectra node.
• Custom Tags Editor for creating, importing, and exporting tag definitions. See Custom
color-coded tags for result table entries.
• Result Exporter processing workflow node (Post-Processing section) for automatically
exporting result tables or specific columns in each result table to spreadsheet or text files.
See Result Exporter node.
• New reporting options for displaying the mzCloud mirror plot, the study name, and the
result file name in a report. The report templates provided with the Compound
Discoverer application display the study name and the file name of the result file in the
page header. The Customize Report dialog box automatically adds the study name and
file name to the page header of new report templates.
For information about adding an mzCloud mirror plot to a report template, see Add
mzCloud mirror plots to a report template.
• An additional compound database—LipidMaps3 Structure Database in the Mass Lists
library. See Mass Lists view.

2
ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS
chromatographic surfaces, RG Sadygov et al. Analytical Chemistry, 2006

3 Sud et al, LMSD: LIPID MAPS structure database, http://www.ncbi.nlm.nih.gov/pubmed/17098933

Thermo Scientific Compound Discoverer User Guide for LC Studies 36

 1 Introduction to Compound Discoverer
Obsolete (n/a) Detect Compounds node in legacy processing workflows

• A new version of the mzCloud Offline Spectral Library (2021B) and two in-silico spectral
libraries for lipids—LipidBlast4 in the Spectral Libraries list. See Spectral Libraries view.
• The Grouping & Ratios page of an analysis shows information on the statistical test that
the analysis will apply by using the selected groups and ratios.
• New Statistical Methods result table that provides detailed information on
transformations (performed by the Differential Analysis node), statistical tests, scaling
methods, gap filling, and QC methods that the analysis performed.

The Compound Discoverer 3.3 SP1 application includes the following enhancements:
• The Fill Gaps node includes a new parameter that lets the user specify a less restrictive
retention time tolerance for filling the gaps for compounds across the input files for the
analysis. For the Gap Filling node, gaps are missing chromatographic peaks for putative
compounds in one or more of the input files for an analysis. See “Fill Gaps node.”
• The Mass List Editor can now open compound lists with a file size of up to 600 MB.
• The Natural Product Atlas database in the mass lists available from the Lists & Libraries
menu has been updated to version 2021_08.
• Peak ratings are now available for chromatographic peaks that the Fill Gaps node
gap-filled by using a matching ion for the missing peak.
• The performance of the Map to BioCyc Pathways node has been improved, reducing the
run time of the mapping process.

Obsolete (n/a) Detect Compounds node in legacy processing

workflows
The Compound Discoverer 3.3 application includes new chromatographic peak detection
and alignment algorithms. These new algorithms have obsoleted the original peak detection
and alignment algorithms in previous versions of the application.

When you reprocess analysis results (result files) for untargeted analyses from previous
versions of the Compound Discoverer application, a not available (n/a) warning appears on
the Detect Compounds node. The current workflow issues table below the Workflow Tree
area on the Workflows page of the Analysis view states that the node is not recognized by the
application.

(n/a) Detect
Compounds

4
Kind et al., LipidBlast in silico tandem mass spectrometry database for lipid identification,
http://dx.doi.org/10.1038/nmeth.2551

Thermo Scientific Compound Discoverer User Guide for LC Studies 37

 1 Introduction to Compound Discoverer
Terminology used in the Compound Discoverer application

You cannot partially reprocess legacy analysis results from untargeted analyses. To reprocess
these results, you must replace the (n/a) Detect Compounds node with the Detect
Compounds node or the Detect Compounds (legacy node) and fully reprocess the analysis.
For details, see “Reprocess a legacy analysis result from an untargeted analysis.”

Terminology used in the Compound Discoverer application

Table 4 describes the terminology that the Compound Discoverer application uses for its
data-processing features.
Table 4. Terminology used in the Compound Discoverer application (Sheet 1 of 3)
Term Description
Analysis An analysis consists of a processing workflow (which is a processing method consisting of
multiple interconnected workflow nodes), a list of input files for processing, and the name
of the result file that the analysis generates. In addition to the input files and the processing
workflow, an analysis can also specify the sample groups and ratios for statistical analyses.

You can select the processing workflow and the input files and set up the study factors and
sample groups for an analysis by using the New Study and Analysis wizard. Or, you can set
up an analysis from within a study.
Compounds For LC studies, a compound (or component) is a chromatographic peak that the application
detected for a specific molecular weight (within the specified mass tolerance) and retention
time (within the specified tolerance). The Features table for a compound lists all the
chromatographic peaks that make up the peak for the compound.
Expected compounds For LC studies, an expected compound is a compound that the application generates by
using the parent compounds and transformations that you specify. You specify the parent
compounds and transformations in the Generate Expected Compounds node of a
processing workflow. After the application generates a list of expected compounds, it
searches for these compounds in the input files that you submit for analysis.
Features Features are chromatographic peaks with specific m/z × RT dimensions that the Detect
Unknown Compounds node detects. The Compound Discoverer application reports the
chromatographic peak areas in counts × seconds.
Gap In an extracted ion current (XIC) trace (chromatogram), gaps are missing data points—that
is, the scan or scans acquired at specific time points in the chromatographic run do not
include mass spectrum peaks for the compound’s mass within the user-specified mass
tolerance.

For the gap filling nodes, gaps are missing chromatographic peaks for putative compounds
in one or more of the input files for an analysis.
Input files Input files are Xcalibur raw data files that you have added to a study. The study lists the
relative location of the raw data files. If you move the raw data files to a different directory
after you add them to a study, you must resolve their location before you start an analysis.

Thermo Scientific Compound Discoverer User Guide for LC Studies 38

 1 Introduction to Compound Discoverer
Terminology used in the Compound Discoverer application

Table 4. Terminology used in the Compound Discoverer application (Sheet 2 of 3)

Term Description
Study factors Study factors are the experimental variables that you are testing for statistically significant
effects on the sample population being studied.

There are three types of study factors:

• Categorical factors include non-quantifiable categories such as organism, matrix, tissue,
gender, and so on.
• Numerical factors include quantifiable variables such as time, amount, concentration,
and so on. You can assign a unit to a numeric study factor; however, the unit is only a
label and is not used in any calculations.
• Biological replicate factors include non-quantifiable categories with samples from
different entities of the same type under the same conditions and provide a measure of
the variability associated with these conditions. Use the biological replicate factor for
nested experiments. You can add only one biological replicate factor to a study.
Study files (studies) Setting up an analysis to process raw data files takes place within the study environment.

Studies include a list of input files with their location, the sample information for each file,
and a list of the analyses run within the study. The sample information includes the file
name, study factor values, and sample type for each sample.

Study files also include the name and location of the folder where the Compound
Discoverer application stores the result files that you generate by running analyses within
the study.

You can open result files from outside a study.

Study folders Every study includes a folder for storing the results of the analyses run within the study. In
addition, you can create multiple higher-level folders for storing the study-specific folders.
See “Directory structure for Compound Discoverer studies.”

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 1 Introduction to Compound Discoverer
LC studies overview

Table 4. Terminology used in the Compound Discoverer application (Sheet 3 of 3)

Term Description
Study templates A study template file is any study file (.cdStudy) that includes defined study factors or a
spreadsheet file (.xlsx) or tab-delimited text file (.txt) that includes all the study information.
As shown in the following example, the required columns for a text or spreadsheet file are
File (names and location of the raw data files), Sample Type, and CF:study factor name (one
column for each study factor).

For information about creating study template files that include all the study information,
see “Create a study template file that contains all the study information.”
Result files Result files contain the results of a specific processing workflow and input file set. Results
files are also known as analysis results. See Chapter 8, “Review the analysis results.”
Processing workflows Processing workflows are node-based processing methods for processing raw data files. You
can access the predefined processing workflow templates and your custom processing
workflow templates only from within a study. See Chapter 6, “Create and edit processing
workflows.”
Parent compounds For targeted analyses, a parent compound is an expected compound that you define in the
Expected Compounds library and then select for analysis in a processing workflow. The
result file from an expected compounds analysis includes an Expected Compounds table
with a Parent Compound column. You can select multiple compounds for an expected
compounds analysis.

In the molecular network viewer, parent compounds are the starting compounds for the
chemical transformations that you specify in the Generate Molecular Networks workflow
node.

LC studies overview
Figure 2 summarizes the workflow for setting up a study and an analysis, submitting a set of
input files for processing, and reviewing and reporting the results of the analysis.

For LC studies, there are two types of analyses—targeted and untargeted. In a targeted
analysis, the application starts with a list of expected compounds. In an untargeted analysis,
the application relies on matching the fragmentation spectra to compounds in a mass spectral
database. You can create processing workflows (processing methods) that combine these two
types of analyses.

Thermo Scientific Compound Discoverer User Guide for LC Studies 40

 1 Introduction to Compound Discoverer
LC studies overview

Figure 2. Compound Discoverer workflow for LC studies

Start the Compound Discoverer application.

Preliminary tasks

–and–
Customize the lists and libraries as applicable. For a If your processing computer has Internet access,
targeted analysis, add the expected compounds to check the communication to the online databases.
the Expected Compounds library.
See Chapter 17, “Test communication to the online
See Chapter 12, “Manage the lists and libraries.” databases.”

Step 1. Create a new study and a new analysis.

In the application toolbar, click the New Study and Analysis icon, , to open the New Study and Analysis
wizard. Then, follow the embedded Help.
When you finish the wizard, the new study page opens as a tabbed page in the application window, and the Analysis
view opens to the right of the study.
See Chapter 3, “Create a new study and an analysis by using the wizard.”

Step 2. Submit the analysis to the job queue.

In the Analysis view, click Run to start the analysis.

If the Run button is not available, open the Workflows page by clicking Edit in the Analysis view to the right of
Processing Step. Then, one by one select any node that has an exclamation mark on its upper-right corner and specify
the missing parameter value. For a targeted analysis, you must specify at least one compound for the Generate
Expected Compounds node. See “Customize the processing workflow.”
After you start the run, the job queue opens as a tabbed page in the application window. See “Control the Job
Queue.”

Step 3. Open the result file from the analysis.

Review and filter the data.
After the job ends, open the result file by double-clicking the job in the job queue.
The result file opens as a tabbed page in the application window, and the toolbar icons for data visualization, filtering,
and reporting become available.
Review the data. Then, filter the data for data reduction as applicable. See Chapter 8, “Review the analysis results.”

Step 4. Create a report.

–or–
Select a report template and print a report. Export the data to an Excel spreadsheet.
See Chapter 11, “Create and print reports.” See “Export the tabular data in a result file to an
external file.”

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 1 Introduction to Compound Discoverer
Start the Compound Discoverer application

Start the Compound Discoverer application

You can start the application from the taskbar or the computer desktop.

Y To start the Compound Discoverer application

Do one of the following:

• From the taskbar, choose Start > All Programs (or Programs) > Thermo Compound
Discoverer.
• From the computer desktop, double-click the Compound Discoverer 3.3 icon, .

The Compound Discoverer window opens with the Start Page displayed as a tabbed
document. As you create studies and process data, the application creates and populates the
recent file lists to the right of the What Would You Like to Do? links.

Figure 3 shows the initial application window with large toolbar icons:
• The icons in the first row are always available.
• Most of the icons in the second and third rows become available when you open a result
file.
Figure 3. Application window with the initial Start Page and large toolbar icons

Toolbar icons for

result pages

Toolbar icons for

reporting

Start Page links

For information about the toolbar icons and application menus, see “The Compound
Discoverer window.”

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 1 Introduction to Compound Discoverer
The Compound Discoverer window

The Compound Discoverer window

The Compound Discoverer window contains a title bar, a menu bar, and a toolbar. From the
application window, you can open all the other application views and pages by choosing a
menu command or clicking a toolbar icon. The Start Page lists the recently opened study files
and result files. See “Start the Compound Discoverer application.”

These topics describe the menu bar, the toolbar, and the recently used files lists on the Start
Page:
• Compound Discoverer menu bar
• Compound Discoverer toolbar
• Change the size of the toolbar icons
• Manage the recently used files lists on the Start Page

Note This user guide uses the following terms to describe the user interface:
• View—A dockable window that you can move to a second monitor.
• Page—A tabbed document. You can have many pages open simultaneously; however,
only one of these pages is the active page.
• Dialog box (modal)— A graphical element that accepts user input. Only one modal
dialog box can be open at a time. When it is open, a modal dialog box blocks you
from working in other parts of the application.
• Pane—A defined area of an application view, page, or dialog box.
• Prompt—A pop-up message box that you must dismiss to continue.

Compound Discoverer menu bar

Table 5 describes the menu commands in the menu bar at the top of the Compound
Discoverer window.
Table 5. Compound Discoverer menu bar (Sheet 1 of 6)
Menu command Description
File menu

These commands are always available.

New Study and Opens the New Study and Analysis Wizard, which takes you
Analysis through the process of selecting the studies folder for your study
subfolders, creating a new study, and starting a new analysis.

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 1 Introduction to Compound Discoverer
The Compound Discoverer window

Table 5. Compound Discoverer menu bar (Sheet 2 of 6)

Menu command Description
Open Study Opens the Open Study dialog box for selecting an existing study
file to open.

The Compound Discoverer study file type has the .cdStudy file
name extension.
Open Result Opens the Open Result File dialog box for selecting an existing
result file or result view file.

You do not need an active software license to open result files.

The file name extension for result files that contain the data
processing results is .cdResult.

The file name extension for files that contain the display layout for
the results tables, graphical views, and filter settings
is .cdResultView.

To restore the default layout for a result file, delete its associated
result view file.
Note You do not need an active software license to open result
files.
Save Saves recent changes to the current active page (selected tab), for
example, the active study page or result page.
Save All Saves recent changes to all the open pages in the application
window.
Recent Studies Displays a list of recent studies that you can open.
Recent Studies > Clear Clears the Recent Studies list.
Recent Results Displays a list of recent results that you can open.
Recent Results > Clear Clears the Recent Results list.
Exit Closes the application.
Reporting menu

These commands are available only when a result page is active.

Create Report Opens the Open Report Design Template dialog box for selecting
a report template to resolve specific data in the result file.
Create Report Opens the Customize Report dialog box for setting up the main
Template properties of a report template.
Edit Report Template Opens the Open Report Design Template dialog box for choosing
an existing report template to edit.

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 1 Introduction to Compound Discoverer
The Compound Discoverer window

Table 5. Compound Discoverer menu bar (Sheet 3 of 6)

Menu command Description
List & Libraries menu

These commands are always available.

Expected Compounds Opens the Expected Compounds view for modifying the list of
expected compounds.
Note The Generate Expected node and Create Pattern Trace
node require compounds from the Expected Compounds
library. The Create Pattern Trace and the Pattern Scoring nodes
require user-specified elemental compositions.
Transformations Opens the Transformations view for modifying the list of
transformations.
Neutral Losses Opens the Neutral Losses view for modifying the list of neutral
losses.
Ion Definitions Opens the Ion Definitions view for modifying the list of ion
definitions.
Adducts Opens the Adducts view for modifying the list of adducts.
Mass Lists Opens the Mass Lists view for modifying the list of mass list files
or editing mass list files.
Spectral Libraries Opens the Spectral Libraries view for modifying the list of
mzVault database files.
Metabolika Pathways Opens the Metabolika Pathways view for modifying the list of
Metabolika pathways or editing a Metabolika pathway.
Compound Classes Opens the Compound Class view for viewing or modifying the
list of compound class libraries.
View menu

The Start Page and Job Queue commands from this menu are always available. The other
View commands are available only when a result file is active.
Start Page Opens the Start Page, which lists the most recently opened result
files and study files.
Job Queue Opens the Job Queue page for viewing the progress of the current
analysis or the processing events of previous analyses.
Result Summary Opens the Summaries view.
Custom Tags Editor Opens the Custom Tags Editor for selecting the number of
custom tags that you want to use for tagging items in the result
tables and the text that you want to display for each tag.

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 1 Introduction to Compound Discoverer
The Compound Discoverer window

Table 5. Compound Discoverer menu bar (Sheet 4 of 6)

Menu command Description
Result Filters Opens the Result Filters view for reducing the number of rows
displayed in selected result tables.
Chromatograms Opens the Chromatograms view for viewing chromatogram plots.
Mass Spectrum Opens the Mass Spectrum view for viewing a spectral tree and the
spectrum scans.
Trend Chart Opens the Trend Chart view for setting up a box-and-whisker
(Box Whisker selection) chart or a trendline chart.
Isotopologues Opens the Isotopologues Chart view.
Distribution Chart
Available only when the active result file includes results from the
Analyze Labeled Compounds node.
Mass Defect Plot Opens the Mass Defect Plot view for examining the relationship
between the mass defects of the detected or expected compounds
and their molecular weights.
Result Charts Opens the Result Charts view for setting up data graphs, such as
scatter plots, histogram charts, bar charts, and pie charts. Use
these views to visualize the data.
Descriptive Statistics Opens the Descriptive Statistics view for viewing a
box-and-whisker plot of all the compounds in the Compounds or
Expected Compounds tables for the selected sample groups.
Differential Analysis Opens the Differential Analysis view for viewing volcano plots
and running differential analyses.
Principal Component Opens the Principal Component Analysis view for evaluating
Analysis multivariate data.
Partial Least Squares Opens the Partial Least Squares Discriminant Analysis view.
Discriminant Analysis
Hierarchical Cluster Opens the Hierarchical Cluster Analysis view.
Analysis
Retention Time Opens the Corrected Retention Times view.
Corrections
Available only when the active result file includes data from
multiple input files. To view the retention time correction curves
for one or more input files, select the input files of interest in the
Input Files table.
Compound Area Opens the Compound Area Corrections view.
Corrections
Available only when the active result file includes data from
Quality Control samples.

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 1 Introduction to Compound Discoverer
The Compound Discoverer window

Table 5. Compound Discoverer menu bar (Sheet 5 of 6)

Menu command Description
Metabolika Pathways Opens the Metabolika Pathways view for viewing the Metabolika
pathways that are mapped to the compounds data.
BioCyc Pathways Opens the BioCyc Pathways view for viewing the BioCyc
pathways that are mapped to the compounds data.

Available only when the active result file includes mapped BioCyc
pathways.
KEGG Pathways Opens the KEGG Pathways view for viewing the KEGG™
pathways that are mapped to the compounds data.

Available only when the active result file includes mapped KEGG
pathways.
mzLogic Analysis Opens the mzLogic Analysis view.
FISh Scoring Queue Opens the FISh Scoring Queue view.
Window menu

Use these commands to apply, save, manage, or reset layouts.

Apply Layout Displays the layouts list for selecting a layout.
Save Layout Opens the Save Layout dialog box for naming the current layout.
Manage Layouts Opens the Manage Result File Layout dialog box for renaming or
deleting layouts.
Reset Layout Closes and reopens the active result file to reset its layout.
Help menu

These commands are always available.

Compound Discoverer Opens the Compound Discoverer Help, which is a compiled Help
Help file with Contents, Index, and Search tabs. The Help contains
context-sensitive topics; that is, pressing F1 opens the Help topic
that corresponds to the current area of the application.
How to Use the Help Opens the Compound Discoverer Help to the Using This Help
topic.
Glossary Opens the Compound Discoverer Help to the table of contents
for the glossary.
Compound Discoverer Displays links to the Compound Discoverer User Guide,
Support Manuals Compound Discoverer Reporting Quick Start, Compound
Discoverer tutorials, and Release Notes.

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 1 Introduction to Compound Discoverer
The Compound Discoverer window

Table 5. Compound Discoverer menu bar (Sheet 6 of 6)

Menu command Description
License Manager Opens the License Manager page where you can activate your
Compound Discoverer license or scan for missing application
features.
Communication Tests Opens the Communication Tests dialog box where you can run
tests to check whether your data processing computer can connect
to the external BioCyc Pathways, KEGG Pathways, mzCloud, and
ChemSpider databases.
Create Bug Report Creates a report of your computer configuration and stores it as a
Compound Discoverer Bug Report (timestamp).zip on your
computer desktop.

To report software errors to Thermo Fisher Scientific, send a

detailed error description with screen shots and attach this bug
report to the email.
Configuration Opens the Configuration page for setting global options, such as
the maximum number of parallel analyses, the study management
setting for automatically saving studies, the color maps, the
mzCloud search settings, and your user credentials for the BioCyc
mapping feature.
About Opens the Compound Discoverer dialog box for viewing lists of
the installed components and processing workflow nodes.

Compound Discoverer toolbar

Figure 4 shows the Compound Discoverer toolbar (when a result page is active).
Figure 4. Compound Discoverer toolbar (with small icons)
Shows the Start page.
Shows the Job Queue page.
Shows the Lists and Libraries Manager.
Reporting
Study icons Data review icons icons

Saves all open items.

Saves the active item.

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 1 Introduction to Compound Discoverer
The Compound Discoverer window

Table 6 describes the icons in the Compound Discoverer toolbar from left to right.
Table 6. Toolbar icons (Sheet 1 of 3)
Icon Description
Study icons
Opens the New Study and Analysis Wizard that takes you through the process
of specifying the studies folder for all your study subfolders, creating a new
study, and starting a new analysis.
Opens the Open Study dialog box for selecting the current version or a
previous version of an existing study.
Opens the Open Result File dialog box for selecting the current version or a
previous version of a result file.
General icons
Saves the currently active item, such as a study or result file.

Saves all the open pages, such as the study pages and the result pages.

Opens the Start Page when it is not already open and makes it the active page.

Opens the Job Queue page when it is not already open and makes it the active
page.
Opens the Lists and Libraries Manager where you can select to open one of the
following editors:
• Expected Compounds—For viewing or modifying a list of compounds
• Transformations—For viewing or modifying a list of transformations
• Neutral Losses—For viewing or modifying a list of neutral losses
• Ion Definitions—For viewing or modifying a list of ion definitions
• Adducts—For viewing or modifying a list of adducts
• Mass Lists—For creating, editing, importing, exporting, or deleting mass
lists
• Spectral Libraries—For creating, editing, importing, exporting, or deleting
mzVault database files
• Metabolika Pathways—For adding, editing, importing, exporting, or
deleting Metabolika pathways.
• Compound Classes—For creating, editing, importing, exporting, or
deleting compound class libraries of fragment structures

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 1 Introduction to Compound Discoverer
The Compound Discoverer window

Table 6. Toolbar icons (Sheet 2 of 3)

Icon Description
Data review icons

Available when a result file is the current page in the application window. When the
respective view is open, brings the view to the forefront or makes the view the active view.
Opens the Summaries view as a docked view.

Available when the Summaries view is closed.

Opens the Custom Tags Editor as a floating window.

Opens the Result Filters view as a floating window.

Opens the Chromatograms view as a docked view.

Opens the Mass Spectrum view as a docked view.

Opens the Trend Chart view as a docked view.

Opens the Isotopologues Distribution Chart view as a docked view.

Available when the opened result file includes an analysis of labeled

compounds.
Opens the Mass Defect Plot view as a docked view.

Opens the Results Chart view as a floating window.

The Results Chart view includes the following pages: Scatter Chart, Histogram
Chart, Bar Chart, and Pie Chart.
Opens the Descriptive Statistics view as a docked view.

Opens the Differential Analysis view as a docked view.

Opens the Principal Component Analysis view as a docked view.

Opens the Partial Least Squares–Discriminant Analysis (PLS–DA) view as a

docked view.
Opens the Hierarchical Cluster Analysis view as a docked view.

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 1 Introduction to Compound Discoverer
The Compound Discoverer window

Table 6. Toolbar icons (Sheet 3 of 3)

Icon Description
Opens the Retention Time Corrections view as a docked view.

Available when the result file includes more than one input file.
Opens the Compounds Area Correction view as a docked view.

Opens the Metabolika Pathways view as a docked view.

Available when the result file includes mapped BioCyc pathways.

Opens the BioCyc Pathways view as a docked view. Available when the result
file includes mapped BioCyc pathways.
Opens the KEGG Pathways view as a docked view. Selecting an item in the
KEGG Pathways result table opens the reference pathway for the item in the
KEGG Pathway view.

Available when the result file includes compounds mapped to KEGG

pathways.
Opens the mzLogic Analysis view as a docked view.

Opens the FISh Annotations Queue view as a docked view.

Reporting icons

Available when a result file (not necessarily the current page) is open in the application
window.
Opens the Open Report Design Template dialog box for selecting a report
template (.cdReportTemplate).
Opens the Customize Report dialog box for setting up a custom report
template.
Opens the Open Report Design Template dialog box for selecting a report
template (.cdReportTemplate).

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 1 Introduction to Compound Discoverer
The Compound Discoverer window

Change the size of the toolbar icons

You can choose between large or small icons for the Compound Discoverer toolbar. By
default, the toolbar displays large icons.

Y To change the size of the toolbar icons

Do one of the following:

• To display small icons in the toolbar, right-click the application toolbar

and choose Show Large Icons.
• To display large icons in the toolbar, right-click the application toolbar
and choose Show Large Icons.

Note The check mark to the left of Show Large Icons indicates that the application is
set to display large toolbar icons.

Figure 5 shows the toolbar set to display large icons.

Figure 5. Compound Discoverer toolbar with large icons

Shortcut menu for the toolbar icon size

Figure 6 shows the toolbar set to display small icons.

Figure 6. Compound Discoverer toolbar with small icons

Shortcut menu for the toolbar icon size

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 1 Introduction to Compound Discoverer
Auto-Hide the Start Page, the Chromatograms view, and the Mass Spectrum view

Manage the recently used files lists on the Start Page

The right side of the Start Page displays lists of the most recently opened study and result files.
You can clear the recent file lists, remove files from these lists, keep one or more files at or near
the top of each list, or open the folder where a specific study file or result file resides.
Table 7. Managing the recent files lists
Task Procedure
Keep files at the top of a recent Click the pin icon to the left of the file name.
files list.
The orientation of the pin changes from to . When
you pin more than one file, the files appear at the top of
the list in the order that you pin them.
Remove files from the recent • To remove a single file, right-click the file and choose
files lists. Remove From List.
• To clear the entire list, right-click any file in the list
and choose Clear List.
Explore the contents of a folder Under the recent files list, right-click a study file or a
where a study file or a result file result file and choose Explore Path.
is stored.
Windows Explorer opens to the folder for the selected
study file or result file.

Auto-Hide the Start Page, the Chromatograms view, and the Mass
Spectrum view
To make more space for other views, you can auto-hide the Start Page and the
Chromatograms and Mass Spectrum views in the Compound Discoverer window. The
auto-hide features collapses each of these items down to a small tab.

Y To use the auto-hide feature

1. Right-click the page tab and choose Dockable.

The Auto Hide command becomes available for the Start Page and the Chromatograms
and Mass Spectrum views. This command remains unavailable for all other dockable
pages.
2. Right-click the page tab and choose Auto Hide.
The tab changes to a vertical tab on the left of the application window.
3. To view the hidden page, click its tab.
4. To hide the page, click anywhere in the application window outside the page borders.

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 1 Introduction to Compound Discoverer
Show, hide, and rearrange the tabbed pages of the application

Show, hide, and rearrange the tabbed pages of the application

As you open top-level views, study files, and result files in the Compound Discoverer window,
they open as tabbed pages (also known as documents) below the toolbar.
• Start Page ( )
• Lists and Libraries manager ( )
• Configuration ( )
• Job Queue ( )
• Report Templates ( Report Template Name)
• License Manager ( )
• Study files ( Study Name )
• Result files ( Result File Name )

Note Excluding the Start Page and Job Queue, views that open from the View menu or
toolbar are not tabbed documents—that is, when they are open, they are not listed in the
open files.

To display, dock, hide, or rearrange the tabbed pages (documents), see these topics:
• Tabbed pages list
• Open a hidden tabbed page
• Tab groups
• Shortcut menu commands that control the layout of the tabbed pages
• Rearrange the tabbed pages and graphical views

Tabbed pages list

Although you can have all the tabbed pages (documents) open simultaneously (including
multiple study files and result files) the number of tabs that the application can display is
limited by the monitor size. As you open more files than the monitor can display, the tabs
begin to disappear from view in the order that you opened the files. To indicate that one or
more tabs are hidden, the Current Tabs icon changes from to .

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 1 Introduction to Compound Discoverer
Show, hide, and rearrange the tabbed pages of the application

The following figure shows a list of open files and pages.

Figure 7. List of open files and pages

Current Tab
icon

List of open files and pages

Open a hidden tabbed page

Y To display an open tabbed page (document) when its tab is hidden

Click the Current Tabs icon, , to display a list of open files. Then, select the
appropriate tabbed page from the list.
The selected page becomes active.

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 1 Introduction to Compound Discoverer
Show, hide, and rearrange the tabbed pages of the application

Tab groups
In the Compound Discoverer window, when two or more tabbed pages (documents) are open
in the same tab group, you can create more tab groups. Each tab group has its own Current
Tabs icon, . Figure 8 shows tab group examples.
Figure 8. Orientation of tab groups
Single tab group Current Tab icon

Two vertical tab groups

Two
horizontal
tab groups

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 1 Introduction to Compound Discoverer
Show, hide, and rearrange the tabbed pages of the application

Shortcut menu commands that control the layout of the tabbed pages
Table 8 describes the shortcut menu commands that control the properties of the tabbed
pages (documents) in the Compound Discoverer window.
Table 8. Shortcut menu for tabbed documents (Sheet 1 of 2)
Command Description
Dockable Activates the Auto Hide command.

Available for the Start Page and the result file views. This
command is not available for the Job Queue page.
Tabbed Document Makes the page a tabbed document.

Available for the Start Page, Job Queue page, License Manager
page, library pages, study pages, result file views, and report
template pages.
Auto Hide Hides the page while leaving the tab visible. Clicking the tab
opens the page. Clicking outside the page closes the page if more
than one tabbed document is open. The location of the tab
depends on the position of the tabbed document in the
application window.

Available for the Start Page and the views in the View menu when
these pages are dockable windows. This command is not available
for the Job Queue page.
Hide Closes the tabbed document.
Move to Previous Tab Changes the position of the tabbed document.
Group
Available only when the application window contains two or more
tabbed groups.
Move to Next Tab Changes the position of the tabbed document.
Group
This command is available only when the application window
contains two or more tabbed groups.
New Horizontal Tab Moves the selected tabbed document to a new horizontal tab
Group group.

Available only when there are two or more tabbed documents that
belong to the same tab group in the application window. Each tab
group has its own Current Tab icon.

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 1 Introduction to Compound Discoverer
Show, hide, and rearrange the tabbed pages of the application

Table 8. Shortcut menu for tabbed documents (Sheet 2 of 2)

Command Description
New Vertical Tab Moves the selected tabbed document to a new vertical tab group.
Group
Available only when there are two or more tabbed documents that
belong to the same tab group in the application window. Each tab
group has its own Current Tab icon.

Rearrange the tabbed pages and graphical views

To make the best use of your screen space, rearrange the graphical views and tabbed pages
(documents) as follows:
• Use the mouse pointer to move the graphical views that are available when you open a
result file from one dock position to another dock position or to a second monitor.
• Use the mouse pointer or the shortcut menu commands to rearrange the tabbed pages
within the application window. For information about using the shortcut menu
commands, see “Shortcut menu commands that control the layout of the tabbed pages.”

Y To move a view or tabbed page to another position by using the mouse pointer

1. Drag the view by its title bar or the page by its tab. As you drag a view or a tabbed page by
its title bar, a guide tool appears. The guide tool consists of four directional arrows (inner
arrows) that are arranged in a diamond pattern around a central circle. In addition to the
guide tool, a directional arrow (outer arrows) appears in the middle of each of the four
window edges.
Figure 9. Guide tool

2. After the guide tool appears, align the pointer with the appropriate directional arrow, and
then release the mouse button.

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 1 Introduction to Compound Discoverer
Show, hide, and rearrange the tabbed pages of the application

Table 9. Rearranging views and tabbed pages by using the mouse pointer
Task Procedure
Move a graphical view to another Drag the pointer to the second monitor.
monitor.
Move the selected view above the second Drag the pointer to the inner up arrow, .
view.

Move the tabbed page to a horizontal

group above the current group.
Move the selected view below the second Drag the pointer to the inner down arrow, .
view.

Move the tabbed page to a horizontal

group below the current group.
Move the selected view to the left of the Drag the pointer to the inner left arrow, .
second view.

Move the tabbed page to a group on the

left.
Move the selected view to the right of Drag the pointer to inner right arrow, .
the second view.

Move the tabbed page to a group on the

right.
Make both views tabbed. Drag the title bar to the tabs icon.

The application displays the first view and creates

a tab for the second view.
Move the selected view to the top or Drag the pointer to the outer top arrow or the
bottom of the window. outer bottom arrow.

Move the tabbed page to the top or

bottom of the window.
Move the first view to the left side or Drag the pointer to the outer arrow at the left of
right side of the window. the window or the outer arrow at the right of the
window.
Move the tabbed page to the left side or
right side of the window.

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 1 Introduction to Compound Discoverer
Supported file formats

Supported file formats

Table 10 describes the file types that the application can recognize or create.
Table 10. Supported file formats (Sheet 1 of 2)
File format Description
Xcalibur RAW file Contains unprocessed data acquired from a high-resolution,
accurate mass (HRAM) Thermo Scientific mass spectrometer with
a Thermo Scientific data system that is layered on the Thermo
Foundation™ platform.
MOL format (.mol), Contains a two-dimensional compound structure. You can open
compressed structure structure files by using the Structure Editor or the Custom
(.mcs), template (.tml) Explanations Editor.
SDF Contains one or more two-dimensional compound structures. You
can import compounds from an SDF file into the Expected
Compounds library.
XLSX or tab-delimited Contains the study information for a set of input files. See “Create
text file a study template file that contains all the study information.”
cdProcessingWF Contains the data processing instructions for the application. To
create a processing workflow, you must start or open an analysis in
a study.

cdAnalysis Stores the processing workflow information.

cdStudy Stores the study information, which includes the names and
locations of the input files, the sample information, and the
relationship between the input files.

cdResult Contains the results produced by processing a set of raw data files
and information about the analysis settings used to process the raw
data.

cdResultView Contains the layout settings that the application uses to display
the available tables and graphical views of a result file. These
settings also include the applied result filters.

Deleting this file erases all the custom layout settings and restores
the display to the default layout settings.

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 1 Introduction to Compound Discoverer
Supported file formats

Table 10. Supported file formats (Sheet 2 of 2)

File format Description
cdReportTemplate Contains the layout for reports that extract data from the
following items in a result file: selected columns in one main table,
selected columns in the related tables, and selected graphical views
(MS1, MS2, and Chromatograms).
Inclusion set (.inclSet) Contains all the parameter settings for generating an inclusion list
with the Generate Xcalibur Inclusion List dialog box.
Filter Set (.filterset) You can use filter set files for data reduction when reviewing and
reporting the data in Compound Discoverer result files. The
application comes with one predefined filter set file—Example
Filter Set.filterset.
Mass list (.masslist) Contains a mass list that is compatible with the Compound
Discoverer mass list editor.
metabolika Contains a metabolic pathway drawing that is compatible with the
Compound Discoverer Metabolika Pathway editor.
mgf, mzML, mzDATA Contains the mass spectral data that can be read by third-party
mass spectrometry applications. To create any of these files types,
use the Export Spectra Node in a processing workflow.
XML You can export each library to an XML file, and you can import
library entries from an XML file.
TAGS Contains a set of user-defined custom tags.
text (.txt) You can save the data points in the graphical views to a text file.
EMF, BMP, JPG, GIF, You can save the images in the graphical views as image files of the
PNG, TIFF following file types: enhanced metafile (.emf ), bitmap (.bmp),
Joint Photographic Group (.jpg), graphic interchange format
(.gif ), portable network graphics (.png), and tagged image file
format (.tiff ).

You can open EMF files in a raster image editor or a vector image
editor.
CSV You can import the contents of a CSV file into a Mass List file.
CLIB You can import the contents of a CLIB file as a Compound Class
list. A compound class list contains the fragment structures that
are common to the named compound class.
DB You can import mzVault libraries into the Spectral Libraries list.
MSP You can export compounds as MSP files that you can then import
into the NIST MS Search application.

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 2

Functional description of the data-processing

features
For an overview of the compound detection, identification, and scoring features in the
Compound Discoverer application, see the following topics:
• Chromatographic peak detection, alignment, and identification for LC Studies
• Chromatographic peak rating filter
• Peak quality factors
• Online compound databases and metabolism pathways
• Local spectral databases, mass lists, and metabolism pathways
• Best scans for composition prediction and spectral matching
• Using mzLogic to score candidates for unknown compounds
• Confidence score for an mzCloud hit
• FISh scoring for proposed structures
• Mass defect types and visualization techniques
• Neutral loss detection and visualization
• Using quality control samples to compensate for batch effects
• Batch normalization for single sequence runs
• Batch normalization for multiple sequence runs (LC studies)
• Stable isotope labeling experiments
• PFAS identification
• Methods for imputing values for missing chromatographic peaks across a set of input files

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 2 Functional description of the data-processing features
Chromatographic peak detection, alignment, and identification for LC Studies

Chromatographic peak detection, alignment, and identification for LC

Studies
For LC-MS/MS data, the application processes the high-resolution scan data as follows:
1. Reads the raw data files.
2. Filters the spectra by the specified filters.

IMPORTANT If the input files are from a FAIMS-MS experiment and any of them
include spectra for more than one FAIMS CV value (also known as CV switching),
you must specify the CV value that you want to process, and all the input files must
include spectra for the user-specified CV value.

If the input files are from an experiment with mass range switching, you must specify
the mass range that you want to process, and all the input files must include spectra
for this mass range.

3. Aligns the input files by their alignment features when the analysis includes multiple
input files and the processing workflow includes the Align Retention Times
(ChromAlign) node or the Alignment Retention Times node.

Note Most of the processing workflow templates in the Common Templates folder
use the Align Retention Times (ChromAlign) node.

The Align Retention Times (ChromAlign) node is new in the Compound Discoverer 3.3
application. This node automatically selects the first sample file in the Files for Analysis
area of an analysis as the reference alignment file. A sample file is an input file assigned
any of the following sample types: Sample, Control, or Standard. After you add input files
to the Files for Analysis area of the analysis, you can select a different sample file as the
reference file.
The legacy Align Retention Times node individually aligns each feature ((m/z × RT)) as
follows:
• When the set of input files includes only one sample group, the node uses the input
file with the most features (landmarks) as the reference file.
• When the set of input files includes multiple sample groups, the node aligns the
features (m/z value × RT) within a group first. Then, aligns the features among the
groups based on which group has the most features.
The new Align Retention Times (ChromAlign) node builds correlation matrices based on
spectral similarities. Then, creates regression curves by using the optimal path in the
correlation matrix.

Tip Use the Retention Time Corrections view and the File Alignments table to review
the corrected retention time of each detected compound in a result file.

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 2 Functional description of the data-processing features
Chromatographic peak detection, alignment, and identification for LC Studies

4. Detects the XIC traces and chromatographic peaks by doing the following:
• For an untargeted processing workflow that includes the Detect Compounds node,
the analysis detects the chromatographic peaks in the XIC traces.
• For a targeted processing workflow that includes the Expected Compounds node, the
analysis searches for the expected compounds in the XIC traces.
Both the Detect Compounds node and the Find Expected Compounds node calculate
the chromatographic peak areas (for relative quantitation) according to the following
parameter settings:
• Use Most Intense Isotope Only:
– True: Displays the area of the chromatographic peak in the XIC trace for the
most intense isotope in the isotope pattern for the compound.
– False: Displays the combined area for all the detected isotopes in the isotope
pattern for the compound.
The Detect Compounds node automatically detect the isotope pattern for organic
compounds with the following elements: C, H, N, O, and S. You have the option to
add Cl and Br to this list.
• Remove Baselines:
– True: Does not include the extra area caused by integrating the area under the
XIC trace down to the baseline.
– False: Drops a perpendicular tangent line from the start and end points of the
chromatographic peak down to the baseline and includes this additional area in
the reported peak area.
5. Groups the compounds across the input files as follows:
• An untargeted processing workflow groups each compound across the input file set
by its MW × RT dimensions.
• A targeted processing workflow groups each expected compound across the input file
set by its formula × MW × RT dimensions.
When you turn on the peak rating filter, the grouping nodes (Group Compounds and
Group Expected Compounds) store only the compounds that pass the filter in the
analysis result. In addition, they do not send these failing peaks to the downstream nodes
(Fill Gaps, Peak Area Refinement, Identification, Pathway Mapping, Compound Scoring)
for further processing, which speeds up the processing time.
Even when you do not turn on the peak rating filter, you can use the Result Filters view to
filter the compounds in the analysis result by using the Peak Rating column or by any of
the peak quality factor (PQF) columns in the compounds tables. By default, the PQF
columns are hidden.
For details, see “Chromatographic peak rating filter.”

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 2 Functional description of the data-processing features
Chromatographic peak rating filter

6. For an untargeted workflow, fills the gaps for missing chromatographic peaks when the
processing workflow includes the Fill Gaps node.
Filling the gaps with nonzero values is necessary for the statistical analyses.
7. For an untargeted workflow, predicts the elemental composition of the compounds when
the processing workflow includes the Predict Compositions node.
8. Assigns annotations to the compounds by using the available information from the
identification and pathway mapping nodes when the processing workflow includes the
Assign Annotations node.

Chromatographic peak rating filter

The new Group Compounds and Group Expected Compounds processing workflow nodes
include a peak rating filter. This filter allows you to remove low-quality chromatographic
peaks without setting an overly restrictive minimum peak intensity threshold in the Detect
Compounds node or the Find Expected Compounds node.

Note An appropriate intensity threshold for chromatographic peaks is difficult to

estimate, especially for untargeted experiments. So, attempting to remove noise-level
peaks by setting a minimum intensity threshold commonly removes low-intensity peaks
that must then be gap-filled to perform statistical analyses.

The new processing workflow templates for untargeted analyses perform the initial peak
detection at a very low minimum peak intensity threshold of 10 000 (minimum intensity, in
ion counts, at the chromatographic peak apex). This low-intensity threshold filters out very
few chromatographic peaks. To remove low-quality or non-reproducible peaks, you can set up
a peak rating filter in the Group Compounds node. This peak rating filter combines peak
quality and peak reproducibility across the input file set.

Note When you submit 10 or more input files (assigned the Control, Standard, Sample,
or Blank sample type) for processing and the analysis includes one or both of the grouping
nodes, the application prompts you to set up a peak rating filter.

The application considers only the following sample types when it calculates the total
number of files for the analysis: Control, Standard, Sample, and Blank. It excludes the
following sample types from the total number of files: Identification Only and Labeled.

The processing workflow templates for targeted analyses still include a relatively high
minimum peak intensity threshold of 1 000 000. So, these templates automatically remove
low-intensity noise-level chromatographic peaks for most analyses. However, when you are
analyzing large data sets with similar samples, you might find it useful to set up a peak rating
filter to remove spurious compounds that are present in only a small subset of the samples.

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 2 Functional description of the data-processing features
Peak quality factors

Note Removing chromatographic peaks that do not pass the peak quality threshold in a
specified number of input files at the grouping stage of the analysis decreases the overall
processing time by streamlining other processing steps, such as gap filling and
identification.

By default, the peak rating filter in the processing workflow templates is not enabled. See
Figure 10.

To enable the filter, you must specify the minimum number of input files (number greater
than or equal to 1) where the chromatographic peak for a putative compound meets or
exceeds the specified peak rating value (0.1 to 10). You can also modify the various peak
quality factors that contribute to the overall peak rating value. See “Peak quality factors.”
Figure 10. Group Compounds node and Group Expected Compounds node parameters

O
OH Group Compounds Group Expected
C

Compounds

To enable this filter, you must specify nonzero values

for these two parameters:
• Peak Rating Threshold
• Number of Files

Peak quality factors

The peak quality factors that contribute to the overall rating (0 to 10) for a chromatographic
peak are as follows:
• FWHM2Base quality factor
• Jaggedness quality factor
• Modality quality factor
• Zig-Zag Quality Factor

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 2 Functional description of the data-processing features
Peak quality factors

The Group Compounds and Group Expected Compounds nodes calculate the peak rating of
the chromatographic peaks for each compound across the set of input files. The Differential
Analysis node recalculates the peak rating values for each chromatographic peak before it
performs a differential analysis based on the peak areas.

For information about the peak rating values in the result tables, see “Peak Rating columns.”
You can filter the compounds in the compounds tables by the Peak Rating column.

For information about the peak quality factor columns in the result tables, see “Peak quality
factor (PQF) columns in the result tables.” You can filter the compounds tables in the analysis
results by the PQF columns.

Note The Detect Compounds (Legacy) node and the Detect Compounds node use
different approaches for isotope grouping:
• The Detect Compounds node uses the peak quality information to group the XIC
traces for common isotopes of C, H, N, O, and S and optionally for Cl and Br. It
ignores XIC traces with low-quality chromatographic peaks for isotope grouping.
• The Detect Compounds (Legacy) node does not use the peak quality information
during grouping. It uses the peak quality information only for filtering after grouping.

When used in a processing workflow that runs only a targeted analysis, the Find Expected
Compounds node includes hard-coded peak quality thresholds for isotope pattern
detection:
• PQF: J (Jaggedness) ≤ 0.4
• PQF: ZZI (Zig-Zag Index) ≤ 0.25
• PQF: M (Modality) ≤ 0.9

When used in a processing workflow that includes a targeted analysis and an untargeted
analysis, the Find Expected Compounds node uses the user-specified peak quality
thresholds in the Detect Compounds node.

The Find Expected Compounds (Legacy) node does not use peak quality information.

When a processing workflow includes untargeted and untargeted analyses, it can include
the Detect Compounds node and the Find Expected Compounds node or the Detect
Compounds (Legacy) node and the Find Expected Compounds (Legacy) node.

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 2 Functional description of the data-processing features
Peak quality factors

FWHM2Base quality factor

The peak quality factor for the separation of the chromatographic peaks compares the peak
width at half-maximum (height) to the peak width at its base.
W
FWHMB2Base = -------h-
Wb

Where:
Wh = the peak width at half the maximum peak height
Wb = the peak width at the base

The calculated value ranges from 0 to 1. As the peak quality increases, the calculated value for
the peak quality factor decreases.
Figure 11. FWHM to base peak quality measurement
Baseline Original Smoothed
120

8.130
100 Peak height

80
Intensity [counts] (10^6)

60
Peak width at half height

40

20
8.056 Peak width
at the base
0
8.1 8.2 8.3 8.4 8.5 8.6 8.7
RT [min]

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 2 Functional description of the data-processing features
Peak quality factors

Jaggedness quality factor

The peak quality factor for jaggedness captures the quality of the chromatographic peak shape
by calculating the number of changes in direction over the length of the intensity vectors.

The calculated value ranges from 0 to 1. As the peak quality increases, the calculated value for
the peak quality factor decreases.
Figure 12. Jaggedness peak quality measurement
Baseline Original Smoothed

60
3.006

50
Intensity [counts] (10^3)

40

30 2.988

20

10

0
2.96 2.97 2.98 2.99 3.00 3.01 3.02 3.03
RT [min]

Modality quality factor

The Modality peak quality factor is the size of the deepest valley (= unexpected change) in the
peak normalized by the intensity of the peak.

The calculated value ranges from 0 to 1. As the peak quality increases, the calculated value for
the peak quality factor decreases.

Modality = --a-
b

Figure 13. Modality peak quality factor measurement

a
Intensity

Retention Time (minutes)

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 2 Functional description of the data-processing features
Online compound databases and metabolism pathways

Zig-Zag Quality Factor

The zig-zag index captures the quality of the chromatographic peak shape by measuring the
mean of all the valleys across the peak, which is then normalized by the intensity of the peak
above the baseline.
Mean ( V i )
Zig-Zag = ------------------------
-
b
The calculated value is greater than zero, and in some cases it can be greater than one. As the
peak quality increases, the calculated value for the peak quality factor decreases.
Figure 14. Zig-zag index peak quality measurement

Vn
Intensity

V1 b Vn + 1

V1

Retention Time (minutes)

Online compound databases and metabolism pathways

When the processing computer has Internet access, the Compound Discoverer application
can access and use the following online databases for compound identification:
• mzCloud
• ChemSpider
• KEGG
• BioCyc

For information about checking the processing computer’s access to these online databases,
see Chapter 17, “Test communication to the online databases.”

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 2 Functional description of the data-processing features
Local spectral databases, mass lists, and metabolism pathways

Local spectral databases, mass lists, and metabolism pathways

The local offline databases that you can use to identify and map compounds with the
Compound Discoverer application include the following:
• mzCloud offline libraries
For LC studies, you can create your own mzVault libraries by using the mzVault 2.3 SP1
application.
For all studies, you can create your own mzVault libraries by exporting the mass spectral
data from a compounds table in the analysis result.
• Metabolika pathways
You can create your own Metabolika pathway drawings by using the Metabolika pathway
editor. See “Create a new Metabolika Pathway file.”
• Mass lists
You can create your own mass lists by using the mass lists editor. See “Create and edit
mass list files.”

Best scans for composition prediction and spectral matching

For each set of raw data files that you submit for processing, the application can select the best
MS1 scan and the best MS2 scan for each compound from different input files. This selection
is done within the compound consolidation nodes—that is, by the Group Compounds node
and the Group Expected Compounds node.

For information about how the application determines and uses the best scans, see these
topics:
• Best MS1 scan for isotope pattern matching
• Best MS2 scan for fragments matching and spectral comparison

Best MS1 scan for isotope pattern matching

To determine the best MS1 scan to use for a compound across a set of input files, the
consolidation nodes select the MS1 scan with the highest resolution and retention time closest
to the peak apex for a compound.

The application sends the isotope pattern information from the best MS1 scan to the
following workflow nodes for further processing:
• The Predict Compositions node for isotope pattern matching
• The Apply Spectral Distance node for calculating the spectral distance between the
assigned elemental composition and the experimental isotope pattern

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 2 Functional description of the data-processing features
Using mzLogic to score candidates for unknown compounds

Best MS2 scan for fragments matching and spectral comparison

To identify compounds by fragmentation data or to determine the spectral similarity between
the fragmentation scans for two different compounds, the application uses the best MS2 scan
for each compound.

To determine which MSn scans to attach to a compound, the application does the following:
1. Searches for MS2 scans for the precursor ion within the RT range of the peak
apex ± FWHM for a compound.
2. If it finds no MS2 scans for the precursor ion within this range, it searches for scans
within the start and end points of the chromatographic peak for a compound, as
determined by the Parameterless Peak Detection (PPD) algorithm.
3. To determine the best MS2 scan, it does the following:
a. Selects the MS2 scan for the preferred ion.
b. If it finds multiple spectrum trees for the preferred ion, it uses the MS2 scan from the
MS1 scan with the highest precursor intensity.

For each compound, the Group Expected Compounds and the Group Compounds nodes
send all the MS2 scans associated with that compound to the following nodes:
• Search mzCloud node
• Search mzVault node

For each compound, the Group Compounds node sends the best MS2 scans to the Apply
mzLogic node.

Using mzLogic to score candidates for unknown compounds

mzLogic uses all the fragmentation scans (full MSn depth) for an unknown compound to
score possible matching candidates.

There are two ways to run the mzLogic scoring algorithm:

• Running an untargeted analysis that includes the mzLogic node
• Running an mzLogic analysis from the mzLogic Analysis view

For information about setting up and running an analysis, see Chapter 4, “Set up, run, and
reprocess analyses.”

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 2 Functional description of the data-processing features
Using mzLogic to score candidates for unknown compounds

Running an untargeted analysis that includes the mzLogic node

Processing workflow templates (processing methods) that include the following terms—
Online Database Searches or mzLogic—in their file names include the Apply mzLogic node
and one or more of the compound identification nodes and pathway mapping nodes.

Tip For information about selecting a processing workflow template for an analysis, see
“Start a new analysis from within an existing study.”

When an mzCloud search yields no identity matches for an unknown compound, the
mzLogic algorithm provides a ranking score for the compound hits from the identification
nodes and pathway mapping nodes.

The mzLogic algorithm can provide a ranking score for the various database search results
when an unknown compound has available data-dependent MS2 scans and similarity results
from an mzCloud similarity search.

Note The ranking score is not a probability score. It is only a measure of how similar the
fragmentation spectra for a putative compound are to closely matching spectra in the
mzCloud spectral database.

During data processing, the Apply mzLogic node does the following:
1. Runs a forward search and a reverse search using the mzCloud service.
2. For compounds that have available MS2 scans, scores all the structure candidates (or the
specified maximum number of candidates) from the attached input nodes.

Note The following nodes can supply structures to the Apply mzLogic node: Search
ChemSpider, Search Mass Lists, Map to BioCyc Pathways, and Map to Metabolika
Pathways.

The mass lists that you select for the Search Mass Lists node must include structures.
The Endogenous Metabolites database 4400 Compounds.masslist file does not
include structures.

3. Adds the following columns to the result tables:

• Adds the #Similarity Results column to the Compounds table. By default, this
column is hidden.
• Adds the mzLogic Score column to the following related tables as applicable:
ChemSpider Results, Mass List Search Results, Metabolika Results, and BioCyc
Results.

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 2 Functional description of the data-processing features
Confidence score for an mzCloud hit

Running an mzLogic analysis from the mzLogic Analysis view

If the processing workflow for a result file did not include the Apply mzLogic node, or if you
suspect that the online mzCloud spectral database now includes more spectral data, use the
mzLogic Analysis view to rank the putative structures for your unknown compounds.

Because the mzLogic Analysis view includes a link to the ChemSpider database where you can
select putative structures, the result file does not need to include structure annotations.

For details, see “mzLogic Analysis view.”

Confidence score for an mzCloud hit

The application provides two scores for comparing a query spectrum to its library hits—the
Confidence score and the Match score.

For details about these scores, see the following topics:

• Factors that affect the Confidence score
• How to use the Confidence score

Factors that affect the Confidence score

The Confidence score is a probability-based library searching and scoring algorithm, primarily
developed to reduce the likelihood of a false positive identification. In essence, it is a measure
of the probability of a correct compound identification calculated from a Bayesian network
extensively trained on searching against the mzCloud database.

The scoring model is based on extracting six observables from a query versus library spectral
pair:
• Spectral similarity (expressed as the spectral match value)
• Relative difference in the collision energies for the query and library spectra
• Polarity of the spectra
• Number of peaks in the spectra
• Relative energies of the query spectrum and library spectrum
• Identity of the compounds that produced the library spectrum and the query spectrum

The final score for a query spectrum versus library spectrum pair is based on the likelihood of
two spectra belonging to the same compound given the observed spectral match, the collision
energy of the unknown, the number of peaks in each spectrum, the polarity of each spectrum,
and the difference in the relative collision energies of the two spectra.

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 2 Functional description of the data-processing features
Confidence score for an mzCloud hit

The following examples illustrate how to use the confidence score and the match score for a
query versus library spectrum comparison.

Example 1: Comparison of spectra with non-specific features (fragment ions)

Suppose that you are identifying 6-hydroxynicotinic acid in your sample and assume that the
representative query spectrum for your sample exactly matches the mzCloud library spectrum,
producing a match score of 100.

When you search the mzCloud library using the standard ID search, which is restricted only
to the product spectra with a matching precursor ion, you find very similar spectra for related
compounds. Because the spectrum is non-specific, any molecule with the same molecular
weight and adduct is likely to have the same non-fragmented spectrum at the lower end of
activation energies. The Confidence algorithm severely penalizes these library search results
because they are based on a non-specific spectral fingerprint (only 1 precursor peak), making
the probability of a correct ID very low.
Figure 15. MS2 HCD 20 product spectrum of 6-hydroxynicotinic acid

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 2 Functional description of the data-processing features
Confidence score for an mzCloud hit

Figure 16 shows the Confidence and Match scores for the three top hits for the low-energy
fragmentation scan of 6-hydroxynicotinic acid. Because the query and library spectra are so
non-specific (with only one fragment peak), the Confidence scores are extremely low
compared to the Match scores.
Figure 16. mzCloud search results for a query spectrum of 6-hydroxynicotinic acid obtained at a
collision energy of 20 HCD

Confidence scores Match scores

Example 2: Comparison of fragmentation-rich spectra

At a higher collision energy of 100 HCD, the fragmentation of 6-hydroxynicotinic acid

produces a much richer fragmentation spectrum. The breakdown curves in Figure 17 show
that this fragmentation energy is close to the optimum for generating characteristic fragments.
Figure 17. Breakdown curves for the HCD fragmentation of 6-hydroxynicotinic acid
Normalized collision energy

m/z

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 2 Functional description of the data-processing features
Confidence score for an mzCloud hit

Figure 18 shows the fragmentation spectrum for 6-Hydroxynicotinic acid at the higher
fragmentation energy (HCD 100).
Figure 18. MS2 HCD 100 product spectrum of 6-hydroxynicotinic acid

The search results against the mzCloud database look very different from the first example at
the lower fragmentation energy. In Figure 19, you see greater separation in the scores between
the true hit (6-hydroxynicotinic acid) and its analogs (false hits). The separation is even more
pronounced in the Confidence score ranking.
Figure 19. mzCloud search results for a query spectrum of 6-hydroxynicotinic obtained at a
collision energy of 100 HCD

Confidence scores Match scores

When you look at the next best library hit, 3-hydroxypiconilic acid, which is a positional
isomer of the true hit, you see different fragmentation energies for the query spectrum
(HCD 100) and the library record (HCD 30). The assumption is that identical compounds
at similar fragmentation energies produce similar fragmentation spectra. So, if you observe

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 2 Functional description of the data-processing features
FISh scoring for proposed structures

similar fragmentation spectra (= a high spectral match score) at different collision energies, it
might mean that the original assumption of identical compounds is incorrect, which the
heavily penalized Confidence score (80.4 spectral match score versus 9.2 confidence score)
reflects for this particular result.
Figure 20. Query spectrum (HCD 100) versus library spectrum (HCD 30)

How to use the Confidence score

Use the Confidence score as an additional metric to prevent conclusions based on poor input
data. Many applications display library search results in a tabular format with only a spectral
match score. But a good match score can be misleading if the fragmentation fingerprint is
non-specific.

When the Confidence score is significantly lower than the Match score, evaluate the possible
reason for this difference.

When the Match score and the Confidence score are both greater than 80%, the confidence
that you are identifying the compound correctly is relatively high.

FISh scoring for proposed structures

The FISh scoring algorithm works with both LC/MSn data and GC CI data.

The FISh scoring algorithm compares the experimental fragmentation spectra for a
compound to the expected fragmentation spectra based on the structure of the compound.
Note In the 3.1 and later versions of the application, the FISh scoring algorithm uses all
the fragmentation scans (in the spectrum tree for a compound), compared to earlier
versions of the application that only used MS2 scans. Therefore, if you reprocess data sets
that you already processed with an earlier version of the application, and these data sets
include MSn scans (where n > 2), the FISh coverage scores might be lower.

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 2 Functional description of the data-processing features
Mass defect types and visualization techniques

For targeted compounds (expected compounds), you can add FISh scoring to the automated
analysis.

For untargeted compounds, you can apply FISh scoring to your proposed structures or
compounds with structures and MS2 or higher spectra.

The FISh scoring algorithm matches the fragment structures in a list of expected fragments to
the centroids in the fragmentation scans of the precursor ions.

When a precursor ion scan is followed by only one fragmentation scan, the node calculates the
FISh coverage score as follows:
# matched centroids
FISh coverage score = -------------------------------------- × 100
# used centroids
where:
# matched centroids represents the number of matched centroids.
# used (matched + unmatched) centroids represents the number of centroids in the
fragmentation scan that are above the user-specified signal-to-noise threshold. The
algorithm skips centroids below the user-specified signal-to-noise threshold.

When a precursor scan is followed by more than one fragmentation scan, the node calculates a
composite score as follows:
( Σ per all scans # matched centroids )
FISh coverage score = -------------------------------------------------------------------- × 100
( Σ per all scans # used centroids )

The FISh scoring algorithm annotates the centroids in the fragmentation scans with the
matching fragment structures. It also provides a FISh Coverage score for data-dependent scans
in the Mass Spectrum view legend and a FISh Coverage score in the compounds table.

Mass defect types and visualization techniques

In the Compound Discoverer application, you can use the mass defect of an elemental
composition to do the following:
• Filter the spectral data during processing to keep or remove expected and detected
compounds by their mass defect.
• Calculate the mass defect of each detected compound by using multiple calculation
methods during processing, and then sort the resulting table of detected compounds by
their mass defect.
• View a plot of the mass defects for the detected compounds versus their molecular
weights to visualize the similarity between the compounds.

Table 11 lists the formulas that the application uses to calculate the mass defect of an
elemental composition.

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 2 Functional description of the data-processing features
Mass defect types and visualization techniques

Table 11. Mass defect types

Mass defect type Formula
Fractional mass exact mass – floor of the exact mass

where:
exact mass = monoisotopic mass of the elemental
composition
Standard mass defect exact mass – nominal mass

where:
nominal mass = integer mass of the elemental composition

The application calculates the integer mass by using the selected

rounding function:
• Floor rounds down
• Ceiling rounds up
• Round rounds to the nearest integer value
Relative mass defect 1e6 × (exact mass – nominal mass)/exact mass
Kendrick mass defect Kendrick mass – nominal Kendrick mass

where:
Kendrick mass = a × (b/c)
a = exact mass of the elemental composition
b = nominal mass of the Kendrick formula
c = exact mass of the Kendrick formula

For more information about using the mass defect feature, see these topics: “Filter By Mass
Defect node,” “Calculate Mass Defect node,” and “Mass Defect Plot view.”

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 2 Functional description of the data-processing features
Neutral loss detection and visualization

Neutral loss detection and visualization

The identification of neutral loss fragments in the fragmentation spectra for an unknown
compound adds confidence to the identification of the compound.

For LC studies, follow these steps to report neutral loss fragments and to visualize the spectral
peaks that are due to neutral losses from higher-mass precursor ions in the fragmentation
scans for compounds in the Compounds table:
1. Add the Search Neutral Losses node to the processing workflow and specify the neutral
losses for the search. See “Search Neutral Losses node.”
The Group Compounds node automatically connects to the Search Neutral Losses node.

Note The m/z value of an expected fragment ion equals the m/z value of the best MS2
ion minus the user-specified neutral loss.

Tip Because the Search Neutral Losses node is downstream of the Group Compounds
node, you can quickly run a neutral loss search by reprocessing a previous analysis. See
“Reprocess an analysis.”

2. After you run an analysis with a processing workflow that includes the Search Neutral
Losses node, open the result file.
The Search Neutral Losses node generates the following:
• The Neutral Losses column in the Compounds table
• The main Neutral Losses table (see Neutral Losses table)
• A related Neutral Losses table for each detected compound
3. To check how many compounds the analysis found for each specified neutral loss, click
the Neutral Losses tab in the main result tables pane.
Figure 21. Neutral Losses table for an analysis with two specified neutral losses

Number of compounds with fragmentation scans

that include these neutral losses

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 2 Functional description of the data-processing features
Neutral loss detection and visualization

4. To make it easier to review the neutral losses for compounds of interest, modify the layout
of the result page as follows:
a. Close the Chromatograms view by clicking the close icon in the upper-right corner of
the view.
b. Click the Compounds tab to open the Compounds table.
c. Right-click the Compounds table and choose Enable Column Fixing. Then, scroll
to the right and click the pin icon to the right of the Neutral Losses column header.
The Neutral Losses column moves to the leftmost column position.
d. Right-click the Compounds table and choose Expand All Column Headers.
The selected neutral losses are visible as subheadings in the Neutral losses column.
e. To sort the neutral losses by one of the neutral losses, select the specific (vertical)
neutral loss heading. Then, click the Neutral Losses column header until the arrow
points down.
f. (Optional) To pin compounds of interest to the top of the table, click the pin icon to
the right of their row numbers.
Figure 22 shows a result table from a processing workflow with the Search Neutral Losses
node with two neutral losses selected: glucuronide and glucuronic acid. The Neutral
Losses column is fixed at the left, and a compound is pinned to the top of the table.
Figure 22. Result file from a processing workflow with the Search Neutral Losses node (with
column fixing enabled and a compound pinned to the top of the table))

Neutral Losses column

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 2 Functional description of the data-processing features
Neutral loss detection and visualization

5. To view specific neutral losses for a compound in the Mass Spectrum view, do the
following:
a. Select the compound in the main Compounds table.
b. Click Show Related Tables at the bottom left of the result page.
c. In the first related tables pane, click the Neutral Losses tab.
d. In the Neutral Losses table, select the neutral loss that you want to visualize in the
mass spectrum.
e. In the Mass Spectrum view, review the fragmentation spectrum with the selected
neutral loss.
6. To return the Mass Spectrum view to the normal view, click another row in the
Compounds table.
Figure 23. Fragmentation spectrum with annotated neutral loss

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 2 Functional description of the data-processing features
Using quality control samples to compensate for batch effects

Using quality control samples to compensate for batch effects

When acquiring raw data files for a large sample set by running an uninterrupted acquisition
sequence, you can use pooled quality control samples to compensate for time-dependent
batch effects. For information about batch effects, refer to the following article: Procedures for
large-scale metabolic profiling of serum and plasma using gas chromatography and liquid
chromatography coupled to mass spectrometry.5

To create a pooled quality control sample, combine a small aliquot from each sample in the
processing batch (input file set to be processed to create one result file). When setting up an
acquisition sequence, bracket the unknown samples by injecting this pooled quality control
sample at regular intervals.

For details about processing the raw data files from a sequence with quality control samples,
see these topics:
• Batch normalization for single sequence runs
• Batch normalization for multiple sequence runs (LC studies)

Batch normalization for single sequence runs

When the processing workflow includes the Apply QC Correction node and the input file set
includes QC samples, an analysis uses the QC samples to create a regression curve of area
versus acquisition time for each detected compound.

Note For information about setting up a processing workflow for a QC-corrected sample
set, see “Apply QC Correction node.” For information about reviewing the corrected
compound areas for a QC-corrected sample set, see “Compound Area Corrections view.”

An analysis does not create a regression curve for a particular compound and does not correct
the areas in the non-QC samples unless all three of these conditions are met:
• It detects the compound in the user-specified minimum percentage of the QC samples.
• The relative standard deviation of the detected peak areas for the compound in the QC
samples before and after correction does not exceed the user-specified thresholds.
• The number of samples acquired between the QC samples does not exceed the
user-specified number.

You can view the results of the batch normalization process in the main compounds result
table (Compounds table) and the Compound Area Corrections view. The Norm. Area
column in the compounds table displays the corrected compound areas. The Compound Area
Corrections view shows the effect of the signal correction on the absolute compound areas.

5
Dunn, W.B.; Broadhurst, D.; Begley, P.; Zelena, E.; Francis-McIntyre, S.; Anderson, N.; Brown, M.; Knowles,
J.D.; Halsall, A.; Haselden, J.N.; Nicholls, A.W.; Wilson, I.D.; Kell, D.B.; Goodacre, R. Human Serum
Metabolome (HUSERMET) Consortium. Nat Protoc. 2011, 6(7), 1060-83.

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 2 Functional description of the data-processing features
Batch normalization for multiple sequence runs (LC studies)

When the application excludes the selected compound during the QC signal correction step,
the Compound Area Corrections view is empty. In addition, the Norm. Area column for the
compound is empty across all the input files, and a filter icon appears on the compounds table
tab. Pointing to the tab displays a tooltip with the number of displayed compounds, detected
compounds, and filtered-out compounds. Clicking the filter icon displays all the detected
compounds, including the compounds with uncorrected peak areas.

For additional information, see Chapter 4, “Set up, run, and reprocess analyses,” and
“Compound Area Corrections view.”

Batch normalization for multiple sequence runs (LC studies)

For LC studies, use the Apply SERRF QC Correction workflow node when you are
processing input files from batches acquired with more than one sequence run, and the time
lapse between the sequence runs was greater than the time lapse between individual sample
runs. SERRF stands for systematic error removal with random forests.

IMPORTANT The input files can comes from different batches, but the parameter settings
for the instrument methods used in these different batches must be the same.

The node determines how to divide the input files into batches as follows:
1. The node orders the input files by their acquisition times.
2. After the node groups the input files by time and determines the largest time gaps, it
attempts to divide the input files into the number of user-specified batches, while
maintaining a minimum of five QC samples per batch. The node assumes that the biggest
gaps in the series of acquisition times are due to the time gaps between batches.
3. If a batch (as determined by a time gap) contains fewer than five QC samples, the node
merges it with the smallest neighboring batches. If the node cannot create multiple
batches with five QC samples each, it assigns all the input files to the same batch. The
SERRF algorithm can process one batch without problems.
4. The node numbers the detected batches, starting with 0, and reports the sequential batch
number (0 to the maximum user-specified batch number) in the Batch column of the
Input Files result table.

For information about adding the Apply SERRF QC Correction node to a processing
workflow, see “Peak area refinement node connections.” For information about the node
parameters, see “Apply SERRF QC Correction node.”

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 2 Functional description of the data-processing features
Stable isotope labeling experiments

Stable isotope labeling experiments

Stable isotope labeling experiments are fundamental to understanding metabolic pathways
and the turnover rate (flux) for the molecules in these pathways. Where traditional approaches
are usually limited to targeted analyses, which detect and quantify known compounds and
their labeled downstream metabolites, the Compound Discoverer application makes full use
of continuous high-resolution accurate-mass (HRAM) full scan data from the Orbitrap™ MS
(coupled to a liquid chromatograph).

Using an unlabeled reference sample, the application detects unknown compounds above a
specified minimum intensity threshold, determines their elemental composition and identity,
and then determines the labeled counterparts (isotopologues) of these compounds in the
samples marked as labeled.

You can use any isotopic label in your experiments; however, when you use a label other than
carbon-13, you must specify the labeled element in the processing workflow.

The application reports the isotopologues and the fractional label incorporation (exchange
rate) for each compound. You can overlay the exchange rate as well as other statistical data
onto pathways using Metabolika™, which is directly integrated into the Compound
Discoverer application.

To acquire and process stable isotope labeled data, do the following:

1. Acquire LC/MS/MS data for a set of samples where at least one sample corresponds to the
unlabeled state of the system.
2. In the Compound Discoverer application, select the following sample types:
• For unlabeled samples, select Sample, Identification Only, Quality Control, or
Blank as appropriate. You must select Sample (or Control or Standard) for at least
one sample.

Note Currently, the application treats Sample, Control, and Standard samples
the same way. This functionality is subject to change in future releases.

• For labeled samples, select Labeled.

3. Select one of the processing workflows in the following folder:
Common Templates\Workflow Templates\LC\Stable Isotope Labeling
4. When using a label other than carbon-13, customize the parameter settings for the
Analyze Labeled Compounds node in the processing workflow. See “Analyze Labeled
Compounds node.”

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 2 Functional description of the data-processing features
Stable isotope labeling experiments

During data processing, the application does the following:

1. Detects and identifies the compounds in the unlabeled samples.
2. Submits the compounds with assigned formulas to the Analyze Labeled Compounds
node which does the following:
a. Generates isotopologues for each detected compound by replacing one occurrence of
an atom at a time by its specified isotope. The formula of the compound or the
user-specified limit defines the number of exchangeable atoms, whichever is smaller.
b. Simulates the isotope pattern for each isotopologue by using its formula and the
spectral resolution of the raw data.
c. Consolidates the isotopologue patterns for each compound to get the final set of
expected masses, considering the specified mass tolerance and the spectral resolution
of the raw data.
d. Generates an XIC trace for each expected mass and detects the chromatographic
peaks.
e. Deconvolves the chromatographic peaks to determine the relative amount of each
isotopologue.
f. Flags compounds containing contaminating masses in unlabeled samples, as well as
unusual isotopologue distributions and insufficient pattern fits.

The Analyze Labeled Compounds node adds the following columns to the Compounds table
in a result file: Labeling Status, Ave. Exchange, and Rel. Exchange Rate. See “Compounds
table (LC studies).”

To determine the presence of contaminating masses, the Analyze Labeled Compounds Node
evaluates the measured isotope pattern versus the fitted isotope pattern (for the expected
isotopologues). It also evaluates the distribution of the measured exchange rates for the
expected isotopologues. If the distribution is not continuous, for example, if the compound
has three exchangeable atoms and chromatographic peak area for the M+2 isotopologue is
significantly less than the chromatographic peak area for the M+1 and M+3 isotopologues,
the node assigns an Irregular Exchange status to the input file.

These flags indicate the following states:

• ( ) Red—Contaminating Mass—The average exchange for the unlabeled sample is
above the 0.1 threshold.
• ( ) Orange—Low Pattern Fit—The measured pattern significantly differs from the fitted
pattern. The SFit value is below the threshold of 20%, the Fitted Coverage value is below
the threshold of 60%, or the Measured Coverage value is below threshold of 60%. To
review these values, see the “Labeled Features table.”

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 2 Functional description of the data-processing features
PFAS identification

• ( ) Blue—Irregular Exchange—The isotopologue exchange rates are discontinuous; for

example, there is a significant valley in the exchange rates profile. This might indicate an
incorrect analysis or a special type of kinetics. However, if this is the typical behavior
expected for your experiments, consider changing the setting for Mark Irregular
Exchanges in the Analyze Labeled Compounds node to False.

• ( ) Green—No Warnings—The measured isotope patterns and the exchange rates are
within acceptable limits.
• ( ) Gray—Compound was not detected in this sample.

PFAS identification
Per- and polyfluoroalkyl substances (PFAS) are a highly stable group of small molecules that
have a wide range of commercial applications. PFAS are highly soluble in water, chemically
stable, persistent in the environment, and can accumulate in the human body over time,
leading to adverse human health effects and potential human health risks. Due to these health
risks and the pervasiveness of PFAS in common household items, some compounds in the
PFAS family have been banned and analytical tests have been developed to check for their
presence.

LC-MS/MS analysis is a common analytical technique used for determining the presence of
per- and polyfluoroalkyl substances in extraction solutions. The Compound Discoverer
application supports the identification of PFAS in raw data files acquired with a Thermo
Scientific high-resolution accurate-mass (HRAM) mass spectrometer. The data files must
include high-quality MS1 full scans and data-dependent MS2 fragmentation scans.

These topics describe how to use the processing workflow template for PFAS analysis that is
provided with the application and how to review the analysis result:
• PFAS processing workflow template
• Review the results of a PFAS analysis

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 2 Functional description of the data-processing features
PFAS identification

PFAS processing workflow template

Use the following processing workflow template to identify per- and polyfluoroalkyl
substances in raw data files acquired with a Thermo Scientific high-resolution accurate-mass
(HRAM) mass spectrometer:
PFAS Unknown ID w Database Searches and Molecular Networks.cdProcessingWF

You can find this processing workflow template in the following folder for LC studies:
Common Templates\Workflow Templates\PFAS\

Note For information about selecting a processing workflow for an analysis, see “Select a
processing workflow for the analysis.”

The PFAS processing workflow template processes the raw data files as follows:
• Performs retention time alignment, unknown compound detection, and compound
grouping across all samples.
Table 12. Customized parameter settings for the Detect Compounds node in the PFAS
processing workflow template
Parameter Default setting for the node Custom setting for PFAS
Min. Peak Intensity 10,000 (1e4) 1,000 (1e3)
Ions [M+H]+1; [M+K]+1; [2M+FA–H]–1; [2M–H]–1;
[M+Na]+1; [M-H]–1 [2M–H+HAc]–1; [M+Cl]–1;
[M+FA–H]–1; [M–2H+K]–1;
[M–H]–1; [M–H+HAc]–1;
[M–H–H2O]–1

• Predicts elemental compositions for all compounds, fills gaps across all samples, and hides
background compounds (by using the Blank samples).
In the Predict Compositions node, the maximum number of fluorine atoms in the
elemental composition of the compound is limited to 50.
Minimum Element Counts: C H F
Maximum Element Counts: C90 H190 Br3 Cl4 F50 N10 O18 P3 S5
• Identifies compounds by using the following:
– The mzCloud™ mass spectral database (data-dependent MS2)
– The EPA DSSTox database in the ChemSpider chemical structure database (formula
or exact mass)
– The following mass lists, which are provided with the application:
– PFAS_NEG, PFAS_NIST, and PFASSTRUCT-2022-04-20

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 2 Functional description of the data-processing features
PFAS identification

• Flags unknown compounds that share common set of fragments by using the Compound
Class Scoring node.
Uses the following compound class files, which are provided with the application: PFAS
General from FluoroMatch Suite.cLib and \PFAS Fine signature fragment_lib.cLib.
• Generates mass defect values in the Compounds table that are based on the selected mass
defect type (Kendrick for identifying homologous series).
Uses the following Kendrick mass: C F2.
• Generates a molecular network to visualize compounds that might be related.
Uses the following transformation: PFAS Chain Shortening (C F2 -> ) under Other.
• Supports the optional scripting node that is available on AnalyteGuru.
https://www.analyteguru.com/t5/Scientific-Library/Compound-Discoverer-PFAS
-Scripting-node/ta-p/20051

For optimal performance of the analysis, do the following:

• Make sure that your raw data files include high-quality MS1 full scans and full scan
data-dependent MS2 scans
• For optimum performance, add at least one blank sample to the input file set.
For matrices where no blank is available, use a suitable sample containing relatively low
levels of PFAS and modify the parameter settings in the Mark Background Compounds
node. For example, increase the ratio for the Max. Sample/Blank parameter setting. The
default ratio is 5 to 1.
• Use three replicates per sample to simplify peak filtering.

Review the results of a PFAS analysis

After you run an analysis using the PFAS processing workflow template that is provided with
the Compound Discoverer application, open the analysis result and review the results.

Note For more information about reviewing the results from an analysis that used the
PFAS processing workflow template that is provided with the application, refer the
following article:
http://assets.thermofisher.com/TFS-Assets/CMD/Application-Notes/an-001826
-lsms-pfas-analysis-workflow-compound-discoverer-an001826-na-en.pdf

Y To review the results of a PFAS analysis

1. Open the analysis result by double-clicking the job on the Job Queue page or by clicking
the analysis result on the Analysis Results page of a study.

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 2 Functional description of the data-processing features
PFAS identification

2. Apply the following result filters to filter the Compounds table to display only high
confidence candidates with matched fragments as follows:
a. Set the following filters:
AND (All of these conditions must be true.)
• Mass Defect Is Between –0.116 and 0.268 In Type Standard MD
• Peak Rating Is Greater Than 3.00 In Any Sample
• Class Coverage Is Greater Than or Equal To 0.25 In Compound Class PFAS
General from FluoroMatch Suite
• Background is False
OR (One of these conditions must be true in addition to the four AND filters)
– mzCloud Best Match Is Greater Than 75.00
– Class Coverage Is Greater Than 0.00 In Compound Class PFAS Fine
Signature Fragment_Lib
– mzCloud Best Sim Match Is Greater Than 75.00
Figure 24. Result filter to reduce the number of compounds displayed in the Compounds
table to high confidence candidates with matching fragments

b. Click Apply.
Only compounds with a high confidence of belonging to the PFAS family remain
visible in the Compounds table.

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 2 Functional description of the data-processing features
PFAS identification

3. Visualize the relationship among the remaining compounds in a scatter plot as follows:
a. In the application menu bar, choose View > Result Charts.
The Scatter Chart plot opens.
b. In the Data Source list, select Compounds.
c. Make the following selections for the three axes:
• For X Data, select Calc. MW.
• For Y Data, select Mass Defect: Kendrick MD [CF2].
• For Z Data, select RT [min].
d. Click Refresh to display the plot.
In Figure 25, data points from the filtered Compounds table are plotted in three
dimensions using the Kendrick MD of approximately 50 Da or exactly one CF2 to
elucidate the presence of homologous PFAS series. Homologous PFAS series will share
the same Kendrick MD but differ in molecular weight by 50 Da and have increasing
retention time based on PFAS chain length. The retention time is color coded as a third
dimension to provide a simple verification of this trend.
Two homologous series are identified at Kendrick MD [CF2] of -0.03 and -0.015
(highlighted by the two red rectangles in Figure 25). In the longer series, there are two
overlapping PFAS with a molecular weight of 349.9471 Da, which corresponds to
perfluoropentanesulfonic acid. To resolve this overlap, one data point is plotted as a
triangle instead of a circle. The compound that corresponds to the blue circle does not
follow the retention time trend of increasing retention with increasing chain length. This
retention time deviation is most likely explained by an alternate branching structure.

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 2 Functional description of the data-processing features
PFAS identification

Figure 25. Scatter chart with a plot of the Kendrick mass defect for C F2 (y axis) against the
Calc. MW of the compound (x axis) and the retention time of the compound (z axis)

C5HF11O3S

C4HF9O3S C6HF13O3S

Overlapping PFAS

4. After you filter the Compounds table to display only potential PFAS, visualize the
molecular network between the compounds as follows:
a. Right-click the Compounds table and choose Molecular Networks > Send to
Viewer.
The Export Molecular Networks dialog box opens.
b. Select the Open Viewer After Export check box, and then click Export.
The viewer opens in a web browser where you can adjust the settings to optimize
clustering. For PFAS, class-based clustering is based on fragmentation and the
detection of homologous series by selecting the PFAS chain shortening
transformation in the Generate Molecular Networks node. This transformation
accounts for the addition or removal of up to ten CF2 moieties that correspond with
the expected differences in chain length for PFAS homologous series.

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 2 Functional description of the data-processing features
Methods for imputing values for missing chromatographic peaks across a set of input files

Figure 26. Molecular Networks viewer with PFAS

Methods for imputing values for missing chromatographic peaks

across a set of input files
For various statistical analyses, zero values within a sample set can lead to erroneous results. To
avoid this type of error, the Compound Discoverer application provides methods for imputing
missing chromatographic peak areas for detected compounds across the set of input files that
you submit for analysis.

For LC studies, you can add one of the following two nodes to the processing workflow to
impute missing peak areas: Fill Gaps or Apply Missing Value Imputation. The processing
workflow templates for LC studies use the Fill Gaps node, which fills the gaps for missing
chromatographic peaks by revisiting the original XIC traces and searching below the noise
threshold. Use the Apply Missing Value Imputation node only if the Fill Gaps node does not
give you the expected results. The Apply Missing Value Imputation node is a peak area
refinement node that does not revisit the original data stream.

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 2 Functional description of the data-processing features
Methods for imputing values for missing chromatographic peaks across a set of input files

For details, see these topics:

• Random Forest imputation method
• Median + Small Value imputation method
• Gap filling method

Random Forest imputation method

The Random Forest method that you can select in the Apply Missing Value Imputation
workflow node of a processing workflow uses a machine learning algorithm that trains itself
on the set of peak profiles of the compounds detected across all input files. For this method,
you specify the number of trainings (iterations) and the number of decision trees for each
training.

Median + Small Value imputation method

The Median + Small Value method that you can select in the Apply Missing Value Imputation
workflow node of a processing workflow uses one of two calculation methods to impute the
area of a missing chromatographic peak. The method it uses depends on whether all or only
some of the samples in each study group are missing the chromatographic peak for a
compound.
• Partially missing peak area—If the compound is detected in one or more input files in a
study group—that is, if the compound is only partially missing from the study group, this
method imputes a value for the missing areas that is close to the mean of the non-missing
values within the same study group. The imputed value is calculated so that the
coefficient of variation (CV) for all the peak areas in the groups (imputed and
experimentally acquired) is similar to the CVs for this compound in other study groups.
• Completely missing peak area—If the compound is not detected in any of the input files
in a study group—that is, the compound is completely absent from the group, the
Median + Small Value method imputes the area for a missing peak by dividing the
smallest chromatographic peak area detected in the input file by 2.

To avoid distorting the CVs of the sample groups with missing or partially missing peaks, this
imputation method does the following:
• Adds a corresponding variability to the mean for a partially missing group.
• Adds the smallest value detected in the input file divided by 2 for a completely missing
group.

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 2 Functional description of the data-processing features
Methods for imputing values for missing chromatographic peaks across a set of input files

• Calculates the typical (or local) standard deviations by using local estimations (depending
on the median of the areas) of the compound CVs. It uses a maximum number of 50
neighbors to estimate a local CV. The number of neighbors is lower than 50 if there are
fewer than 100 compounds with at least three sample-replicate values in the dataset. After
it estimates the local CVs, it removes the local outliers and estimates the local median
CVs with the remaining data.
• Calculates the mean (or minimum value) plus the added variability as a random value
(positive or negative). The added variability follows a Gaussian distribution that is
centered at the mean (or minimum value) with a standard deviation that corresponds to
the estimated typical standard deviation for similar area values for other study groups in
the analysis.

Gap filling method

For LC studies, the Fill Gaps node of a processing workflow calculates the area of missing
chromatographic peaks as follows.
1. Calculates the detection limit for each missing ion as an area of a simulated Gaussian peak
that starts and ends at a zero intensity baseline. To calculate the area of the Gaussian peak,
the node uses the expected peak width and the maximum spectrum noise in the expected
retention time range multiplied by the S/N threshold.
2. Searches for the missing ion with the expected m/z × RT dimensions against all detected
ions (in the mass list generated by the Detect Compounds node) while ignoring the
assigned adduct type. If it finds a match (ion with the expected m/z × RT dimensions), it
uses the ion’s area to fill the gap and displays Filled by Matching Ion for the Fill Status.
3. If the node does not find a matching ion, it attempts to detect the peak at a lower
intensity threshold by using the new peak detection algorithm in the detect compounds
node (the new Detect Compounds node or the Detect Compounds (Legacy) node. If it
detects a chromatographic peak at a lower threshold, it uses the integrated peak area to fill
the gap and displays Re-detected Peak for the Fill Status.
4. If the node does not find a chromatographic peak by using a lower intensity threshold, it
fits a Gaussian peak to the XIC trace for the expected m/z range and displays Filled by
Simulated Peak for the Fill Status.
5. If the filled area is still zero or lower than the detection limit, the node uses the detection
limit value to fill the gap and displays Filled by Spectrum Noise for the Fill Status.
6. If the node cannot fill the gap, it displays Area Could Not Be Filled for the Fill Status.

For details about the parameter settings for the Fill Gaps node, see “Fill Gaps node.”

Thermo Scientific Compound Discoverer User Guide for LC Studies 96

 3

Create a new study and an analysis by using the

wizard
Use the New Study and Analysis Wizard to create a new study and set up a new analysis.
Before you start the wizard for the first time, review the available sample types and the
directory structure for studies.

Note For information about the terminology used in the Compound Discoverer
application, see “Terminology used in the Compound Discoverer application.”

Preliminary information:
• Available sample types
• Directory structure for Compound Discoverer studies
• Create a study template file that contains all the study information

To set up a new study and a new analysis, follow these steps:

1. Start the New Study and Analysis Wizard.
2. Define the study type, name the study, and optionally select a study template and a
processing workflow.
3. Add input files to the new study.
4. Characterize the new input files.
5. (Optional) Extract study factor values from the file names of the input files.
6. (Optional) Set up the sample groups and ratios for a new analysis.
7. Prepare to submit the analysis to the job queue.

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 3 Create a new study and an analysis by using the wizard
Available sample types

Available sample types

Table 13 describes the sample types that the application supports and how it uses these sample
types.

For information about selecting the sample types, see “Select the sample types.”
Table 13. Sample types
Sample type Application use
a
Sample Detects the compounds in the sample.
Controla Detects the compounds in the sample.
Blank Detects the compounds in the sample. When the processing
workflow includes one or both Mark Background Compounds
nodes, marks these components as background compounds.
Identification Only Does not report the chromatographic peak areas for the
(LC studies only) compounds detected in this sample type. Uses the fragmentation
scans in this sample type for component identification when the
processing workflow includes the Group Compounds node.
Quality Control Detects the compounds in the sample. Pools the QC samples to
determine a group area for each detected compound for area
normalization.
Standarda Detects the compounds in the sample.
Labeled Determines the formulas for the compounds in the labeled
(LC studies only) samples.
a
The application attributes the same functionality to the Sample, Control, and Standard sample types. You can use
the Control and Standard sample types to label your control or standard samples; that is, you can use these sample
types as an additional study variable for grouping.

Directory structure for Compound Discoverer studies

Figure 27 shows the hierarchy of the study folders. The studies folder is the top-level folder for
all your studies or a particular set of studies. Each study folder within the studies folder holds
one study file (.cdStudy) and one or more result files (.cdResult).

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 3 Create a new study and an analysis by using the wizard
Directory structure for Compound Discoverer studies

Note You can create more than one top-level folder for your studies. Each time you open
the New Study and Analysis Wizard, it opens to the last opened top-level folder.

Study files include a list of input files with their location, the sample information for each
file, and a list of the analyses run within the study. The sample information includes the
file name, study factor values, and sample type for each sample.

Result files contain the results of an analysis in tabular form. In addition, you can access
multiple views for visualizing the analysis results when you open a result file in the
application window.

Figure 27. Studies folder structure

Top-level folder

My Studies Study folders in the Files in each study folder

top-level folder

Study 1 Study 1.cdStudy File A1.cdResult

Study 2 Study 2.cdStudy File B1.cdResult

Study 3 Study 3.cdStudy File C1.cdResult

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 3 Create a new study and an analysis by using the wizard
Create a study template file that contains all the study information

This figure shows an example of the directory hierarchy for a study named Omeprazole Study
with one result file. The individual study folder and the study file share the same name.
Top-level folder where the application stores the individual study folders
Individual study folder

Contents of the
Omeprazole Study
folder

Create a study template file that contains all the study information
There are two ways to create a study template file.

For details, see the following topics:

• Manually create a template that includes all the study information
• Edit a spreadsheet for use as a study template

For information about selecting a study template file for a new study, see “Define the study
type, name the study, and optionally select a study template and a processing workflow.”

Manually create a template that includes all the study information

If you have already run an analysis that includes the study information for all your input files,
you can export the study information from the result file to a spreadsheet. After you export
the information to a spreadsheet, you must edit the information to make it compatible with
the New Study and Analysis Wizard.

Y To export the study information in a result file to a spreadsheet

1. Open a result file that includes the study information of interest.

2. Click the Study Information tab.
3. Click the Field Chooser icon, , in the upper-left corner of the active table.
4. In the Field Chooser dialog box, clear all the check boxes except those for the CF: study
factor name, File Name, and Sample Type. Then, close the dialog box.
5. Right-click the Study Information page and choose Export > As Excel.

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 3 Create a new study and an analysis by using the wizard
Create a study template file that contains all the study information

6. In the Export to Excel dialog box, select the folder where you want to store the Excel
spreadsheet, select the All Items option, select the Open File After Export check box,
and then click Export.
The exported spreadsheet opens in the spreadsheet application.
7. Change the File Name column heading to File.
8. Save the spreadsheet.

Edit a spreadsheet for use as a study template

If you already have a spreadsheet with all the study information you need, you can edit the
spreadsheet to make the information available to the New Study and Analysis Wizard.

Y To edit a spreadsheet for use as a study template

1. Open the Excel spreadsheet application and create a new spreadsheet.

2. Set up columns with the following column headers:
• Column A: File
• (Optional) Column B: Sample Type
If the spreadsheet does not include a Sample Type column, the application assigns the
Sample as the sample type for all the input files.
• Column C and higher:
– For a categorical study factor, type CF: study factor name.
– For a numerical study factor, type NF: study factor name.
You can append a unit to the end of a numerical study factor, for example,
NF: Solution [mL].
– For a biological replicate factor, type BF: study factor name.
If you do not label the study factor columns CF:, NF:, or BF:, the application treats
them as categorical study factors.
3. Add the following information to the columns:
• Column A: complete directory path and file name for each input file
• Column B: sample type for each input file
• Column C and higher: study factor value for each input file
4. Save the file as a spreadsheet file.

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 3 Create a new study and an analysis by using the wizard
Start the New Study and Analysis Wizard

Start the New Study and Analysis Wizard

To create a new study, you use the New Study and Analysis Wizard. You can start the wizard
in several ways.

Y To start the New Study and Analysis Wizard

Do one of the following:

• From the menu bar, choose File > New Study and Analysis.
• In the toolbar, click the Create a New Study and Analysis icon, .
• On the Start page under What Would You Like to Do?, click New Study and
Analysis.
The New Study and Analysis Wizard opens to the Study Name and Processing Workflow
page (step 1 of 5).
The wizard has embedded “How To” instructions that you open by clicking the light bulb
icon, , in the lower-left corner. In addition, there is a context-sensitive Help topic for
each page of the wizard. To open the context-sensitive Help for the current page of the
wizard, press the F1 key on your computer keyboard.

Define the study type, name the study, and optionally select a study
template and a processing workflow
To start the New Study and Analysis Wizard, see “Start the New Study and Analysis Wizard.”
The wizard opens to the Study Name and Processing Workflow page.

Use the Study Name and Processing Workflow page (step 1 of 5) of the New Study and
Analysis Wizard to do the following:
• Select the study type: LC or GC (chromatography type = liquid chromatography or gas
chromatography).
• Name the current study. This step automatically creates a study folder and a study file
with the same name. See “Directory structure for Compound Discoverer studies.”
• Select a current folder or create a new top-level folder for storing all the study folders or a
subset of the study folders.
• (Optional) Select a template file for the study.
A study template file is either a study file that includes defined study factors or a
tab-delimited text file or spreadsheet file that includes all the study information. The
study information includes the location, sample types, and study factors for all the input
files in a study.
• (Optional) Select a processing workflow for the analysis.

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 3 Create a new study and an analysis by using the wizard
Define the study type, name the study, and optionally select a study template and a processing workflow

Note You can select a processing workflow after you create the study.

Figure 28. New Study and Analysis Wizard – Study Name and Processing Workflow page

Displays the embedded Help to the left of the page

For more information about the Study Name and Processing Workflow page of the wizard, see
these topics:
• Select the study type
• Name the new study, select the top-level studies folder, and optionally select a study
template
• Select a processing workflow for the analysis

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 3 Create a new study and an analysis by using the wizard
Define the study type, name the study, and optionally select a study template and a processing workflow

Select the study type

The New Study and Analysis Wizard is open to the Study Name and Processing Workflow
page. See “Start the New Study and Analysis Wizard.”

Y To select the study type

In the Study Type area, do one the following:

• Select the GC option for a GC study.
• Select the LC option for an LC study.

The Workflows list in the Processing area includes the processing workflow templates that are
available for the study type that you selected.

Note The wizard retains this selection (LC or GC) after you close it. The next time you
create a new study, the Study Type area displays your last selection.

You can process either GC/MS data or LC/MS data from within a study; you cannot
process both types of data from within the same study. After you create a study, you
cannot modify its study type.

You can perform step 1 through in any order—that is, naming the study, selecting the
studies folder, and selecting a processing workflow are independent of each other.

Name the new study, select the top-level studies folder, and optionally select a
study template
The New Study and Analysis Wizard is open to the Study Name and Processing Workflow
page and you have selected the study type. See Start the New Study and Analysis Wizard and
Select the study type.

Y To name a new study, select the top-level studies folder, and optionally select a study
template
1. In the Study Name and Directory Structure area, type a name for the new study in the
Study Name box.

Note When you create a new study, the application uses the study name that you
specify for two items: the study file (.cdStudy) and the study folder where it stores the
study file. The application stores the result files from the analyses run within the study
in this named study folder. For details, see “Directory structure for Compound
Discoverer studies.”

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 3 Create a new study and an analysis by using the wizard
Define the study type, name the study, and optionally select a study template and a processing workflow

Note The first time you create a study, the studies folder is undefined and the Studies
Folder box is empty and outlined in red. If you have already created at least one
studies folder, the Studies Folder box is populated with the name and location of the
last studies folder that you created.

2. Use the current folder name and location that is displayed in the Studies Folder box or do
the following to select an existing folder or create a new folder:
a. Click the browse icon to the right of the Studies Folder box.
Figure 29. Undefined studies folder

The Select Folder dialog box opens.

Figure 30. Select Folder dialog box

b. Browse to an existing folder or use the New Folder command to create a new folder.

The name and location of the new folder appear in the Studies Folder box.

Note You can store all your study folders in a single top-level folder or categorize
your studies by setting up multiple top-level folders. See “Directory structure for
Compound Discoverer studies.”

Tip To create two studies with the same name but different data types, store the
two studies in different folders.

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 3 Create a new study and an analysis by using the wizard
Define the study type, name the study, and optionally select a study template and a processing workflow

3. (Optional) To select a study template file, click the browse icon, , next to the Study
Template File box. Then, do one of the following:
• To import only the study factors for the study, browse to and select a study file
(.cdStudy).
• To import all the study information, browse to and select a text file or a spreadsheet
file that contains the study information in a compatible format.

Note To create a spreadsheet that contains all the study information, see “Create
a study template file that contains all the study information.”

Select a processing workflow for the analysis

You can select a processing workflow (workflow template) on the Study Name and Processing
Workflow page of the New Study and Analysis Wizard or on the Workflows page of an
analysis.
• For information about opening the New Study and Analysis wizard, see “Start the New
Study and Analysis Wizard.”
• For information about starting a new analysis from within a study, see “Set up a new
analysis from within an existing study.”
• For information about opening th Workflows page of an analysis, see “Select a workflow
template.”

Y To select a processing workflow for the current analysis

Do either of the following:

• Select a processing workflow from the Workflow list.
The Workflow list displays the processing workflow files in the Common Templates
folder for the study type that you selected in New Study and Analysis Wizard. Before
you select a processing workflow on the Study Name and Processing Workflow page
of the wizard, select the study type: GC or LC.
• Select a processing workflow or result file from another folder by clicking the browse
icon, , next to the Workflow list.
When you select a processing workflow file, the file name appears in the Workflow
list. When you select a result file, the following text appears in the Workflow list:
Imported from: File name
where:
File name is the file name of the result file
If the processing workflow includes a description, the description appears in the
Workflow Description box below the Workflow list.

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 3 Create a new study and an analysis by using the wizard
Add input files to the new study

If you are creating a new study and a new analysis in the New Study and Analysis Wizard,
click Next to go to the Input File Selection page of the wizard.

Add input files to the new study

Use the Input File Selection page of the New Study and Analysis Wizard to select all the input
files for the new study or only those input files that you want to process with the current
analysis. If you click Finish before you add files to the study, the wizard saves the named study
to the named folder and closes.

For information about starting the wizard and defining the study, see “Define the study type,
name the study, and optionally select a study template and a processing workflow.”

Note The example Xcalibur RAW files for the tutorials are on the Compound Discoverer
USB key in the software media kit or in the software media that you downloaded from the
Life Sciences and Mass Spectrometry Software Download and Licensing Portal website
page. The software installation process does not install the example files on your
processing computer.

Y To add raw data files

1. On Input File Selection page of the wizard, click Add Files.

2. Browse to the appropriate folder, select the Xcalibur RAW files of interest, and click
Open.
Figure 31. Input File Selection page of the wizard

The file names of the selected files appear in the Files box, the number of files that you
selected appears below this box, and the Next button becomes available.

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 3 Create a new study and an analysis by using the wizard
Add input files to the new study

Figure 32. Input File Selection page with selected files (brown O-rings and red O-rings)

Number of files field

Tip To remove any of the added files, select them and click Remove Files.

3. Do one of the following:

• Click Next to continue to the Input File Characterization page.
• Click Finish to create the new study and close the wizard.

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 3 Create a new study and an analysis by using the wizard
Characterize the new input files

Characterize the new input files

You can set up the sample information for the input files in a study in two ways:
• You can use the Input File Characterization page (step 3 of 5) of the New Study and
Analysis Wizard that opens after you add new input files on the Input File Selection page
of the wizard.

–or–
• You can use the Input File Characterization dialog box that opens when you add input
files to an existing study.

The sample information includes the sample type and study factor values for each sample.

For information about starting the New Study and Analysis Wizard, see “Start the New Study
and Analysis Wizard.”

Note In an existing study, you can do the following:

• Use the Input File Characterization dialog box to add and edit the study factors and
set up the sample information for additional input files.
• Add and edit the study factors on the Study Definition page.
• Manually select the sample types and study factor values on the Samples page.

Figure 33 shows the Input File Characterization page of the wizard.

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 3 Create a new study and an analysis by using the wizard
Characterize the new input files

Figure 33. Input File Characterization page of the wizard (with 12 O-rings)
Opens the Extract Sample Information from Sample Names dialog box
Automatically assigns the defined study factor values

To characterize the input files for a study, follow these steps as applicable:
1. Select the delimiters for parsing the file names.
2. Add or edit the study factors.
3. To select or assign the study factor values to the samples (in the Samples area), see the
following topics as applicable:
• Automatically assign the study factor values
• Manually select the study factor values
• Reset the sample assignments
4. Select the sample types.

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 3 Create a new study and an analysis by using the wizard
Characterize the new input files

Select the delimiters for parsing the file names

You can select the delimiters for parsing a file name on the Input File Characterization page of
the New Study and Analysis Wizard or in the Input File Characterization dialog box. For
information about opening the Input File Characterization page or dialog box, see
“Characterize the new input files.”

Y To select the delimiters that separate the factors in the file names

1. Select the check box or check boxes of the delimiter or delimiters for the input file names.

For example, the underscore character is the delimiter that separates the study factors
from the other parts of the file name in the following file names:
In this case, the study factors are O-ring color and solvent. The O-ring colors are red and
brown. The solvents are water and ethanol.

Blank_100EtOH_1 Blank_H2O_1
Blank_100_EtOH_2 Blank_H2O_2
Red_100EtOH_1 Red_H2O_2
Red_100EtOH_2 Red_H2O_1
Brown_100EtOH_1 Brown_H2O_1
Brown_100EtOH_2 Brown_H2O_2

2. If the delimiter is not available, select the Other check box and type the delimiter
character in the box.

Add or edit the study factors

A study can include many study factors. You can add and edit the study factors on the Input
File Characterization page of the New Study and Analysis Wizard or the Study Definition
page of an existing study.

For details, see these topics:

• Add categorical study factors
• Add numeric study factors
• Add biological replicate study factors
• Delete study factors
• Duplicate study factors
• Edit study factors

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 3 Create a new study and an analysis by using the wizard
Characterize the new input files

Add categorical study factors

You can add study factors when you create a new study, when you add files to an existing
study, and on the Study Definition page of an existing study.

Y To add a categorical study factor to a study

1. From the menu bar at the top right of the Study Factors pane, choose Add > Categorical
Factor.
The categorical factor editor appears with [new factor] automatically selected.
Figure 34. Categorical factor editor

2. Select the [new factor] text and type the name of the factor.
For example, type Color.
3. For each item that you want to add to the Items list, do the following:
a. In the Items box (to the left of the Add button), begin typing a factor.
For example, type Red for one of the Color study factor items.
If the file name contains a character delimiter (underscore, hyphen, comma, space,
plus, or other defined character) and you selected the check box for this delimiter, the
editor automatically enters the appropriate text in the Items box as you start typing.
Otherwise, you must type all the characters for the item.

Note The file name parsing feature is not available on the Study Definition page
of an existing study, so you must type all the characters for the item.

The Add button becomes available.

Add button

b. Click Add.
The current item appears in the Items list.

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 3 Create a new study and an analysis by using the wizard
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4. To save the study factor, click Apply.

The factor editor collapses to show only the study factor name and the Items list. The
items appear in ascending order.

Tip To continue editing the study factor, click Edit. The editor expands, providing
access to the study factor name and items.

Add numeric study factors

You can add study factors when you create a study, when you add files to an existing study,
and on the Study Definition page of an existing study.

Y To add a numeric factor to a study

1. From the menu bar at the top right of the Study Factors pane, choose Add > Numeric
Factor.
The numeric factor editor appears with [new factor] automatically selected.
Figure 35. Numeric factor editor

2. Type a factor name to replace [new factor], for example, Replicate.

3. Point to the right of Factor Unit and, in the box that appears, type a unit for the factor if
applicable.
The Factor Unit is only a text label; however, it must start with a letter.
4. For each numeric value that you want to add to the Values list, do the following:
a. In the box next to the Add button, type a numeric value.
The Add button becomes available.

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 3 Create a new study and an analysis by using the wizard
Characterize the new input files

Figure 36. Entering numeric values in the values box

Add button

b. Click Add.
The value appears in the Values list in ascending order.
5. To save the study factor, click Apply.
The factor editor collapses to show only the study factor name and the Values list.
Figure 37. Numeric factor with a list of values

Tip To continue editing the study factor, click Edit. The editor expands, providing
access to the study factor name and items.

Add biological replicate study factors

You can add study factors when you create a study, when you add files to an existing study,
and on the Study Definition page of an existing study.

You can add only one biological replicate factor to a study. Use the biological replicate factor
for nested statistical models—that is, for studies that include one study factor nested within
another study factor.

Y To add a biological replicate factor to a study

1. From the menu bar at the top right of the Study Factors pane, choose Add > Biological
Replicate Factor.
The biological replicate factor editor appears with [new factor] automatically selected.
Figure 38. Biological replicate factor editor

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 3 Create a new study and an analysis by using the wizard
Characterize the new input files

2. Type a factor name to replace [new factor].

3. For each item that you want to add to the Items list, do the following:
a. In the Items box (next to the Add button), type a study factor item.
The Add button becomes available.
b. Click Add.
The current item appears in the Items list.
4. To save the study factor, click Apply.
The factor editor collapses to show only the study factor name and the Items list. The
items appear in alphabetical order.

Tip To continue editing the study factor, click Edit. The editor expands, providing
access to the study factor name and items.

Delete study factors

You can delete study factors in the Study Factors pane on the Study Definition page or the
Study Factors pane on the Input File Characterization page or dialog box.

Y To delete a study factor from a study

1. In the Study Factors pane, click in the title bar of the factor.

Note Because the application cannot recognize whether a study factor is in use, this
prompt appears even when you attempt to delete an undefined study factor.

2. At the prompt, click Yes to delete the study factor.

Duplicate study factors

You can use the Copy and Paste commands to duplicate and create new study factors in the
Study Factors pane on the Study Definition page or the Study Factors pane on the Input File
Characterization page or dialog box.

Y To create a new study factor by using the Copy and Paste commands

1. In the Study Factors pane, select the factor that you want to copy.
The title bar of the selected factor turns blue.
2. Click Copy. Then, click Paste.
A copy of the selected factor appears.

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 3 Create a new study and an analysis by using the wizard
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Edit study factors

You can edit study factors as you create a new study with the wizard, in Study Factors area of
the Input File Characterization dialog box when you add more files to an existing study, and
in the Study Factors area on the Study Definition page of an existing study.

Y To edit a study factor

1. In the factor title bar, click Edit.

The text entry box and the Add and Delete buttons appear. For a numeric factor, the
Factor Unit box also appears.
2. To change the unit for a numeric factor, select the current unit and type a new unit.
3. To add more entries to the Items or Values list, type alphanumeric text in the appropriate
box, and then click Add.
4. To delete an entry, select the entry and click Delete.
When an entry is in use, it is unavailable. To delete a value that is in use, you must first
undo its assignment to any sample.

Automatically assign the study factor values

After you set up the study factors for a study, you can assign the study factor values to each
sample. If the input file names follow a consistent pattern and the study factor values are
completely defined, clicking Assign on the Input File Characterization page (or dialog box)
assigns the study factor values to the samples.

Note You can only manually assign study factor values on the Samples page of an existing
study.

Y To automatically assign the study factor values to a sample set

1. If you have not already set up the study factors, set them up. See “Add or edit the study
factors.”

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 3 Create a new study and an analysis by using the wizard
Characterize the new input files

Figure 39. Input file Characterization page with two study factors—Color and Solvent

2. In the command bar of the Input File Characterization page or dialog box, click Assign.
The application assigns the study factors to the samples. See Figure 40.

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 3 Create a new study and an analysis by using the wizard
Characterize the new input files

Figure 40. Input file Characterization page with assigned sample types and study factors

3. Check the study factor columns, verify the sample assignments, and manually assign the
study factor values if necessary.

Manually select the study factor values

After you set up the study factors for the study, you can select the study factor values for each
sample. If the input file names do not follow a consistent pattern or do not include the study
factor values or you are selecting the values on the Samples page of an existing study, you have
to manually select these values.

Y To manually select the study factor values

On the Input File Characterization page (or dialog box) or on the Samples page of an
existing study, do the following:
• To select the factor values for a single sample, select the appropriate value from the
list in each factor column.
• To select the same value for a consecutive sample range, drag the pointer across the
rows of interest. Then right-click and choose Set Factor To > Value.
• To select the same value for nonconsecutive samples, hold down the CTRL key and
click the samples of interest. Then right-click and choose Set Factor To > Value.

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 3 Create a new study and an analysis by using the wizard
Characterize the new input files

Reset the sample assignments

On the Input File Characterization page (or dialog box), you can use the Reset button in the
command bar to automatically clear the sample assignments. The Samples page of a study
does not have a command bar.

Y To clear the assignments in the Samples pane

In the command bar, click Reset.

Clicking Reset resets the Sample Type and study factor assignments—that is, it resets the
sample type to Sample and the study factor values to n/a for all the samples.

Note To edit the values for a study factor, you must first clear the sample assignments
if the values are assigned to samples.

Select the sample types

You can select the sample type for the study samples from any of these locations:
• The Samples pane of the Input File Characterization page (page 4 of the wizard)
• The Samples pane of the Input File Characterization dialog box
• The Samples page of an existing study

By default, the selected sample type for each input file is Sample. Clicking Assign on the Input
File Characterization page (or dialog box) automatically assigns the Blank sample type to
samples with a file name that includes “blank” as a delimited value (for example,
solvent_blank_1.raw, where the underscore character is the delimiter).

Y To select a sample type other than the default assignment

In the Samples pane (any location), do any of the following:

• To select the sample type for a single sample, select a sample type from the dropdown
list in the Sample Type column. See “Available sample types.”
• To assign the same sample type to a consecutive sample range, use the SHIFT key to
select a range of samples. Then, right-click and choose Set Sample Type To >
Sample Type.
• To assign the same sample type to nonconsecutive samples, use the CTRL key to
select the samples. Then, right-click and choose Set Sample Type To > Sample Type.

Tip To select a row, click a column without a list.

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 3 Create a new study and an analysis by using the wizard
Extract study factor values from the file names of the input files

Extract study factor values from the file names of the input files
Use the Extract Sample Information From Sample Names dialog box to automate the setup
and assignment of the study factors. This dialog box is accessible from the Input File
Characterization page of the New Study and Analysis Wizard or from the Input File
Characterization dialog box that opens when you add input files to a study.

Note For the extraction and assignment process to work, you must select the study factor
portions of an example input file name and define these portions appropriately as
categorical, numerical, or biological replicate factors.

When the undefined portions of the file name are not exactly the same for all the samples
that you want to characterize, you can mark the text to be ignored or you can manually
assign or edit the study factor values for these samples after returning to the Input File
Characterization page or dialog box.

Y To extract the sample information from the sample names

1. Open the Input File Characterization page (step 3 of 5) of the wizard or the Input File
Characterization dialog box from within an existing study.

Note When you are working within an existing study, the Input File Characterization
dialog box opens when you add files to the study. You cannot open the Input File
Characterization dialog box to characterize raw data files that are already linked to the
study.

2. Click Advanced.
The Extract Sample Information From Sample Names dialog box opens with the first file
name displayed in the Regular Expression Builder box and the file names of all the
selected input files listed below it. See Figure 41.

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 3 Create a new study and an analysis by using the wizard
Extract study factor values from the file names of the input files

Figure 41. Extract Sample Information From Sample Names dialog box

Inserts a regular expression

that does the following:
• Ignores a text string.
• Defines a biological variable.
• Defines a categorical variable.
• Defines a numerical variable.

3. If the Regular Expression Builder box does not contain a representative sample name,
right-click a representative sample name in the Sample Name column and choose Use
Name of Selected Sample as Regular Expression Template.
Figure 42. Urine_0-4hr_01 sample name selected

Right-click command

The selected sample name replaces the nonrepresentative sample name.

Figure 43. Urine 0-4hr file name to be used as the regular expression template

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 3 Create a new study and an analysis by using the wizard
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4. For a representative sample name, do the following:

• For each categorical study factor, select the corresponding study factor item and click
[A-Z].
For example, select 0-4hr and click [A-Z].
The CategoricalVariable_1 column appears to the right of the sample names. In this
example, the application extracts the categorical study factor for the
Urine_Predose_01 sample. The column is not populated with study factor values for
the remaining samples for two reasons:
– The remaining portions of the sample names are not the same (for example, _01
and _02).
– The default expression for a categorical factor does not recognize the hyphen
special character in the 0-4hr, 4-8hr, and 8-12hr time points.
• For each numeric study factor, select the corresponding study factor value and click
[0-9]. For example, select 1 and click [0-9].
For this example, the following expression replaces the file name:
Urine_(?<CategoricalVariable_1>[0-9A-Z]+)_ (?<NumericalVariable_1>[0-9]+)
–and–
Only the study factor values for these file names appear in the table:
Urine_Predose_01 and Urine_Predose_02.
Figure 44 shows the new regular expression in the regular expression builder box. This
expression cannot interpret the time points that include hyphens (0-4hr, 4-8hr, 8-12hr).
Only “Predose” matches the expression, which is looking for an alphanumeric string.
Figure 44. Building a regular expression with the default categorical and numeric operators

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5. If the study factor columns do not populate as expected, modify the regular expression
operators within the square brackets.
Table 14. Examples of regular expression operators
Operator Quantifier Matching pattern
[0-9] none A single integer
[0-9] + One or more integers
[A-Z] none One alphabetic character
[0-9A-Z] none One alphanumeric character
[0-9A-Z] + One or more alphanumeric characters
[0-9A-Z-] + One or more alphanumeric characters, one or more
hyphens, or both (for example, 555-0000)
[0-9A-Z] [0-9A-Z] + One or more alphanumeric characters, a space, and
one or more alphanumeric characters (for example,
ABC 123)

For example, to populate the rows for the other file names with defined time periods, add
a hyphen to the operators in the square brackets. Figure 45 shows the hyphen character
added to the operator set for a categorical factor.
Figure 45. Hyphen building block added to the regular expression for a categorical factor
Original operator set = [0-9A-Z]
Modified operator set = [0-9A-Z-]

6. If the sample names include extra text that differs from sample to sample and does not
define a study variable, exclude this text from the regular expression by selecting it and
clicking .

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 3 Create a new study and an analysis by using the wizard
Extract study factor values from the file names of the input files

Note Figure 46 and Figure 47 show a different sample set than the previous figures.

For example, in the sample set shown in Figure 46, exclude all the characters to the right
of the categorical variable by selecting _01_MDF and clicking .
Figure 46. Selecting the text that you want to exclude from the expression

The application ignores the extra text

when extracting the study factor values
from these sample names.

The regular expression builder replaces the selected text with the following expression:
(?:.+)?
Figure 47 shows the result of these actions:
• Selecting the time period (0-3) as a categorical variable
• Adding a hyphen to the categorical variable expression
• Selecting “_01_MDF” as text to ignore
Figure 47. Regular expression that defines the categorical variable and the text to ignore

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 3 Create a new study and an analysis by using the wizard
Extract study factor values from the file names of the input files

7. To enter the study factor names, type the study factor names in the column-heading
boxes.
For example, replace CategoricalVariable_1 with Time Period and NumericalVariable_1
with Replicate (Figure 45 and Figure 48).
Figure 48. Study factors renamed

Edited study factor names

Tip You can edit the study factor names in two ways:
• In the column-heading boxes, replace the default column headings with the study
factor names.
• On the Input File Characterization page, edit the study factors.

8. Click OK to return to the Input File Characterization page where you can modify the
values in the study variable columns if necessary.

Tip The Regular Expression Builder does not assign sample types. To assign Blank as
the sample type, click Assign on the Input File Characterization page after selecting
the appropriate delimiters.

For example, select the Underscore check box on the Input File Characterization page
and click Assign, for the following file name: Solvent_Blank_1.

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Table 15 describes the parameters in the Extract Sample Information From Sample Names
dialog box.
Table 15. Extract Sample Information From Sample Names dialog box parameters
Parameter Description
Regular Expression Builder

Initially displays the first file name in the Sample Name list. Use this file name (or a
different file name in the list) to build a regular expression that extracts the study factor
values for the file names in the Sample Name list.
Buttons
[0-9] Identifies a numeric factor.

Clicking [0-9] replaces the selected text with the following

expression: (?<NumericalVariable_1>[0-9]+)
[A-Z] Identifies a categorical factor.

Clicking [A-Z] replaces the selected text with the following

expression: (?<CategoricalVariable_1>[0-9A-Z]+)
[A-Z] Identifies a biological replicate factor.

Clicking [A-Z] replaces the selected text with the following

expression: (?<ReplicateVariable_1>[0-9A-Z]+)
Excludes text that does not define a study variable and does not
follow a pattern.

Clicking replaces the selected text with the following

expression: (?:.+)?
Columns
Sample Name Displays the file names of the selected input files.
CategoricalVariable_1 Displays the extracted items for this factor. You can edit the
column heading.
NumericalVariable_1 Displays the extracted values for this factor. You can edit the
column heading.
ReplicateVariable_1 Displays the extracted values for this factor. You can edit the
column heading.

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 3 Create a new study and an analysis by using the wizard
Set up the sample groups and ratios for a new analysis

Set up the sample groups and ratios for a new analysis

Use the Sample Groups and Ratios page of the New Study and Analysis Wizard or the
Grouping & Ratios page of an analysis within an existing study to set up the sample groups
that you want to compare and the group ratios that you want to include in the result file.

Note The Sample Groups and Ratios page of the New Study and Analysis Wizard is the
fourth page of the wizard. To open the fourth page of the wizard, you must select one or
more input files on the second page of the wizard.

Note When you start a new analysis in an existing study, you must manually add the
input files to the Files for Analysis area of the Analysis view.

IMPORTANT Do not create ratios with sample groups that have an n/a assignment for a
study variable. To use a sample group in a ratio, you must replace the n/a assignment with
a study factor value.

Follow these topics:

1. Set up the sample groups for an analysis
2. Set up the group ratios

The Study Variables area contains a File check box, a Sample Type check box, and an
additional check box for each study factor you created on the Input Files Characterization
page of the wizard or the Study Definition page of the current study.

Figure 49 shows the Sample Groups and Ratios page of the wizard. The Generated Sample
Groups area lists the input files for the analysis.

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 3 Create a new study and an analysis by using the wizard
Set up the sample groups and ratios for a new analysis

Figure 49. Sample Groups and Ratios page of the wizard

Set up the sample groups for an analysis

To set up the sample groups for an analysis, follow these procedures:
1. Select the study variables for the sample groups
2. Review the generated sample groups and fix any assignment errors
3. Do the following as appropriate:
• Change the hierarchy of the study variables
• Change the sort order of the study variables

Select the study variables for the sample groups

You select the study variables that you want to group on one of these pages:
• Grouping & Ratios page of an existing analysis

Note To start a new analysis from within an existing study, click New Analysis in the
study command bar. Or, reprocess an existing analysis on the Analysis Results page of
a study.

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Set up the sample groups and ratios for a new analysis

• Sample Groups and Ratios page of the New Study and Analysis Wizard

Note The Sample Groups and Ratios page of the New Study and Analysis Wizard is
the fourth page of the wizard. To open the fourth page of the wizard, you must select
one or more input files on the second page of the wizard.

Y To select the study variables for sample grouping

In the Study Variables area of the page, select the check boxes for the study variable or
variables for sample grouping.
Selected study variables have a light green background, a dark green handle ( ) on the
left, and a Sorting icon ( )on the right.

Primary study variable

Secondary variable

Review the generated sample groups and fix any assignment errors
After you select the study variables for sample grouping, the Generated Sample Groups area
displays the generated sample groups.

The hierarchy of the selected study variables in the Study Variables area affects the sample
group names and the denominator list for bulk ratio generation. See “Change the hierarchy of
the study variables.”

The naming scheme for the study groups in the Generated Sample Groups area is as follows:
• Group names (green) consist of the common values for the selected study variables.
• Sample names (blue) consist of a unique ID and the input file name.

Following data processing, the result file displays the chromatographic peak areas for
individual samples and the named sample groups.

When selecting the study variables generates an n/a sample group that includes Sample,
Control, or Standard sample types, the application highlights the selected study variable and
the n/a group in red and displays the following error message:
There are samples with unset study variables selected for grouping.

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Set up the sample groups and ratios for a new analysis

Figure 50. Error message for unset study variables

Y To fix an assignment error on the Sample Groups and Ratios page of the wizard or the
Grouping & Ratios page of an analysis within an existing study
1. Check the sample type and study factor assignments of the input files as follows:
• If you are creating a new study, in the New Study and Analysis Wizard, return to the
Input File Characterization page.
• If you are modifying an existing study, open the Samples page.
2. Do any of the following:
• Assign study factor values to the Sample, Control, or Standard sample types. If
necessary, create new study factor values for these samples.
• For LC studies, change the sample type assignment for samples without a study factor
value to Blank, Identification Only, or Quality Control as appropriate.
3. Do one of the following:
• In the New Study and Analysis Wizard, return to the Sample Groups and Ratios page
and verify the assignments.
• In an existing study where you have started a new analysis, return to the Grouping &
Ratios page.

Change the hierarchy of the study variables

You can set up the group ratios on the Grouping & Ratios page of an existing analysis or on
the Sample Groups and Ratios page of the New Study and Analysis Wizard.

The hierarchy of the selected study variables in the Study Variables area affects the sample
group names and the denominator list for bulk ratio generation.

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Y To change the hierarchy of the study variables

Place the pointer over the handle ( ) to the left of a variable name. When the move
cursor ( ) appears, drag the variable up or down in the list.
Figure 51. Changing the hierarchy of the study variables

Original hierarchy ------> Dragging the variable ------> New hierarchy

up in the list

Move cursor

Change the sort order of the study variables

The sort order of the study variables affects the denominators to be used in the Bulk Ratio
Generation area on the Grouping & Ratios page of an existing analysis or on the Sample
Groups and Ratios page of the New Study and Analysis Wizard.

Y To change the sort order of the study variables

Click the Sorting icon for the study variable that you want to sort by and choose Sort
Ascending or Sort Descending.
Figure 52. Sort order shortcut menu for the study variables

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Set up the group ratios

You can set up group ratios individually in the Manual Ratio Generation area or automatically
by using the bulk ratio generator.

For details about setting up the group ratios, see the following topics:
• Set up the group ratios individually
• Set up the group ratios by using the bulk ratio generator

The application assumes you are setting up the group ratios for a differential analysis. When
you set up at least one group ratio, information about the statistical test that the Differential
Analysis node will perform appears in the Generated Ratios area.

Tip The Differential Analysis node is a post-processing node in the processing workflow
for an analysis. When you set up group ratios for an analysis that does not include the
Differential Analysis node, a validation prompt appears when you submit the analysis to
the job queue. If you do not want the analysis to perform a differential analysis, you can
click Ignore to dismiss the prompt and start the run.

The workflow templates provided with the application that include Statistics in their file
names include the Differential Analysis node.

Table 16. Messages in the Generated Ratios area (Sheet 1 of 2)

Setup Message
Non-nested design
Two group comparison Hypothesis test performed by a two-tailed student's t-test
(which assumes that the means for the two groups are not
equivalent). P-values are adjusted by the
Benjamini-Hochberg algorithm.
Multi-group comparison Hypothesis test performed by a one-way ANOVA model
with Tukey as post-hoc test. P-values are adjusted by the
Benjamini-Hochberg algorithm.
Nested design
Two group comparison Hypothesis test performed by a multivariate paired t-test
(assuming equal variance). P-values are adjusted by the
Benjamini-Hochberg algorithm.
Multi-group comparison Hypothesis test performed by an unpaired ANOVA
model with Tukey as post-hoc test. P-values are adjusted
by the Benjamini-Hochberg algorithm.

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Table 16. Messages in the Generated Ratios area (Sheet 2 of 2)

Setup Message
Alert message with a yellow background
Non-nested design for ratios Nested design is not applicable. For a nested design, the
with biological samples same biological samples must be present in all sample
groups.

Set up the group ratios individually

You can set up the group ratios on the Grouping & Ratios page of an existing analysis or on
the Sample Groups and Ratios page of the New Study and Analysis Wizard.

Y To set up group ratios one by one

In the Manual Ratio Generation area of the page, select a group from the Numerator list,
select a group from the Denominator list, and click Add Ratio. Repeat this step for each
pair of groups that you want to compare.

Set up the group ratios by using the bulk ratio generator

You can set up the group ratios on the Grouping & Ratios page of an existing analysis or the
Sample Groups and Ratios page of the New Study and Analysis Wizard.

Note The hierarchy of the selected study variables in the Study Variables area affects the
sample group names and the denominator list for bulk ratio generation and the sort order
of the study variables affects the denominators to be used in the Bulk Ratio Generation
area. For details, see “Change the hierarchy of the study variables,” and

Y To automatically set up one or more ratios

1. Modify the sort order and hierarchy of the study variables as appropriate.
2. In the Bulk Ratio Generation area, select one or more denominators and click Add
Ratios.

When you select more than one variable in the Study Variables area and the selected
variables have multiple values, the Select/Deselect Item in All Groups icon, , appears
when you place the pointer near a denominator in the Denominators to Be Used area.
To automatically select multiple check boxes for the same value in all groups, select one of
the check boxes for the value, and then click the Select/Deselect Item in All Groups
icon, .

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Set up the sample groups and ratios for a new analysis

Figure 53. Two study factors and multiple groups

3. To modify the group ratio list, do either of the following:

• To remove a ratio, click the delete icon ( ) to its left.
• To clear the entire list, click Clear All.

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 3 Create a new study and an analysis by using the wizard
Prepare to submit the analysis to the job queue

Prepare to submit the analysis to the job queue

The first time you use the New Study and Analysis Wizard, read the instructions on the final
page of the wizard (step 5 of 5).

Clicking Finish on the Input File Selection page (after selecting input files), on the Input File
Characterization page, or on the final wizard page opens the study page and the Analysis view.
The Analysis view contains the selected input files. If you selected a processing workflow on
the Study Name and Processing page of the wizard, the Workflow box on the Analysis view
displays the name of the processing workflow, and the Workflows page contains the
processing workflow.

Before starting a run, you can edit the study, the processing workflow, the input file list, and
the result file name. Some of the defined processing workflows require customization. For
example, for a targeted analysis, you must select the target compounds for the Generate
Expected Compounds node. For information about customizing a processing workflow, see
“Customize the processing workflow.”

If the processing workflow is valid and the Analysis view contains one or more input files, the
Run command at the top right of the Analysis view is available.

If the Run command is unavailable, you must fix the analysis errors. See “Troubleshoot
common analysis errors.”

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 4

Set up, run, and reprocess analyses

To set up and submit new analyses, review the details of completed analyses, or reprocess
analyses, see these topics:
• Set up a new analysis from within an existing study
• Troubleshoot common analysis errors
• Submit an analysis to the job queue and fix any validation issues
• Control the Job Queue
• Review or reprocess an analysis
• Analysis view parameters

These topics describe how to set up additional tables, lists, or files for use in a processing
workflow:
• Set up individual isotope patterns by using the Isotope Ratio Editor
• Create an isotope patterns list by using the Pattern List Editor
• Extract analog and PDA traces

Set up a new analysis from within an existing study

You can set up a new analysis by beginning with an empty Workflows page, an empty
Grouping & Ratios page, and an empty Analysis view. Or, you can set up a new analysis by
reprocessing an analysis from the Analysis Results page.

Tip You cannot set up the sample groups and ratios on the Grouping and Ratios page
without first adding the appropriate input files to the Analysis view.

To set up a new analysis from within an existing study, follow these steps:
1. Start a new analysis from within an existing study
2. Select a workflow template
3. Customize the processing workflow

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Set up a new analysis from within an existing study

4. Select the input files for the new analysis

5. Edit the file name for the result file to be generated by the analysis
6. Select the study variables and set up the group ratios for a comparison analysis

For information about reprocessing an analysis, see “Reprocess an analysis.”

Start a new analysis from within an existing study

This topic describes how to start a new analysis from within an existing study. For
information about reprocessing an existing analysis, see “Reprocess an analysis.”

Y To start a new analysis from within an existing study

1. Open the study. See “Open an existing study.”

2. In the study command bar, click New Analysis.
The Workflows tab and the Grouping & Ratios tab appear to the right of the study page
tabs and an empty Analysis view opens to the right of the tabbed pages. Both the
Workflows and Grouping & Ratios pages are empty.

Tip You can also start a new analysis by opening an analysis template.

Select a workflow template

On the Workflows page of an analysis, you can select a workflow template from a directory
folder, create a new processing workflow, or load a processing workflow from a result file.

The following procedure describes how to select a processing workflow template or load an
existing processing workflow from a result file. For information about creating a new
processing workflow from scratch, see Chapter 6, “Create and edit processing workflows.”

Y To select a workflow template

1. Click the Workflows tab.

Command bar

Workflow box

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Set up a new analysis from within an existing study

2. In the Workflow Tree area on the Workflows page, create a new processing workflow or in
the Workflows command bar, do one of the following to select an existing processing
workflow:
• To select a standard processing workflow from the Common Templates folder, click
Open Common, select the folder for the field of interest, select one of the provided
processing workflow templates, and click Open.
The file name appears in the Workflow box, and a description of the processing
workflow appears in the Description box.
• To select a processing workflow from another folder, click Open, locate the
processing workflow file (.cdProcessingWF) of interest, and click Open.
The file name appears in the Workflow box.
• To load the processing workflow that you previously used to process a specific result
file, click Open, locate the result file (.cdResult) of interest, and click Open.
3. To customize the processing workflow, see the next topic, “Customize the processing
workflow.”

Customize the processing workflow

In the Compound Discoverer application, you can customize processing workflows only from
within a study. To open an analysis from within an existing study, see “Start a new analysis
from within an existing study.”

Table 17 lists the workflow nodes in processing workflows within LC studies that require
custom settings.
Table 17. Workflow nodes that require customization for an LC study (Sheet 1 of 2)
Node Required customization
Generate Expected From the Compound list, select library compounds.
Compounds
In the defined workflow templates, this selection is empty.
Create FISh Trace From the Compound list, select a library compound.

In the defined workflow templates, this selection is empty.

Create Pattern Trace In the Isotope Ratios box, enter an elemental composition
formula—for example, C15S or C17S.

In the defined workflow templates, the formula has been

preset to C15S.
Note If you add the Create Pattern Trace node to a processing workflow, the Isotope
Ratios box is empty until you populate it.

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Table 17. Workflow nodes that require customization for an LC study (Sheet 2 of 2)
Node Required customization
Search Mass Lists From the Input Files list, select mass lists.

In the defined workflow templates, one of the preinstalled

mass lists is pre-selected, according to the vertical market.
Search mzVault From the mzVault Library list, select mzVault libraries.

In the defined workflow templates, one or more of the

preinstalled mzCloud Offline for mzVault libraries are
selected.
Compound Class Scoring From the Compound Classes list, select a Compound Class
file.
Pattern Scoring For the Isotope Patterns parameter, set up an isotope pattern.

In the defined workflow templates, the pattern has been set to

C15S. You can define and add more ratios.

For LC studies, Thermo Fisher Scientific has optimized most of the parameter settings in the
defined processing workflow templates by the area of study (vertical market). Table 18 lists the
parameters that usually require a different setting, regardless of whether you use one of the
defined templates or create your own processing workflow.
Table 18. Parameter modifications for workflow nodes
Node Parameter settings to optimize or modify
Create Analog Trace Select the trace of interest.
Create Mass Trace Select the trace of interest.
Generate Expected Set up the dealkylation and transformation steps and select
Compounds the appropriate ions.
Search nodes Select the libraries or lists of interest.
Detect Compounds For the recommended minimum peak intensity settings for a
(Legacy) specific mass spectrometer model, see Table 19.
Group Compounds Set up a peak rating filter to remove low-quality
chromatographic peaks from the analysis.
Group Expected Set up a peak rating filter to remove low-quality
Compounds chromatographic peaks from the analysis.

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Table 19 lists the recommended range for the minimum peak intensity setting in the Detect
Compounds (Legacy) node for an LC study. The optimal setting depends on the sensitivity of
the mass spectrometer.

IMPORTANT Unless you are creating a new analysis for comparison with legacy analyses,
Thermo Fisher Scientific recommends that you use the new Detect Compounds node
instead of the Detect Compounds (Legacy) node. With the new Detect Compounds
node, you can use the peak rating filter to eliminate compounds for further processing and
from the analysis result unless their chromatographic peaks pass the peak quality threshold
in a specified number of input files.

Table 19. Recommended minimum peak intensity range

Minimum peak intensity
Mass spectrometer
(chromatographic peak height)
Q Exactive, Q Exactive Plus™, Q Exactive HF 500 000 to 1 000 000
Orbitrap Fusion, Orbitrap Lumos™, Orbitrap ID-X™ 50 000 to 100 000
Exactive, Exactive Plus™, Orbitrap Elite™, Orbitrap Velos 100 000 to 500 000
Pro™
LTQ Orbitrap XL™, LTQ Orbitrap Velos™ 25 000 to 100 000

Select the input files for the new analysis

Follow this procedure to select the input files for a new analysis from within an existing study.
If you are reprocessing a previous analysis, the Files for Analysis area of the Analysis view
includes its input files. If you are starting a new analysis, the Files for Analysis area is empty.

Y To select the input files that you want to process

1. Open the study of interest and start a new analysis. See “Start a new analysis from within
an existing study.”
2. On the Input Files page or the Samples page of the study, select the files of interest.
3. Right-click the selection and choose Set As Input File, or drag the files of interest to the
Files for Analysis area of the Analysis view.

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Set up a new analysis from within an existing study

Figure 54. Dragging input files to the Analysis view

The following items appear in the Analysis view:

• The file name of the last input file appears in the Result File box.
• The Run command becomes available if the Workflows page contains a valid
processing workflow.
• When you add more than one input file to the Files for Analysis area, the By File
check box becomes available.
If the Caution symbol in the Processing Step title bar remains, the processing workflow
contains an error. See “Troubleshoot common analysis errors.”

Go to the next topic, “Edit the file name for the result file to be generated by the analysis.”

Edit the file name for the result file to be generated by the analysis
After you add the input files to be processed to the Analysis view, the application
automatically populates the Result File box with the file name of the first input file. You can
edit the file name.

Y To change the name of the result file for an analysis

In the Analysis view, select the default file name in the Result File box and type the new
name.

Go to the next topic, “Select the study variables and set up the group ratios for a comparison
analysis.”

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Troubleshoot common analysis errors

Select the study variables and set up the group ratios for a comparison analysis
To run a differential analysis automatically, you must define the sample groups and ratios for
the new analysis.

Note When the processing workflow includes the Differential Analysis node, the Analysis
Validation confirmation box opens if the analysis does not include defined sample groups
and ratios on the Grouping & Ratios page of the analysis.

Y To set up sample groups and ratios for a new analysis

1. If you have not already opened an existing study and started a new analysis, do the
following:
a. Open an existing study. See “Open an existing study.”
b. Click New Analysis in the study command bar.
c. On the Workflows page of the analysis, select a workflow template or set up a
processing workflow. See “Select a workflow template.”
d. Select the input files for the analysis. See “Select the input files for the new analysis.”
2. On the Grouping and Ratios page of the analysis, select the study variables and set up
group ratios.

For details about selecting the variables for the analysis and setting up group ratios, see “Set up
the sample groups and ratios for a new analysis,” which describes how to set up the sample
groups and ratios on the Sample Groups and Ratios page of the New Study and Analysis
Wizard.

Go to the next topic, “Troubleshoot common analysis errors.”

Troubleshoot common analysis errors

After you set up an analysis, you must troubleshoot the analysis if a Caution symbol appears
in the Analysis view and the Run button is unavailable.

Tip For LC studies, the application does not know the polarity of the scan data or whether
the data contains data-dependent or data-independent fragmentation (acquisition) scans.
For best results, check the following:
• When the processing workflow contains any of these nodes—Create Mass Trace,
Create FISh Trace, or Create Pattern Trace—verify that the ion polarity setting
matches the data.
• When the processing workflow contains the Create FISh Trace node, verify that the
setting for Fragmentation Mode matches the data.

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Y To troubleshoot an analysis

1. In the Analysis view, point to the Caution symbol, , to display the list of missing
analysis items, or check the error information in the Current Workflow Issues pane
(Figure 56) below the Post-Processing pane on the Workflows page.
2. Using the information provided in the list of missing items, fix the analysis errors until
the Caution symbol disappears. See Table 20.
Figure 55. Error messages for a defined processing workflow in an LC study

For example, Figure 55 shows the error message that appears before you customize the
defined processing workflow provided in the Common Templates folder:
Degradants w Statistics Expected w FISh Scoring and Unknown ID w Online and
Local Database Searches.cdProcessing WF
Figure 56 shows the corresponding error messages in the Current Workflow Issues pane.
Figure 56. Current Workflow Issues pane with issues for an LC study

In addition, each workflow node that is missing a value for one of its parameters has an
exclamation mark, , in its upper-right corner.
To fix the analysis errors for this example, you must select a compound for the Create
FISh Trace node, one or more compounds for the Generate Expected Compounds node,
and a mass list for the Search Mass Lists node.

Tip You can update all the libraries and lists when an analysis is open—that is, the
available selections in the workflow nodes that include selections from these libraries
and lists automatically update when you modify the associated libraries and lists.

Go to “Submit an analysis to the job queue and fix any validation issues.”

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To troubleshoot common analysis errors, see Table 20.

Note To troubleshoot validation issues, which occur after you submit a run, see
“Common validation issues.”

Table 20. Common analysis errors

Error message Error Solution
The workflow does not contain a You have not added the Input Files Add the Input Files node to the
start node. node to the workflow. beginning of the workflow.
No input files defined. You have not added input files to the Add input files from the Input files or
Files for Analysis area. Samples page to the Files for Analysis
area.
The current workflow does not You have not set up a processing Select or set up a processing workflow
contain any nodes. workflow on the Workflows page. on the Workflows page.
Node Name Missing value for The processing workflow contains a Make the appropriate selections in
parameter “Parameter Name” node that requires a custom the affected workflow nodes.
parameter setting.
Node Name Missing connection for You have not connected node to the Make the appropriate node
“Connection Information” processing workflow. connections.

Submit an analysis to the job queue and fix any validation issues
To submit an analysis to the job queue, understand the validation issues that might occur, and
control the job queue, see these topics:
• Submit an analysis to the job queue
• Common validation issues

Submit an analysis to the job queue

After you set up an analysis and troubleshoot any analysis errors, the Run command becomes
available.

Y To submit an analysis to the job queue

1. Decide whether you want to create one result file for the entire set of input files or one
result file for each input file.
• To create a single result file, leave the By File check box clear.
• To create a separate result file for each input file, select the By File check box.
2. (Optional) In the Result File box, type a name for the result file to overwrite the default
name.

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3. In the Analysis command bar, click Run.

If the analysis contains no validation issues, the Job Queue page opens. See “Control the
Job Queue.”
If the analysis contains issues, the Analysis Validation Issues prompt opens.
4. If a warning prompt appears, do the following:
a. Read the warning message. See “Common validation issues.”
b. Do one of the following:
• To modify the analysis, click Abort and remedy the error.
• To start data processing, click Ignore.

Common validation issues

If the Analysis Validation Issues prompt appears when you submit and analysis, see Table 21
to troubleshoot common validation issues.
Table 21. Validation issues (Sheet 1 of 2)
Validation issue Remedy
The peak rating filter in the Group When appropriate, set up an appropriate
Compounds node, the Group Expected peak rating filter in the Group Compounds
Compounds node, or both nodes is not node, the Group Expected Compounds
enabled. node, or both nodes.
The processing workflow includes the • On the Sample Groups and Ratios page,
Differential Analysis node, but you have not set up the appropriate sample groups
set up sample groups and ratios. and ratios.
• On the Workflows page, delete the
Differential Analysis node.

–or–
• Do not change the analysis settings and
click Ignore.
The analysis includes sample groups and On the Workflows page, add the
ratios, but the processing workflow does not Differential Analysis node to the workflow.
include the Differential Analysis node.
IMPORTANT If the analysis does not include sample ratios or the Differential Analysis
node, the application does not run a differential analysis, and the Compounds and
Expected Compounds tables in the result file does not include the following columns:
Ratios, Log2 Fold Change, P-value, and Adj. P-value.

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Control the Job Queue

Table 21. Validation issues (Sheet 2 of 2)

Validation issue Remedy
The processing workflow includes On the Workflows page, add the Assign
Compound Identification nodes or Pathway Compound Annotations node to the
Mapping nodes, but it does not include the workflow.
Assign Compound Annotations node.
IMPORTANT For an untargeted analysis in an LC study, the application does not assign
names or formulas to compounds in the Compounds table of a result file if the processing
workflow does not include the Assign Compound Annotations node.
The processing workflow includes the Assign Click Ignore.
Compound Annotations node, but the
processing workflow does not include any of –or–
the compound identification or pathway
Add one or more compound identification
mapping nodes.
or pathway mapping nodes to the processing
workflow.

Control the Job Queue

When you submit an analysis for processing, the Job Queue page opens (Figure 57). You can
also open the Job Queue page by choosing View > Show Job Queue from the menu bar.

The application can process two runs simultaneously. If you submit a second run while the
first run is being processed, the status of the second run changes to Not Queued, Running, or
Execution Failed. If you submit a third run while the application is processing the first two
runs, its status changes to Waiting.
Figure 57. Job Queue list with runs in various processing states
Command
bar

Job Queue list

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 4 Set up, run, and reprocess analyses
Control the Job Queue

To work with the jobs on the Job Queue page, see the following instructions.
• Open the Job Queue page
• Cancel a run
• Promote a run
• Remove completed or failed jobs from the Job Queue
• Refresh the Job Queue list
• Open a result file from the Job Queue page
• Display verbose messages on the Job Queue page
• View the processing steps for a job
• Filter the Job Queue list
• Job Queue page parameters

Open the Job Queue page

The Job Queue page automatically opens when you submit a job for processing. You can close
the page by clicking the Close icon on the right side of its tab.
Figure 58. Command bar on the Job Queue page

Y To open a hidden Job Queue page

From the Compound Discoverer menu bar, choose View > Show Job Queue.
The Job Queue page opens as a tabbed document.

Cancel a run
You can cancel a run before it ends—that is, you can cancel a run when it is in the Waiting or
Running state.

Y To cancel a run that is being processed

1. On the Job Queue page, select the run that you want to cancel.
2. In the command bar on the Job Queue page, click Abort.
When you cancel a run, its status changes to Aborted, and the application does not create
a result file for the run.

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Promote a run
If the application has not started processing a job, you can promote the job one position at a
time. You cannot promote a job to a position in front of a job that is already running—that is,
you cannot pause a run in progress to promote a job in front of it.

Y To promote a run

1. On the Job Queue page, select a job that is waiting in the job queue list.
2. Click Promote.

Remove completed or failed jobs from the Job Queue

Y To remove completed or failed jobs from the Job Queue list

1. On the Job Queue page, select the jobs that you want to remove.
2. In the command bar on the Job Queue page, click Remove. Then, at the prompt, click
OK.
The selected jobs disappear from the Job Queue list. The application does not remove the
result files from the study.

Refresh the Job Queue list

Y To refresh the Job Queue list

In the command bar on the Job Queue page, click Refresh.

Open a result file from the Job Queue page

Y To open a result file from the job queue list

On the Job Queue page, do one of the following:

• Select the completed run of interest and click Open Results in the command bar.
• Double-click a completed run of interest.
The Results page for the selected run opens as a tabbed document in the application
window.

Display verbose messages on the Job Queue page

By default, the application only displays high-level processing information on the Job Queue
page. To display all the available processing information, you can display the verbose
messages.

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Control the Job Queue

Y To display verbose messages in the Job Queue list

Select the Display Verbose Messages check box.

View the processing steps for a job

By default, the application displays one entry for each job in the job queue, but you can
expand each entry for the job to display its processing steps.

Y To view the processing steps for a job

On the Job Queue page, click the expand icon, , to the left of the job row.

Filter the Job Queue list

Y To filter the job queue list

Note Use the filters for the column that you want to sort by. For example, to display
only the runs that you ended before completion, follow this procedure.

1. Click the icon, , to the left of the Execution State filter list and select Equals.

2. In the Execution State filter list, select Aborted.

The job queue list displays the canceled runs only.

3. To undo filtering, close and reopen the Job Queue page.

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Job Queue page parameters

Table 22 describes the command bar and progress table on the Job Queue page.
Table 22. Job Queue page features (Sheet 1 of 2)
Command or table
Description
column
Command bar
Abort Stops processing and removes the selected job from the queue.

Selecting a job that is being processed makes this button available.

Promote Promotes the selected job to the next earlier and available run
position. For example, if you have queued four jobs with two
actively running and two waiting, promoting the fourth job after
moves it to the third position, where it is still waiting. As soon as
the application completes one of the first two jobs, it starts the
promoted job. You cannot promote a job in front of a job that is
already running. You can promote a job multiple times, but you
can only promote it one position at a time.
Remove Selecting one or more completed jobs makes this button available.
Removes the selected jobs from the job queue, but does not
remove the runs from the Analysis Results page of the study.
Refresh Refreshes the job queue list.
Open Results Opens the result files for the selected, completed jobs.
Display Verbose Displays more messages of less importance. When this check box
Messages is clear, the Job Queue displays no more than a few messages for
each workflow node.
Table columns
Execution Order Displays the execution order of the submitted jobs that are waiting
to start. The application does not display an execution order for
the jobs that are currently running. When multiple jobs are
waiting to run, you can promote any of the runs with an execution
order greater than 1.

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Control the Job Queue

Table 22. Job Queue page features (Sheet 2 of 2)

Command or table
Description
column
Execution State Displays the status of the job.
• Not Queued—The application takes a finite length of time to
start a job after you click the Run command.
• Running—The application is currently processing the job.
The application can process two jobs simultaneously. When
you submit an analysis as a batch, each input file is processed
as a separate job.
• Aborted—You canceled the job while the application was
processing the analysis.
• Execution Failed—The application was unable to complete
the job.
• Waiting—The application has not begun to process the job.
• Completed—The application has completed the analysis and
you can open the result file.
Details Displays whether the job ran with or without warnings.
Progress Displays the progress of the run as a percentage.
Type Displays the job type.
Name Displays the name of the result file.
Submitted At Displays the date and time when you submitted the run to the job
queue.
Study Displays the name of the study.
Data Source Displays the location and file names of the input files for the
current job.
Description Displays the description that you typed in the Description box on
the Workflows page.

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Review or reprocess an analysis

Review or reprocess an analysis

When you submit a run to the job queue, the run appears in the list of analyses on the
Analysis Results page of the current study.

Use the Analysis Results page of a study to review or reprocess a completed analysis or to open
a result file. An analysis consists of a processing workflow, optional sample groups and ratios,
and the selected input files.

Note The Execution State on the Job Queue page updates more quickly than the
Execution State on the Analysis Results page.

For details, see these topics:

• Analysis Results page parameters
• Review an analysis
• Reprocess an analysis
• Reprocess a legacy analysis result from an untargeted analysis

Analysis Results page parameters

Table 23 describes the command bar and progress table on the Analysis Results page of a
study.
Table 23. Analysis Results page parameters (Sheet 1 of 2)
Feature Description
Command bar

Selecting an analysis in the list on this page makes these commands available.
Open Result Opens the selected result file.
Reprocess Opens the Analysis view with the list of input files that were used
for the selected analysis. The Workflows page contains the
processing workflow, and the Grouping & Ratios page contains
the sample groups and ratios used for the selected analysis.
Search box Use this box to type text to search for.
Search For Use this dropdown list to select the column to search by.
Table columns
Execution State Displays the status of the analysis.
Creation Date Displays the date and time when you submitted the run to the job
queue.
File Name Displays the file name of the result file.

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Review or reprocess an analysis

Table 23. Analysis Results page parameters (Sheet 2 of 2)

Feature Description
Description Displays the description of the processing workflow that you or
the originator typed in the Description box on the Workflows
page.
Below the table
Show Associated Opens a locked Processing Step area that shows the names of the
Analysis/Hide processing workflow and result file and a list of the input files for
Associated Analysis the analysis.
Shortcut menu commands
Copy with Headers, See these topics:
Copy, Clear Selection,
Cell Selection Mode, • Copy table entries to the clipboard
and Enable Row • Group table rows
Grouping
Open Result Opens the selected result file.
Open Containing Opens the folder that contains the result file.
Folder
Show Details Opens the Analysis Sequence Details window where you can view
the analysis processing workflow in the Workflow Tree pane and
the Processing Step information in the Analysis view. You cannot
start runs from this window.
Reprocess Same functionality as the Reprocess command in the command
bar.

Review an analysis
Use the Analysis Sequence Details window to review an analysis.

Y To review an analysis

1. On the Analysis Results page of a study, right-click the analysis and choose Show Details.
The Analysis Sequence Details window opens and displays the processing workflow in the
Workflow Tree pane and the result file name and input files in the Processing Step pane.
2. To view the parameter settings for a workflow node, select it in the Workflow Tree pane.
The parameter settings appear in the Parameters pane at the left.

Note The Processing Step is locked, preventing you from reprocessing the analysis
from this window.

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 4 Set up, run, and reprocess analyses
Review or reprocess an analysis

Figure 59. Analysis Sequence Details window showing the parameter settings for the Detect
Compounds node (LC study)

Reprocess an analysis
You can reprocess an entire analysis or only the post-compound detection portions of an
analysis.

Note Because result files (analysis results) for untargeted analyses from previous versions
of the Compound Discoverer application contain an obsolete Detect Compounds node,
you cannot partially reprocess these legacy analysis results. You can fully reprocess these
legacy analyses after you replace the “not available” node with the current Detect
Compounds node or the Detect Compounds (Legacy) node. See “Reprocess a legacy
analysis result from an untargeted analysis.”

Y To reprocess an analysis

1. On the Analysis Results page of a study, right-click the analysis and choose Reprocess.
• If the Analysis view is open and contains information for an analysis that you have
not yet submitted to the job queue, the following prompt appears:
The analysis was not started. Do you really want to discard the analysis?

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Review or reprocess an analysis

• If the Analysis view is closed, it reopens with the settings from the selected analysis. In
addition, the Grouping & Ratios tab and Workflows tab appear to the right of the
study tabs.
2. If prompted, do the following:
a. Check the Analysis view and decide whether you want to discard the current settings.
b. Click Yes to replace the current settings in the Analysis view with the settings from
the selected analysis. Otherwise, click No to return to the in-progress analysis.
3. Do one of the following:
• To reprocess the entire analysis, go to step 5.
• To reprocess only part of the processing workflow, go to step 4.

Note For LC studies, you can add or reprocess any of the Peak Area Refinement
nodes, Pathway Mapping nodes, Search nodes, and Compound Scoring nodes
without reprocessing the entire workflow.

You must reprocess the entire workflow to reprocess any of the nodes for Spectrum
Processing, Trace Creation, Compound Detection, or Expected Compounds (except
for the Merge Features node).

4. To reprocess only part of the processing workflow or add workflow nodes downstream of
the core processing workflow, do the following:
a. Click the Workflows tab.
The processing workflow appears in the Workflow Tree (Reprocess) area. All the
nodes are white with a gray tab, which indicates that they are not set for reprocessing.

Tip When you attempt to reprocess an analysis result from a previous version of
the Compound Discoverer application, some of the processing workflow nodes
are obsolete and unavailable for reprocessing. The gear icon and n/a label indicate
obsolete workflow nodes.

You cannot directly reprocess analysis results with obsolete processing workflow
nodes. To reprocess analysis results from previous versions of the Compound
Discoverer application, you must replace the obsolete workflow nodes with
comparable nodes on the Workflow Nodes page.

b. Do any of the following:

• Right-click any of the nodes currently in the workflow that you want to reprocess
and choose Reprocess.
• Add downstream workflow nodes.
The selected nodes and any related nodes revert to their original color, and the Run
command becomes available in the Analysis view.

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Review or reprocess an analysis

Note If you are only partially reprocessing the existing input files, the Source File
row appears in the Analysis view. You cannot edit the source file name.

c. If you are partially reprocessing the data, consider changing the result file name.
If you do not change the result file name, the application automatically appends a
number to the file name when you submit the run.
d. Go to step 7.
5. To reprocess the entire processing workflow, right-click the Input Files node and choose
Reprocess. Then, at the prompt, click OK.
6. If necessary, make changes to the sample groups and ratios on the Grouping & Ratios
page and the settings in the Analysis view.

Note When you change any of the settings on the Grouping & Ratios page or the
files for analysis in the Analysis view, the application automatically reprocesses the
entire processing workflow.

7. To start the analysis, click Run.

Reprocess a legacy analysis result from an untargeted analysis

You cannot partially reprocess an analysis result from a previous version of the Compound
Discoverer application if the processing workflow for the analysis includes the (n/a) Detect
Compounds node.

Y To fully reprocess the analysis result from a legacy analysis

1. On the Analysis Results page of the legacy study, right-click the analysis and choose
Reprocess.
• If the Analysis view is open and contains information for an analysis that you have
not yet submitted to the job queue, the following prompt appears:
The analysis was not started. Do you really want to discard the analysis?
• If the Analysis view is closed, it reopens with the settings from the selected analysis. In
addition, the Grouping & Ratios tab and Workflows tab appear to the right of the
study tabs.
2. If prompted, do the following:
a. Check the Analysis view and decide whether you want to discard the current settings.
b. Click Yes to replace the current settings in the Analysis view with the settings from
the selected analysis. Otherwise, click No to return to the in-progress analysis.
3. To open the Workflows page of the analysis, click the Workflows tab or click Edit to the
right of Processing Step (Partially Reprocessing).

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 4 Set up, run, and reprocess analyses
Review or reprocess an analysis

4. Review the processing workflow:

• If the processing workflow includes the (n/a) Detect Compounds node, you must
replace the node.
• If the processing workflow also includes the Find Expected Compounds (Legacy)
node, you must replace the (n/a) Detect Compounds node with the Detect
Compounds (Legacy) node.
• If the processing workflow does not include the Find Expected Compounds (Legacy)
node, you can replace the (n/a) Detect Compounds node with the Detect
Compounds node or the Detect Compounds (Legacy) node.
5. Replace the (n/a) Detect Compounds node with an available detect compounds node as
follows:
a. Click the (n/a) Detect Compounds node to select it and press the Delete key.
b. Click the Workflow Nodes tab at the bottom right of the Workflow Tree area.

Note If the processing workflow includes the Find Expected Compounds

(Legacy) node, only the Detect Compounds (Legacy) node is available.

c. On the Workflow Nodes page, drag one of the detect compounds nodes to the
Workflow tree area.
The detect compounds node automatically connects to the Merge Features node and
the Group Compounds node, but the Align Retention Times node does not
automatically connect to the detect compounds node.

Note When you replace the (n/a) Detect Compounds node with the Detect
Compounds (Legacy) node and you want the node to yield results that are similar
to the previous version of the Compound Discoverer application, keep the default
setting of False for the Use Peak Quality for Isotope Grouping parameter.

The User Peak Quality for Isotope Grouping parameter is an advanced parameter
under Isotope Pattern Detection.

d. Connect the Align Retention Times node to the detect compounds node.
6. Make other changes to the processing workflow as appropriate.
7. To start the analysis, click Run.

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 4 Set up, run, and reprocess analyses
Analysis view parameters

Analysis view parameters

The Analysis view appears to the right of the analysis pages when you start a new analysis or
open an existing analysis template. Table 24 describes the parameters in the Analysis view.
Table 24. Analysis view parameters (Sheet 1 of 2)
Parameters Description
Title bar
By File check box Available when you add more than one input file to the Files for
Analysis area.
• Clear (default setting)—The application creates one result file
as it processes the input files in the Files for Analysis area.
• Selected—The application creates one result file for each
input file in the Files for Analysis area.
Run command Submits the analysis to the job queue.

Available when the Workflow Tree pane on the Workflows page

contains a valid processing workflow and the Files for Analysis
area contains a list of input files.
Save command Opens the Save Analysis Template dialog box where you can
provide a file name for the analysis template and save it to an
appropriate directory.
Closes the Analysis view, the Workflows page, and the Grouping
& Ratios page.
Processing Step area
Edit Opens the Workflows page.
If the analysis includes errors, such as missing parameter settings
or no input files, a Caution symbol appears to the far right of the
Processing Step. To display the error list, point to the Caution
symbol. For more information, see Table 20.
Workflow By default, the text matches the text in the Workflow box on the
Workflows page. You cannot change the text in the Analysis view.
To change the name of the processing workflow, edit the text on
the Workflows page. To select a different processing workflow, see
“Start a new analysis from within an existing study.”
Result File Specifies the file name for the result file. This box is empty until
the Files for Analysis area lists at least one input file.

The name of the first input file automatically populates the Result
File box. If the analysis creates only one result file, you can type a
name for the result file in the Result File box.

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Set up individual isotope patterns by using the Isotope Ratio Editor

Table 24. Analysis view parameters (Sheet 2 of 2)

Parameters Description
Source File Displays the filename of the original result file.

Available when you set up an analysis for partial reprocessing.

Files for Analysis: (#) Displays the number of input files in the Files for Analysis area.
Files for Analysis area After you add the input files from the Input Files page or the
Samples page of the study to this area, this area displays the names
of the input files. See “Select the input files for the new analysis.”

Set up individual isotope patterns by using the Isotope Ratio Editor

For LC studies, use the Isotope Ratio Editor dialog box to set up the pattern and the required
isotopes for the Create Pattern Trace node or the Pattern Scoring node.

For LC studies, you can access the Isotope Ratio Editor dialog box from the Create Pattern
Trace node or the Pattern Scoring node.

To set up an isotope pattern, see the following topics as applicable:

• Open the Isotope Ratio Editor
• Define an isotope pattern from an elemental composition
• Copy an elemental composition from the Expected Compounds library
• Set up a custom isotope pattern
• Export a mass spectrum from a raw file to the Clipboard
• Isotope Ratio Editor parameters

Open the Isotope Ratio Editor

Use the Isotope Ratio Editor dialog box to set up isotope patterns.

Y To open the Isotope Ratio Editor dialog box

1. Open or create a processing workflow on the Workflows page of an analysis.

For information about starting a new analysis, see “Set up a new analysis from within an
existing study.”
2. For LC studies, add one or both of these nodes to the processing workflow: Create
Pattern Trace or Pattern Scoring.
3. For LC studies, click the Create Pattern Trace node or the Pattern Scoring node in the
Workflow Tree pane.

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Set up individual isotope patterns by using the Isotope Ratio Editor

The parameters for the node appear in the Parameters pane.

4. To display the browse icon, click the Isotope Ratios box.
5. Click the browse icon, .
For the Create Pattern Trace node, the Isotope Ratio Editor dialog box opens. For the
Pattern Scoring node, the Pattern List Editor dialog box opens.
6. To open the Isotope Ratio Editor dialog box for the Pattern Scoring node, click Add
Patterns in the Pattern Editor dialog box.

Define an isotope pattern from an elemental composition

Y To set up the pattern for a compound by using its elemental composition

1. Open the Isotope Ratio Editor dialog box. See Open the Isotope Ratio Editor.
2. In the Isotope Ratio Definition Type area of the Isotope Ratio Editor dialog box, select
the Define from Elemental Composition Formula option.
Figure 60. Isotope Ratio Editor dialog box with an isotope pattern for a defined elemental
composition

3. In the Elemental Composition box, type or paste the alphanumeric elemental

composition of the compound of interest.
The application automatically populates the Mass Shift and Intensity [%] columns by
using these default settings:
• Intensity threshold: 0.10%

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Set up individual isotope patterns by using the Isotope Ratio Editor

• Resolution: 60 000
• Charge: 1

Tip To enter an elemental composition for a labeled compound, use brackets to

identify the type and number of labeled atoms for each element.

For example, to enter the elemental composition of omeprazole where only one of the
carbon atoms has been replaced with carbon-13, type C16 [13]C H19 N3 O3 S.

4. Refine the settings for the intensity threshold, resolution, and charge, as appropriate and
in any order:
• In the Int. Threshold [%] box, type the relative intensity threshold.
The application removes isotopic peaks below this relative intensity threshold from
the Mass Shift versus Intensity [%] table.
• In the Resolution box, type the resolution for the scans.

Note The scan header in the raw data file lists the resolution of each scan, and the
instrument method that is associated with the raw data file lists the resolution of
each scan event.

• In the Charge box, type or select the charge state of the ions.
The application uses the charge state to display the theoretical mass spectrum in the
graphical display.
5. Select the check boxes of the required peaks.

Copy an elemental composition from the Expected Compounds library

You can copy the elemental composition of a compound in the Expected Compounds library
to the Clipboard, and then paste it to other places in the application where the input is an
elemental composition.

Y To copy an elemental composition from the Expected Compounds library

1. If the Isotope Ratio Editor dialog box is open, close it.

2. From the menu bar, choose Libraries > Expected Compounds.
The Expected Compounds library opens.
3. Right-click anywhere on the page and choose Cell Selection Mode.
4. Click the elemental composition of interest.
The table cell turns a lighter blue than the remaining cells in the table row.
5. Right-click the highlighted cell and choose Copy.

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 4 Set up, run, and reprocess analyses
Set up individual isotope patterns by using the Isotope Ratio Editor

6. Open the Isotope Ratio Editor dialog box. See Open the Isotope Ratio Editor.
7. Right-click in the Elemental Composition box and choose Paste.

Set up a custom isotope pattern

Y To set up a custom isotope pattern

1. Open the Isotope Ratio Editor dialog box. See Open the Isotope Ratio Editor.
2. Select the Custom Isotope Ratio Pattern option.
Below the Isotope Ratio Definition Type area, the available parameters change.
Figure 61. Custom Isotope Ratio Pattern view

3. To set up the custom isotope ratio pattern, do one of the following:

• Type values in the Mass Shift and Intensity boxes.
• Click Get from Composition Formula.
The application uses the text in the hidden Elemental Composition box.
• Click Get from Clipboard.
The application uses the mass spectrum data that you copied to the Clipboard.

Export a mass spectrum from a raw file to the Clipboard

This topic describes how to export a mass spectrum from the FreeStyle 1.8 browser
application to the Clipboard. For later versions of the FreeStyle application, refer to the
FreeStyle Help system.

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 4 Set up, run, and reprocess analyses
Set up individual isotope patterns by using the Isotope Ratio Editor

Y To export a mass spectrum from a raw data file to the Clipboard

1. From the FreeStyle™ data-visualization application, do the following:

a. Open the raw data file that contains the mass spectrum of interest and make the mass
spectrum view or the spectrum list view the active view.
b. In the Exports area of the Spectrum Workspace Options toolbar, click Exports to
open the dropdown list. Then, select Export Selection AS.
c. In the Copy to Clipboard/Export dialog box, select the To CSV File option and click
OK.
d. In the Export Data dialog box, select a folder, name the file, and click Save.
The spreadsheet opens in a spreadsheet application.
2. In the spreadsheet application, select up to 20 rows of m/z and intensity values and copy
them to the Clipboard. Do not select the spectrum header information.

Isotope Ratio Editor parameters

Table 25 describes the parameters in the Isotope Ratio Editor dialog box. For information on
how to open the editor, see Open the Isotope Ratio Editor.
Table 25. Isotope Ratio Editor dialog box parameters (Sheet 1 of 3)
Parameter Description
Isotope Ratio Definition Type

These two options define the parameters that appear below the Isotope Ratio Definition
Type area.
Define from Elemental Selecting this option makes the following features visible:
Composition Formula
• Elemental Composition box
• Int. Threshold [%] box
• Resolution box
• Charge box

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Set up individual isotope patterns by using the Isotope Ratio Editor

Table 25. Isotope Ratio Editor dialog box parameters (Sheet 2 of 3)

Parameter Description
Custom Isotope Ratio Selecting this option makes the following features visible:
Pattern
• Get from Composition Formula button
• Get from Clipboard button
• Bar graph of Intensity [%] versus the m/z ratio of the isotopic
mass peaks
• Data entry table where you define a custom isotope pattern in
terms of the mass shift and intensity of each mass peak

Use this option to create a custom isotope pattern.

Elemental composition view

Selecting the Define from Elemental Composition Formula option makes the following
parameters visible: Elemental Composition, Int. Threshold [%], Resolution, and Charge.
Elemental Specifies the elemental composition of the compound of interest.
Composition
When you type a composition in this box, the application
automatically creates a table of mass shifts and intensities.

Default: Empty (unless you have already specified the elemental

composition in the Isotope Ratios box under General Settings for
the Pattern node)
Int. Threshold [%] Specifies the intensity threshold of the isotope pattern.

Default: 0.10; range: 0–100

Resolution Specifies the resolution of the isotope pattern.

Default: 60 000; range: 2–1 000 000 000

Charge Specifies the charge of the ion fragment.

Default: 1; range: 1–100

Graph of Intensity [%] versus m/z value

Displays a graph of the full isotope distribution in the mass shift and intensity table.

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Set up individual isotope patterns by using the Isotope Ratio Editor

Table 25. Isotope Ratio Editor dialog box parameters (Sheet 3 of 3)

Parameter Description
Mass shift and intensity table

Use this table to specify the required peaks in the isotope pattern.

When you select the Define from Elemental Composition Formula option, the application
automatically populates this table; you cannot edit the entries.
Required Specifies whether the isotope is required.

(for an isotope pattern • When the check box is selected, the isotope is required.
defined from a
• When the check box is clear, the isotope is not required.
user-specified
elemental composition)
Mass Shift Specifies the mass shift from the pattern base peak (A0).
Intensity [%] Specifies the relative intensity [%] of the isotope to the pattern
base peak.
Rows Specify the values for the isotopes.
Custom isotope ratio pattern view

Selecting the Custom Isotope Ratio Pattern option makes the following buttons visible: Get
from Composition Formula and Get from Clipboard.
Get from Composition Creates an isotope pattern for an elemental composition formula.
Formula The application reads the elemental composition that you entered
in the Elemental Composition box before selecting the Custom
Isotope Ratio Pattern option.
Get from Clipboard Imports the isotope pattern from the Clipboard. You can export a
custom pattern to the Clipboard from the spectrum list view in
the FreeStyle application or from a third-party software
application.
Graph of Intensity [%] versus m/z value

Displays a graph of the full isotope distribution in the mass shift and intensity table.
Mass shift and intensity table

When you select the Custom Isotope Ratio Pattern option, you can edit the mass shift and
intensity values for the isotope pattern.

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Create an isotope patterns list by using the Pattern List Editor

Create an isotope patterns list by using the Pattern List Editor

Use the Pattern List Editor to set up a table of isotope patterns.

Y To create a list of isotope patterns for the Pattern Scoring node

1. Add the Pattern Scoring node to a processing workflow.

For LC studies, the Group Compounds node automatically connects to the Pattern
Scoring node.
The blue exclamation mark in the upper-right corner of the node indicates that you need
to define a parameter setting inside the node.

2. In the Workflow Tree area on the Workflows page, select the Pattern Scoring node.
The parameters pane for the Pattern Scoring node opens at the left.
3. In the Isotope Patterns box, type the elemental composition formulas for the defined
isotope patterns that you want to compare. Separate each pattern with a semicolon and a
space—for example, C15S; C17S.
4. Click the more icon, , to the right of the Isotope Patterns box.
The Pattern List Editor opens. The table contains the elemental compositions that you
entered.
Figure 62. Pattern List Editor

5. Select the isotope pattern that you want to edit, and then click Edit Pattern.
The Isotope Ratio Editor dialog box opens. To edit the pattern, see Set up individual
isotope patterns by using the Isotope Ratio Editor.
6. For each pattern that you want to add, click New, and then set up the isotope pattern in
the Isotope Ratio Editor.

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 4 Set up, run, and reprocess analyses
Create an isotope patterns list by using the Pattern List Editor

After you add a pattern, it appears in the Patterns table of the Pattern List Editor dialog
box. The Name and Elemental Composition columns display the elemental composition
of the pattern. The text in the Name column is editable.
7. Click OK to close the Pattern List Editor dialog box.
The isotope patterns appear in the Isotope Patterns box of the Pattern Scoring node.

Table 26 describes the commands and table columns in the Pattern List Editor dialog box.
Table 26. Pattern List Editor parameters
Parameter Description
Commands
New Opens the Isotope Ratio Editor dialog box for setting up an
isotope pattern.
Delete Deletes the selected pattern.
Edit Opens the Isotope Ratio Editor dialog box for editing the
selected pattern.
Columns
Name By default, displays either the elemental composition for each
isotope pattern that you create with a defined elemental
composition or the text “CustomPattern #” for each isotope
pattern that you create by setting up a custom isotope ratio
pattern.

You can edit the text in this column.

Elemental Composition Displays the elemental composition for each isotope pattern
that is based on a defined elemental composition.
Is Custom Pattern Displays an X for each isotope pattern that is based on a
custom isotope ratio pattern.
# Isotopes Displays the number of isotopes in the defined pattern that
are above the intensity threshold.
# Isotopes Required Displays the number of isotopes required to calculate the
SFit% score.
Charge Displays the charge state used to simulate the isotope pattern.

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Extract analog and PDA traces

Extract analog and PDA traces

For LC studies, you can extract analog and PDA traces from the raw data.

Note To extract UV traces and PDA traces in the same analysis, you must add two Create
Analog Trace nodes to the processing workflow. Set up one node to extract UV traces and
the other node to extract PDA traces.

For details, see these topics:

• Extract analog traces
• Extract PDA traces

Extract analog traces

For LC studies, you can extract analog traces from the raw data.

Analog traces include data from a UV-Vis detector, analog data from LC devices controlled by
the Xcalibur data system or an equivalent Thermo Scientific application, and analog signals
from devices connected to the analog channels on the communications panel of your mass
spectrometer.

Y To extract UV or analog traces from the raw data

1. Add the Create Analog Trace node to the processing workflow.

The Input Files node automatically connects to the Create Analog Trace node.
2. In the Workflow Tree area on the Workflows page, select the Create Analog Trace node.

Note For details about this node, see “Create Analog Trace node.”

3. In the Parameters pane, under General Settings, select UV or Analog from the Trace Type
list.
4. In the RT offset [min] box, type the offset time, in minutes, for the UV-Vis or Analog
trace.
If there is a time difference between when the sample enters the mass spectrometer and
the UV-Vis or analog detector’s flow cell, use the offset time to align the chromatographic
traces. A value of 0 indicates that the UV-Vis or analog detector and the mass
spectrometer simultaneously detected the sample.
5. In the Custom Label box, type text to identify the trace in the Specialized Traces table of
the result file window.

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Extract analog and PDA traces

Extract PDA traces

For LC studies, you can extract traces acquired by a photodiode array (PDA) detector from
your raw data.

Y To extract a PDA trace from the raw data

1. Add the Create Analog Trace node to the processing workflow.

The Input Files node automatically connects to the Create Analog Trace node.
2. In the Workflow Tree area on the Workflows page, select the Create Analog Trace node.

Note For details about this node, see “Create Analog Trace node.”

3. In the Parameters pane, under General Settings, do the following in any order:
• In the Trace Type list, select PDA.
• In the RT offset [min] box, type the offset time, in minutes, for the PDA traces.
If there is a time difference between when the sample enters the mass spectrometer
and the PDA detector’s flow cell, use the offset time to align the chromatographic
traces. A value of 0 indicates that the PDA detector and mass spectrometer
simultaneously detect the sample.
• In the Custom Label box, type text to identify the trace in the Specialized Traces table
on the result file page.
4. In the PDA Settings area, do any of the following:
• To extract a plot of the average intensity of the scanned wavelength range versus time,
select True for Total Scan.
This trace is labeled as a Total Scan in the Specialized Traces table.
• To extract a plot of the spectrum maximum of the scanned wavelength range versus
time, select True for Spectrum Maximum.
This trace is labeled as a Spectrum Maximum in the Specialized Traces table.
• To extract a plot for a specified wavelength range, select True for Wavelength Range.
Then, type the wavelength range in the Min. and Max. Wavelength boxes.

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Edit existing studies

In the Compound Discoverer application, you process your raw data files (run analyses)
within the study environment. The following topics describe how to edit an existing
Compound Discoverer study:
• Study files
• Open an existing study
• Study page commands and tabs
• Edit the study description and the study factors
• Add input files to an existing study
• Remove input files or update their location
• Edit the sample type and study factor values
• Save the study file if you turned off the auto-save feature

For information about adding and editing study factors, see “Add or edit the study factors,” in
Chapter 3.

Study files
When you create a study with the New Study and Analysis wizard, the application creates a
study file (.cdStudy) and a study folder. The study file contains a list of input files (Xcalibur
RAW files) with their associated sample information and a list of analyses with their associated
result files (.cdResult). The sample information includes the sample type of each input file
and the relationship between the input files.

When you open an existing study, it opens as a tabbed document with a command bar and a
set of tabbed pages: Study Definition, Input Files, Samples, and Analysis Results.
• The Study Definition page contains an editable list of the study factors. See “Edit the
study description and the study factors.”
• The Samples page contains editable lists of the sample type and study factor values for
each input file. See “Edit the sample type and study factor values.”

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 5 Edit existing studies
Open an existing study

• The Input Files page tracks the location of the input files. These input files typically reside
outside the study folder—for example, they might reside on your processing computer,
on a shared server, or on the data system computer where they were acquired. If you
delete or rename an input file from the specified folder location after you add it to a study,
this warning symbol, , appears to the left of the ID column for the deleted file.
Pointing to the warning symbol displays the expected location of the missing file and
instructions for resolving the issue. See “Resolve the location of the input files in a study.”
• The Analysis Results page tracks the result files generated by analyses run within the
study. Result files reside within the study folder.

Open an existing study

You can open an existing study from the Start Page, the File menu, or the toolbar.

The Start Page lists the 20 most recent studies. The study name appears in blue hypertext.
Pointing to the study name underlines it.
Figure 63. Application window and Start Page
Open an Existing Study
toolbar icon Menu bar

Open Study button Study name in

on the Start Page blue hypertext

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Open an existing study

Y To open an existing study

Do one of the following:

• From the Start Page, under What Would You Like to Do?, click Open Study to open the
Open Study dialog box. Select a study file and click Open.
• From the Start Page, under Recent Studies, click the study name of interest.
• From the application menu bar, choose File > Open Study to open the Open Study
dialog box. Then, select a study file and click Open.
• From the application toolbar, click the Open an Existing Study icon, , to open the
Open Study dialog box. Select a study file and click Open.

The study opens to the Analysis Results page, which is the last page of four pages. The study
tab includes an image of two racked test tubes, , on the left, the study name in the middle,
and a close icon, , on the right.

Tip On the study tab, an asterisk to the right of the study name indicates unsaved
changes.
Figure 64. Analysis Results page of a study
Study tab

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Study page commands and tabs

Study page commands and tabs

The study page includes a command bar and four tabbed pages.
Table 27. Study page parameters (Sheet 1 of 2)
Command or page Description
Commands

The Add Files, New Analysis, and Open Analysis Template commands are independent of
the active page within the study. The Remove Files command is only active when a file is
selected on the Input Files page or the Analysis Results page.
Add Files Opens the Open dialog box where you select the input files
(Xcalibur RAW files) that you want to include in the study.
Remove Files Executes one of two actions:
• Removes the selected files on the Input Files page when it
is the active page.
• Removes the selected analysis results on the Analysis
Results page when it is the active page.
Open Containing Folder Opens the folder that contains the selected file.

This command is only available for the Input Files and

Analysis Results pages.
New Analysis Opens the Analysis view and adds the Workflows tab to the
tab set on the study page. The Workflows page is
unpopulated.

This command is unavailable when the Analysis view is open.

Open Analysis Template Opens the Analysis Template dialog box where you select an
analysis template.

This command is unavailable when the Analysis view is open.

Tabbed pages
Study Definition Use to set up study factors and view the study name, file
location, creation date, modification date, and description on
this page.
Input Files Use to track the status and resolve the location of input files,
as this page lists the file ID, file name, file type, and sample
information for each input file.

Clicking Add Files opens the Input File Characterization

dialog box and the Input Files page, if it is not already open.

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Edit the study description and the study factors

Table 27. Study page parameters (Sheet 2 of 2)

Command or page Description
Samples Use to select the sample type and study factors for each raw
data file.
Analysis Results Use to access the result files created within the study, review
the analysis details, and reprocess an analysis.

Edit the study description and the study factors

Use the Study Definition page of a study to edit the existing study factors, to set up new study
factors, and to edit or add a description of the study.

For information about adding and editing the study factors, see Add or edit the study factors
in Chapter 3
Figure 65. Study definition page of a study

Note If you selected a study template with study factors when you created the study or
added study factors by using the Input File Characterization page of the New Study and
Analysis wizard, the Study Factors area contains the defined factors.

Y To add or edit a description of the study

Type or edit the description in the Study Description area.

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Table 28 describes the parameters on the Study Definition page of a study.

Table 28. Study Definition page parameters (Sheet 1 of 2)
Parameter Description
Study Summary pane
Study Name Displays the study name.
Study Directory Displays the file location where the study is stored.
Study Type Displays the study type: GC or LC. After you create a study,
you cannot change its study type.
Last Changed Displays the date and time of the last saved change to the
study.
Creation Date Displays the creation date of the study file.
Study Description pane

Use this pane to enter and store a description of the current study.
Study Factors pane

Use this pane to set up or edit the study factors.

Menu commands
Paste Pastes the entries in the copied factors below the existing
factors.
Copy Copies the selected factors to the Clipboard.
Add > Biological Replicate Opens a blank biological replicate editor. You can use the
Factor biological replicate factor to create nested studies.
Add > Categorical Factor Opens a blank categorical factor editor.
Add > Numeric Factor Opens a blank numeric factor editor. The numeric factor
editor only accepts numeric values.
Factor box
Title bar Displays the editable factor name.
Buttons and icons
Apply Saves the current entries in the factor editor.
Cancel Closes the item or value entry box and removes any entries
made during the current editing session. Does not remove
previously saved entries.
Deletes the factor from the study.
Add Adds an item to a categorical factor or a numeric value to a
numeric factor.

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Add input files to an existing study

Table 28. Study Definition page parameters (Sheet 2 of 2)

Parameter Description
Delete Deletes the selected item or value from the list in the
respective Items or Values area.
Text entry boxes
[new factor] Type a factor name in this box.
Item box Type the name of an item that you want to add to the Items
list for a categorical factor in this box.
Value box Type a numeric value that you want to add to the Values list
for a numeric factor in this box.

Add input files to an existing study

Use the Add Files button on the study command bar to add input files to a study.

Y To add input files to an existing study

1. Open the study. See “Open an existing study.”

2. On the study command bar, click Add Files.
3. In the Add Files dialog box, select the files of interest and click Open.
The Input File Characterization dialog box opens.
4. Select the sample types and study factor values for the new samples. See “Characterize the
new input files.”
5. Click OK.
The Input Files page of the study opens.

Remove input files or update their location

Use the Input Files page to remove or update the location of the input files in an existing
study. The input files for the Compound Discoverer application are Xcalibur RAW files
acquired by a Thermo Scientific HRAM mass spectrometer.

Tip To add input files to an analysis, drag the files of interest from the Input Files page to
the Analysis view. See “Set up a new analysis from within an existing study.”

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Remove input files or update their location

For details, see the following topics:

• Display the location of the input files for a study
• Remove input files from a study
• Resolve the location of the input files in a study
• Input Files page parameters

Display the location of the input files for a study

Y To display the file path for an input file

1. On the Input Files page of a study, select the input file of interest.
2. Below the table, click Show Details.
The Samples page opens below the input files table.
3. Click the Files tab.
Figure 66 shows the hidden Files page that lists the full file name of the selected input file,
including its directory location.
Figure 66. File path of selected input file

Show Details or Hide Details command

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Remove input files or update their location

Remove input files from a study

Follow this procedure to remove input files from a study.

Note Removing input files from a study does not delete them from their directory
location.

Y To remove input files from a study

1. On the Input Files page, select the rows to remove and click Remove Files in the study
command bar.
Depending on whether you have run an analysis with the selected input files, one of the
following confirmation boxes appears:
• If you have not run an analysis, the Remove Input File confirmation box appears.
• If you have run an analysis, the Remove Analysis Result Files confirmation box
appears.
2. Do one of the following:
• In the Remove Input File confirmation box, click Yes to remove the input files from
the study.
–or–
• In the Remove Analysis Result Files message box, click Remove Files to remove the
input files and their associated analyses from the study.
When you remove an input file from the study, the analyses associated with the input
file disappear from the Analysis Results page, but the result files (.cdResult) remain in
the study folder.

Resolve the location of the input files in a study

Typically, the study file resides in the study folder and the raw data files that the study points
to reside in a separate folder—for example, an Xcalibur\data\subfolder.

If the network or directory path changes between the study and the raw data files, an
exclamation symbol ( ) appears to the left of the file ID.

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Remove input files or update their location

Figure 67. Exclamation symbol for missing input file, Find Missing Files command, and Files page
of the Details section

Y To resolve the input files list when you move a study or the Xcalibur RAW files

1. On the Input Files page of a study, display the details for the missing files and check their
original location.
2. If you know where the files are currently stored, add the files to the study by doing any of
the following:
• Open the Add Files browser by clicking the Add Files command in the Study page
command bar. Then, select the files and click Open.
• Right-click the row for the missing file and choose Find Missing Files. Then, in the
Browse for Folder dialog box, browse to the holding folder, select the Xcalibur RAW
files, and click OK.

The Adding Files confirmation box opens. The progress remains at 0.0% until you click
OK.

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Remove input files or update their location

Figure 68. Adding Files confirmation box with progress information

3. Click OK to continue.
The Adding Duplicate Files message box opens. The progress again remains at 0.0% until
you click OK.
4. Click OK to continue.
The application restores the connection between the study and the raw data files.

Input Files page parameters

Table 29 describes the parameters on the Input Files page of a study.
Table 29. Input Files page parameters (Sheet 1 of 2)
Parameter or feature Description
Show Details/Hide Details Displays or hides the Samples and Files subpages.
Columns
Error Displays an exclamation mark, , if the file is missing.
ID Displays a unique ID in the following format: F#, where # is
a unique integer. If you remove a file, and then add it again,
the application updates the ID number.
Name Displays the file name of the raw data file.
File Type Displays the file type of the input file. The Compound
Discoverer application supports Xcalibur RAW files (.raw).
Sample Information Displays the sample type and any other selected study
factors.
Hidden pages (Samples and Files)
Samples page
Sample Displays a unique identifier for the input file.

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Remove input files or update their location

Table 29. Input Files page parameters (Sheet 2 of 2)

Parameter or feature Description
Sample Identifier Displays the file name of the raw data file.
Sample Type Displays the sample type. See “Available sample types.”
Study factor columns Displays the study factor values. You can modify the study
factor selections.

Changing the factor values and sample types on the Input

Files page also updates these items on the main Samples
page.
Files page
ID Displays a unique ID (reserved for future implementation).
Name Displays the file name and directory location of the raw data
file.
Date Modified Displays the acquisition date and time of the raw data file.
Size Displays the size of the raw data file in bytes.
Shortcut menu for the Input Files page
Set As Input File Adds the selected input file to the Files for Analysis area in
the Analysis view.

Available when the Analysis view is open.

Find Missing Files Opens the Browse for Folder dialog box. Browse to the
folder where the file is stored and click OK. Then, click OK
to close the confirmation message.

Available when the Input Files table contains missing files.

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Edit the sample type and study factor values

Edit the sample type and study factor values

If you have not already characterized the samples in a study or you want to change their
characteristics, use the Samples page of an existing study.

Tip To open the Samples page of a study, click the Samples tab.
Figure 69. Samples page and its shortcut menu

Filter
row

Shows the file information. Shortcut menu

To select or modify the sample types and study factor values or view the file information on
the Samples page, see the following topics as applicable:
• Edit the sample identifier on the Samples page
• Edit the sample types on the Samples page
• Edit the study factor values on the Samples page
• View the file information on the Samples page

Edit the sample identifier on the Samples page

To make it easier to identify each sample in a study, you can modify the text in the Sample
Identifier column.

Y To edit the text in the Sample Identifier column

1. Point to the sample cell.

The Edit icon appears.

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Edit the sample type and study factor values

2. Click the Edit icon, .

3. Place the cursor in the cell, and then type or paste the new text.

Edit the sample types on the Samples page

For information about sample types, see “Available sample types.”

Y To edit the sample types of the input files in a study

Tip To select a row, click a column that does not include a dropdown list.

Do any of the following:

• To select the sample type for a single sample, select Sample, Control, Blank, Quality
Control, Identification Only, Standard, or Labeled from the Sample Type list.
• To assign the same sample type to a consecutive sample range, use the SHIFT key to
select a range of samples. Then, right-click and choose Set Sample Type To >
Sample Type.
• To assign the same sample type to nonconsecutive samples, use the CTRL key to
select the samples. Then, right-click and choose Set Sample Type To > Sample Type.

Edit the study factor values on the Samples page

Y To edit the study factor values for the input files in a study

Do any of the following:

• To select the factor values for a single sample, select the appropriate value from the
list in each factor column.
• To select the same value for a consecutive sample range, drag the pointer across the
rows of interest. Then right-click and choose Set Factor To > Value.
• To select the same value for nonconsecutive samples, hold down the CTRL key and
click the samples of interest. Then right-click and choose Set Factor To > Value.

Tip To select a row, click a column that does not include a dropdown list.

View the file information on the Samples page

Y To view the file name and location for a selected sample

Click Show Associated File at the bottom left of the Samples page.
The following details appear—the full file name and location, the file size in kilobytes,
and the acquisition time of the Xcalibur RAW file.

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Edit the sample type and study factor values

Samples page parameters

Table 30 describes the parameters on the Samples page of a study.
Table 30. Samples page parameters
Parameter Description
Show/Hide Associated Shows or hides the file information for a selected sample.
File
Columns
Error Displays an error symbol.
Sample Displays a unique number for the sample (S#).
File Displays a unique number for the input file (F#).
Sample Identifier Displays the file name of the raw data file.
Sample Type Specifies the sample type for each sample.

For LC studies, the available selections are Sample, Control,

Standard, Blank, Quality Control, Identification Only and
Labeled.

For information about the sample types, see “Available sample

types.”
Study factor columns Specifies the study factor values for each sample.

You can edit the study factor values.

Columns in hidden rows
ID Displays a unique file identifier.
File Name Displays the file name and directory location of the Xcalibur RAW
data file.
File Size Displays the size of the Xcalibur RAW data file in bytes.
File Time Displays the acquisition date and time of the Xcalibur RAW data
file.
Shortcut menu commands

For information about the Copy with Headers, Copy, Clear Selection, and Cell Selection
Mode commands, see “Common operations for manipulating data tables.”
Set Sample Type To Assigns the selected sample type to a sample range.
Set Factor To Assigns the selected study factor value to a sample range.
Set As Input File Adds the selected input file to the Files for Analysis area in the
Analysis view.

Available when the Analysis view is open.

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 5 Edit existing studies
Save the study file if you turned off the auto-save feature

Save the study file if you turned off the auto-save feature
By default, the application saves the study file after you submit an analysis and when you close
the study file. However, you can change this behavior by turning off the auto-save feature.

IMPORTANT If you turn off the auto-save feature, the application prompts you to save
your changes when you attempt to close a study file with unsaved changes. See “Turn off
the auto-save feature for studies.”

Unsaved changes include, for example, the last completed run on the Analysis Results
page, new input files on the Input Files page, new study factors or study factor values on
the Study Definition page, new sample assignments on the Samples page, and other study
parameters.

Y To save a study file

Do one of the following:

• Choose File > Save All from the menu bar. Or, click the Save All Open Items icon,
, in the toolbar.
–or–
• Click the study tab to make it the active page. Then, choose File > Save from the
menu bar, or click the Save the Currently Active Item icon, , in the toolbar.

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 6

Create and edit processing workflows

The application uses a node-based method to create processing workflows (processing
methods) for the analysis of raw data files. You can create your own custom processing
workflows (cdProcessingWF), use one of the many defined processing workflow templates
provided with the application, or customize one of the existing processing workflow
templates.

Note The parameter settings for the workflow nodes in the defined processing workflow
templates are not necessarily the same as the default settings for the workflow nodes
themselves. The parameter settings in the processing workflow templates provided with
the application are optimized by the field of study (vertical market).

For details about editing and creating processing workflows, see these topics:
• Processing workflow templates
• Workflows page
• Edit an existing processing workflow
• Defined processing workflow templates for LC studies
• Create a completely new processing workflow for LC studies
• Connect the workflow nodes for an LC study
• Save a custom processing workflow as a template

Note For LC studies, the application provides more than 30 defined processing workflow
templates organized by field of study.

Processing workflow templates

The Compound Discoverer application uses a node-based processing workflow (processing
method) to analyze the MS data acquired with a high-resolution, accurate-mass LC/MS or
GC/MS instrument.

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 6 Create and edit processing workflows
Workflows page

In addition to analyzing the MS data, the application can display chromatograms from the
following detectors:
• A photo-diode array (PDA) detector or an ultraviolet-visible (UV-Vis) detector that is
controlled by a Thermo Scientific data system
• An analog detector that is connected to the mass spectrometer’s analog input channels

Workflows page
Within an existing study, you use the Workflows page to select, create, and edit processing
workflows. The Workflows page is a tabbed page that opens to the right of the tabbed study
pages when you start a new analysis or reprocess an existing analysis. You cannot edit a
processing workflow from outside a study.

For details about the Workflows page, see the following topics:
• Open the Workflows page
• Workflows page command bar
• Workflows page shortcut menu

Open the Workflows page

Figure 70 shows the initial layout for a new study and analysis after you close the wizard.
Figure 70. Layout for the study and analysis pages after exiting the wizard
Workflows tab Edit button

Closing a study erases the analysis settings, and reopening a study opens only the study pages.

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 6 Create and edit processing workflows
Workflows page

Y To open the Workflows page

Do one of the following:

• Use the New Study and Analysis wizard to set up a new study and a new analysis.
Then, click the Workflows tab in the set of tabbed pages or Edit in the Analysis view.
• Open an existing study, click New Analysis in the Study command bar, and then
click the Workflows tab.
• From the Analysis Results page of a study, select an analysis, click Reprocess, and
then click the Workflows tab.
The Workflow Tree and Workflow Nodes panes appear. For a new analysis, the Workflow
Tree pane is empty. For an existing analysis or an analysis created by using the wizard, the
Workflow Tree pane usually contains a processing workflow.
Figure 71 shows an empty analysis in the Analysis view at the right, an empty Workflow
Tree pane in the middle, and the Workflow Nodes pane for an LC study at the left.

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 6 Create and edit processing workflows
Workflows page

Figure 71. Workflows page without a selected processing workflow

Workflow nodes list Command bar

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Workflows page

Workflows page command bar

Table 31 describes the Workflows page commands.
Table 31. Workflows page commands
Command Description
Open Opens the Open Workflow dialog box for locating and opening a
processing workflow.
Open Common Opens the Open Workflow dialog box to the following folder
where the application installs the three common processing
workflow templates:
C:\Users\Public\Public Documents\Thermo\Compound
Discoverer 3.3\Common Templates
Save Opens the Save Workflow dialog box for selecting a folder and
entering a file name for the processing workflow in the Workflow
Tree pane.
Save Common Opens the Save Workflow dialog box to the folder where the
application installs the common processing workflow templates.
Saves the current processing workflow in the Workflow Tree pane
to the Common Templates folder.
Auto Layout Automatically formats the layout of the workflow nodes.
Clear Clears the Workflow Tree pane.

Workflows page shortcut menu

Table 32 describes the commands in the shortcut menu for the Workflow Tree pane or a
workflow node.
Table 32. Workflow Tree pane and workflow node shortcut menu commands (Sheet 1 of 2)
Command Description
Cut Removes the node from the workflow.

Selecting any workflow node makes this command available.

Copy/Paste Adds a copy of the selected node to the Workflow Tree pane.

Selecting a workflow node that can appear more than once in a

workflow makes this command available.
Auto Layout Automatically formats the layout of the workflow nodes.

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Edit an existing processing workflow

Table 32. Workflow Tree pane and workflow node shortcut menu commands (Sheet 2 of 2)
Command Description
Hide Node Numbers Turns the numbering on or off.
Reprocess Sets the selected node for reprocessing or sets the selected node
and its related nodes for reprocessing.

Available for an analysis that you have set up for reprocessing

[Workflow Tree (Reprocess)].

Edit an existing processing workflow

You can modify a processing workflow by adding and deleting workflow nodes and by
changing the parameter settings in the workflow nodes.

The application automatically connects some of the workflow nodes as you add them to a
processing workflow. But for some of the workflow nodes, you must make the appropriate
connections. When a node is missing a connection, a Caution symbol appears in its
upper-right corner.

Several workflow nodes require custom parameter selections. When a workflow node is
missing a custom parameter selection, an exclamation mark appears in its upper-right corner.

For details, see these topics:

• Fix a workflow node that has a caution symbol
• Fix a workflow node that has an exclamation mark
• Add a workflow node to a processing workflow
• Delete a workflow node from a processing workflow
• Edit the parameter settings for a workflow node

Fix a workflow node that has a caution symbol

When the node is missing a connection, a Caution symbol, , appears in its upper-right
corner.

Y To fix a workflow node that is labeled with a Caution symbol

1. To view the validation errors, point to the Caution symbol in the Analysis view.
A missing connection begins with the following text:
Missing connection for

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Edit an existing processing workflow

2. Make the appropriate node connections.

See Connect the workflow nodes for an LC study.
If the node is also missing a required parameter selection or the selected item is not found
in its corresponding list or library, an exclamation mark appears after you fix the missing
connection. See “Fix a workflow node that has an exclamation mark.”

Fix a workflow node that has an exclamation mark

To edit a processing workflow, you must open it from the Workflows page within a study.

An exclamation mark, , appears in the upper-right corner of a node when the node is
missing a required parameter selection or the selected item is not found in its corresponding
list or library. See “Troubleshoot common analysis errors.”

Y To fix a workflow node that is labeled with an exclamation mark

1. To view the validation errors, point to the Caution symbol in the Analysis view or review
the issues described in the Current Workflow Issues pane below the Post-Processing
Nodes pane.
For a missing parameter selection, the issue description includes the following text:
Missing value for parameter ‘Node’
2. To fix the workflow node error, select the node in the Workflow Tree pane.
Figure 72. Missing parameter value for the Search Mass Lists node

Empty Mass Lists box

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Edit an existing processing workflow

3. In the Parameters of ‘Workflow Node’ pane to the left, make a selection for the missing
parameter value.

Add a workflow node to a processing workflow

To edit a processing workflow, you must open it from the Workflows page within a study.

Y To add a node to the processing workflow

1. Select the node in the Workflow Nodes pane and drag it to the Workflow Tree pane.

Note A Caution symbol appears in the upper-right corner of a workflow node that is
missing a connection. Because a missing connection takes priority over a missing
parameter setting, if a workflow node is also missing a parameter setting, a blue circle
with an exclamation mark appears after you fix the missing connection.

2. If necessary, make the appropriate node connections. See Connect the workflow nodes for
an LC study.
3. To display the parameters for a workflow node, click the node in the Workflow Tree pane.
The Parameters pane lists the parameters for the selected node.
4. Edit the parameter settings for the node.

Note For an LC study that includes a targeted analysis and an untargeted analysis, the
processing workflow must include either the Detect Compounds (Legacy) node and the
Find Expected Compounds (Legacy) node or the Detect Compounds node and the Find
Expected Compounds node.

Delete a workflow node from a processing workflow

To edit a processing workflow, you must open it from the Workflows page within a study.

Y To delete a node from a processing workflow

1. Right-click the node in the Workflow Tree pane and choose Cut.
2. Check whether any validation issues appear.
3. (Optional) To save the processing workflow for reuse, click Save. Then, rename the
workflow if necessary, select an appropriate folder, and click Save.

Tip If you use the processing workflow for the current analysis, you can reuse the
processing workflow without saving it. After you successfully run the analysis, you can
rerun it by selecting the completed analysis on the Analysis Results page of a study.

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Edit the parameter settings for a workflow node

To edit a processing workflow, you must open it from the Workflows page within a study.

Y To edit the parameter settings for a workflow node

1. In the Workflow Tree pane, select the node.

The Parameters page opens with the parameters for the selected node.
2. Click Show Advanced Parameters below the Parameters page title bar.
If the node contains hidden advanced parameters, the advanced parameters appear below
the basic parameters.
When you place the cursor in the box to the right of the parameter name, information
about the parameter appears at the bottom of the Parameters page.
3. Enter the appropriate values or make the appropriate selection for each parameter.
For more information about each parameter, see Chapter 7, “Workflow nodes.”

Defined processing workflow templates for LC studies

These topics describe the provided templates and how the application processes data to find
expected compounds for a targeted analysis or detect and identify unknown compounds for
an untargeted analysis:
• Targeted processing workflows for expected compounds
• Untargeted processing workflows for identifying unknown compounds
• Nomenclature for the provided processing workflow templates
• Defined processing workflow templates

Targeted processing workflows for expected compounds

Use the Expected Compounds workflow nodes to run an analysis that targets known
analytes—for example, the metabolites of a specific drug.

Figure 73 shows the workflow tree in the following processing workflow file:
MetID w Stats Expected w FISh Scoring and Background Removal.cdProcessingWF

This processing workflow uses the Generate Expected Compounds and Find Expected
Compounds nodes to find expected parent1 compounds and their dealkylation, dearylation,
and transformation products. FISh Scoring is applied to explain the fragments in the
fragmentation spectra based on in silico fragment prediction of the parent and
dealkylation/dearylation products.

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Figure 73. Processing workflow for a metabolism study

During this targeted analysis, the following processes occur:

1. The Input Files Node sends the file names and location of the input files to the connected
nodes (typically the Select Spectra node, Create Analog Trace node, or both of these
nodes).
2. The Select Spectra Node filters the MS scan data.

1 A parent compound is the initial compound in a reaction or metabolic pathway.

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IMPORTANT Because the Find Expected Compounds node requires full (MS1) scans,
do not filter out all the full (MS1) scans for a targeted analysis.

Because the FISh Scoring node requires fragmentation scans to provide a

confirmation score for the expected precursor ions, do not filter out the fragmentation
scans when the processing workflow includes this node.

3. The Align Retention Times node chromatographically aligns features (chromatographic

peaks with the same m/z × RT dimensions) across the input files in a sample set by using
the specified alignment algorithm. The node finds features that are common across most
samples. These are called landmark features. It then builds regression curves based on
those landmark features.
The Align Retention Times (ChromAlign) node builds correlation matrices based on
spectral similarities. It then builds regression curves by using the optimal path in the
correlation matrix. The node uses a reference file to build these matrices. The reference
input file can be any input file assigned the Sample, Control, or Standard sample type.

IMPORTANT The alignment algorithm looks for matching features (chromatographic

peaks with the same m/z × RT dimensions) in the input files. The alignment
algorithm can align input files that include polarity switching data; it cannot align
input files that include only positive polarity scans with input files that include only
negative polarity scans.

4. The Generate Expected Compounds node creates a list of expected compound ions by
using the following user-specified parameter settings:
• Parent compound or compounds
• Number of dealkylation and dearylation steps
• Number and type of transformation steps
• List of possible adduct ions
The Generate Expected Compounds node passes the following information to the Find
Expected Compounds node for each expected compound:
• Parent compound or compounds
• Elemental composition of the expected neutral compound
• Molecular weight of the expected neutral compound
• Whether the expected compound is a product of a dealkylation step
• Transformations required to produce the expected compound
• Composition change between the parent and expected compound

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It also passes the following information for each expected compound ion:
• Charge
• Theoretical m/z value

Note The Generate Expected Compounds node does not send information to a result
table. It sends information to the Find Expected Compounds node, which requires
input from at least one Generate Expected Compounds node. The Filter By Mass
Defect node can also process the input from one or more Generate Expected
Compounds nodes.

5. The Find Expected Compounds node performs the following steps by using the full
(MS1) scan data from the Align Retention Times node and the information from the
Generate Expected Compounds node (or multiple Generate Expected Compounds
nodes):
a. Creates a set of mass tolerance and intensity tolerance fit parameters for each
expected compound ion (m/z value) by using the theoretical m/z value for the ion, the
user-specified mass tolerance, the theoretical isotope pattern for the ion, and the
user-specified intensity tolerance for the isotopic ions.
b. For each expected compound ion, the Find Expected Compounds (Legacy) node
does the following:
i. Checks each full (MS1) scan that passes through the connected data processing
node for centroids that match the mass and intensity tolerance rectangles. The
pattern search (set of rectangles) looks for the base peak (most intense centroid)
of the pattern first.
In most cases, the base peak is the A0 centroid for the monoisotopic ion. But in
some cases, for example, in compounds that contain two bromine atoms or four
chlorine atoms, the isotopic peaks have a higher intensity than the monoisotopic
peak.
ii. Draws a filtered XIC trace by summing the centroids found for each data point.
If a data point does not contain the user-specified number of matching isotopes
and the theoretical intensity of the missing isotope was above the noise threshold,
the node assigns a zero intensity value to the data point (see Figure 74).

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Figure 74. Filtered XIC trace with a zero intensity data point
Integrated chromatographic peak
(shaded area) Filtered XIC trace (blue)

Zero intensity data point

c. For each expected compound found, the Find Expected Compounds (Legacy) node
creates a summed trace by summing the XIC traces of the associated expected
compound ions.
d. Detects and integrates the chromatographic peaks in each XIC trace. Does not report
chromatographic peaks with an apex peak height that is below the user-specified
minimum (chromatographic) peak intensity. If the average peak width of the peaks in
the processed retention time range is greater than the setting for the Average Peak
Width parameter, the Find Expected Compounds node rejects all of the
chromatographic peaks.
The Find Expected Compounds node passes the following information to the Expected
Compounds per File table for each expected compound that it finds in an input file:
• RT (min)—Retention time of the chromatographic peak apex.

Note If the node finds more than one adduct ion for an expected compound, the
chromatogram is a summed trace.

• Best SFit [%]—Best spectral fit score between the measured and expected isotope
patterns for the expected compound ions. When the node finds only one adduct ion,
the best spectral score is equal to the score for the adduct ion that it found.
• Max # MI—Maximum number of matched isotopes for any of the adduct ions.
When the node finds only one adduct ion, the maximum number of matched
isotopes is equal to that of the adduct ion that it found.
• #Adducts—Number of adduct ions that it found.

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• Area—Total area of the chromatographic peaks for the found adduct ions of the
expected compound. Peak areas are reported in counts × seconds.
• Parent Area%—Relative area of the chromatographic peak for the expected
compound as compared to the total area of all found peaks for the expected
compound.

Note The parent area is the chromatographic peak area of the expected
compound, rather than the area of the compound listed in the Parent Compound
column. The compounds listed in the Parent Compound column are the library
compounds that you selected in the Generate Expected Compounds node.

6. The Group Expected Compounds Node groups the chromatographic peaks by their
molecular weight × retention time (MW × RT) dimensions across the input file set and
creates the Expected Compounds table.2
When you enable the peak ratings filter, the node filters out expected compounds that do
not pass the peak quality threshold in the specified number of input files.
You can select between two peak integration models:
• Most Common Ion—Reports the chromatographic peak area of the most common
adduct ion detected across the samples.
• All Ions–Reports the summed areas of all the adduct ions detected in each sample.
This node also selects the best hit ions for each compound across the input file set:
• Selects the best ion and related MS1 scan for each compound as the one with the
highest resolution and the highest intensity for the preferred ion. When you open a
result file, the mass spectrum view displays the MS1 scan for the best ion across the
input file set.
• Selects the best fragmentation data by using the user-specified preferred precursor ion
with the highest intensity that has data-dependent MS2 scans.

Note You use the Preferred Ions parameter in the Group Expected Compounds node
to specify the preferred ions.

7. When the input file set includes blank samples (Sample Type: Blank), the Mark
Background Compounds node compares the peak areas of the compounds (same parent
compound, molecular weight, and retention time) that are found in both the blank
samples and the non-blank samples, and labels these compounds as Background
Compounds if their peak areas do not meet the specified threshold.
8. When the spectrum data in the input files includes fragmentation scans (MS2, MS3,
MSn), the FISh Scoring node compares the best fragmentation scan for an expected

2
For result files generated in Compound Discoverer 2.0, the Group Expected Compounds node also added the
Best Compounds column to the Expected Compounds per File table. The Workflow page of the Result
Summary view displays the Best Compound criteria for updated result files.

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compound across the input file set to the expected structures. The scoring process can add
considerable processing time.
9. When the processing workflow includes both the Find Expected Compounds node and
the Detect Compounds node, the Merge Features node consolidates the chromatographic
peaks that these nodes find in the main Merged Features table. The consolidation is based
on the m/z × RT dimensions of the features.

Note The Merge Features node also creates the Merged Features table that is related
to the Manual Peaks table. When you manually integrate a chromatographic peak for
a specialized trace such as a UV trace, you can compare the selected peak in the
Manual Peaks table to the peaks in the related Merged Features table. The application
populates the related Merged Features table with the chromatographic peaks that fall
within the retention time window specified in the Merge Features node—that is, the
application populates the Merged Features table that is related to the Manual Peaks
table with chromatographic peaks that have a similar retention time to the selected
manual peak.

10. When the processing workflow includes any of the search nodes, the application searches
the selected databases.

Note You can connect the Group Expected Compounds node to any of the search
nodes and any of the mapping nodes.

11. When the analysis includes group ratios, the Differential Analysis node runs the
differential analysis.

After the analysis finishes, you can open the result file.

Figure 75 shows a schematic of the main and related result tables for the targeted workflow
shown in Figure 73. The Structure Proposals table is empty until you populate it.

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Figure 75. Result tables for a basic targeted workflow (with the Create Analog Traces and Merge
Features nodes)

Expected
Expected Expected
Expected Expected Merged
Merged Expected
Expected Input
Input
Compounds
Compounds Compounds Formulas Features
Features Features
Features per
per File
File Files
Files
per File

Structure
Structure Expected
Expected Expected
Expected Expected
Expected Expected Expected
Proposals
Proposals Compounds
Compounds Compounds
Compounds Compounds
Compounds Compounds Compounds
per
perFile
File per
per File
File
Expected
Expected Expected
Expected Expected Expected
Expected
Compounds
Compounds Formulas
Formulas Compounds Compounds
Features Merged
per
perFile
File per
per File
File per
per File
File Features

Expected
Expected Merged Related Related
Related Expected
Formulas
Formulas Features Structures Structures
Structures Formulas
Expected
Merged
Merged Expected
Expected Transformations
Transformations Compounds Chromatogram
Chromatogram Specialized
Specialized
Features
Features Features per File
Features per File Peaks
Peaks Traces

Chromatogram
Chromatogram Input
Input File
Peaks
Peaks Files
Files Alignments

Related
Related
Structures
Structures

Input
Input
Files
Files

Specialized
Specialized Study
Study Statistical
Statistical
Traces
Traces Information
Information Methods
Methods

Input
Input Input
Files
Files Files

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You can connect the Group Expected Compounds node to any of the search nodes and
mapping nodes.
Figure 76. Group Expected Compounds node connected to the mapping nodes and the search
nodes

Adding the search nodes to the processing workflow adds the main and related tables shown
in Figure 77 to the result file.
Figure 77. Additional result tables generated by the search nodes

Expected mzCloud Results mzVault Results ChemSpider Mass List

Compounds Results Search Results

mzCloud Results Expected Expected Expected Expected

Compounds Compounds Compounds Compounds

mzVault Results mzCloud Results mzCloud Results mzCloud Results mzCloud Results

ChemSpider mzVault Results mzVault Results mzVault Results mzVault Results

Results

Mass List ChemSpider ChemSpider ChemSpider ChemSpider

Search Results Results Results Results Results

Mass List Mass List Mass List Mass List

Search Results Search Results Search Results Search Results

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Adding the mapping nodes to the processing workflow adds the following result tables to the
result file:
• Main: Metabolika Results, Metabolika Pathways, KEGG Pathways, BioCyc Pathways,
and BioCyc Results
• Related result tables for specific expected compounds: Metabolika Results, Metabolika
Pathways, KEGG Pathways, and BioCyc Pathways, and BioCyc Results
• Related result tables for specific Metabolika results: Expected Compounds and
Metabolika Pathways
• Related result tables for specific Metabolika pathways: Expected Compounds and
Metabolika Results
• Related result tables for specific KEGG pathways

You can connect the Group Expected Compounds node to the following peak refinement
nodes: Mark Background Compounds and Scale Areas. You can add these nodes, and then
reprocess the data set without reprocessing the entire workflow, as these nodes use only the
data provided by the grouping node.

Untargeted processing workflows for identifying unknown compounds

Figure 78 shows the workflow tree for the metabolomics processing workflow that is provided
with the application:
Untargeted. Metabolomics with Statistics Detect Unknowns with ID using Online
Databases and mzLogic.cdProcessingWF

This processing workflow uses the Detect Compounds node to find chromatographic peaks
for unknown compounds (MW × RT) and the Predict Compositions node to determine the
possible elemental compositions of the unknown compounds. It also determines the possible
identity of the unknown compounds as follows:
• The Search ChemSpider node searches selected databases of MS1 scans by using the
molecular weight or predicted formulas when available.
• The Search mzCloud node searches the mzCloud database of fragmentation scans by
using the molecular weight or predicted formulas when available.
• The Map to Metabolika Pathways searches the pathways for the detected compounds.
When the application finds a matching compound, it maps the pathway for ease of
viewing.

The Assign Compound Annotations node assigns the following annotations to the detected
compounds: Name, Formula, and Structure. The Apply mzLogic node combines mzCloud
similarity searching (MS2 and MSn) with structure similarity matching to rank putative
database results.

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Figure 78. Processing workflow that finds and identifies unknown compounds

During this untargeted analysis, the following processes occur:

1. The Input Files node sends the file names and location of the input files to the Select
Spectra node.
2. The Select Spectra node filters the MS scan data.

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3. The Align Retention Times node chromatographically aligns the input files in a sample
set.
4. The Detect Compounds (legacy) node does following:
• Detects contiguous mass traces in the full (MS1) scans by using the parameter
settings for the mass tolerance and intensity threshold.
• Detects chromatographic peaks in the contiguous mass traces.
• Groups isotopes.
• Applies peak quality filters for isotopic features.
• Groups adducts by using the user-specified ions and base ions lists.
• Reports the unknown compounds (MW × RT) by occurrence in the Compounds per
File table.

IMPORTANT Make sure that the Preferred Ions list for the Group Compounds node
includes the selections in the Base Ions list (advanced parameter) for the Detect
Compounds node.

5. The Group Compounds node uses the specified mass and RT tolerances to group
chromatographic peaks with the same MW × RT values in the Compounds table.
You can select between two peak integration models:
• Most Common Ion—Reports the chromatographic peak area of the most common
adduct ion detected across the samples.
• All Ions–Reports the summed areas of all the adduct ions detected in each sample.
When you enable the peak ratings filter, the node filters out compounds that do not pass
the peak quality threshold in the specified number of input files.
It then sends the best fragmentation data across the input files to the Search mzCloud
node and Predict Compositions node.
This node also selects the best hit ions for each compound across the input file set:
• Selects the best ion and related MS1 scan for each compound as the one with the
highest resolution and the highest intensity for the preferred ion. When you open a
result file, the mass spectrum view displays the MS1 scan for the best ion across the
input file set.
• Selects the best fragmentation data by using the user-specified preferred precursor ion
with the highest intensity that has data-dependent MS2 scans.
The Predict Compositions node and the search nodes use the best hit ions.

Note You use the Preferred Ions parameter in the Group Compounds node to specify
the preferred adducts.

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6. The Search mzCloud node searches the mzCloud database for matching and similar
fragmentation spectra.
7. The Predict Compositions node predicts the elemental compositions of the unknown
compounds.
8. The Map to Metabolika Pathways node searches the Metabolika pathways for matching
compounds.
9. The Search ChemSpider node searches the ChemSpider database for matching
compounds.
10. The Fill Gaps node fills in missing peaks or peaks below the detection threshold (specified
in the Detect Compounds node) for subsequent statistical analysis.

IMPORTANT You can substitute the Fill Gaps node with the Apply Missing Value
Imputation node. For details, see “Apply Missing Value Imputation node.”

Do not use the Apply Missing Value Imputation node when the processing workflow
includes either of the QC correction nodes.

11. If the analysis includes QC samples, the Apply SERRF QC Correction node normalizes
the chromatographic peak areas in the input files that you assigned the sample type of
Sample.
12. The Mark Background Compounds node determines the background compounds in the
blank samples (Sample Type: Blank) and labels these compounds as background
compounds.
13. The Differential Analysis node runs a differential analysis on the defined sample ratios
and calculates the p-values.
14. The Assign Compound Annotations node assigns and compares the annotations provided
by the Predict Compositions, Search ChemSpider, Search mzCloud, and Search Mass
Lists nodes.
15. The Apply mzLogic node runs a forward search and a reverse search using the mzCloud
service. For compounds that have available MS2 scans, it scores all the structure
candidates (or the specified maximum number of candidates) from the attached input
nodes. Adds the following columns to the result tables: #Similarity Results (Compounds
table) and mzLogic Score (search result tables).

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For information about the result tables that this processing workflow generates, see
Chapter 10, “Descriptive information for the result tables.”

Figure 79 shows a schematic of the main and related tables for a basic untargeted workflow.
Figure 79. Result tables for an untargeted workflow

Compounds Compounds per File Features per File mzCloud Results

Structure Proposals Compounds Compounds per File Compounds

Compounds per File Features per File Fill Gaps*

mzCloud Result Hits

Predicted Compositions Input Files Chromatogram Peaks

mzCloud Result Hits

File Alignments

Metabolika Results

mzCloud Results

ChemSpider Results

Filled Gaps*

Metabolika Pathways

ChemSpider Results Input Study Metabolika Pathways

Files Information
Compounds Compounds
Compounds per File Input Files

Study
Information

File Ion Definitions

Alignments

Statistical Methods
* By default, the Filled Gaps table is hidden.

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Nomenclature for the provided processing workflow templates

When you open a defined processing workflow on the Workflows page of an analysis,
descriptive text appears in the Description box. Read and understand the description before
you use the workflow. The Description box does not enlarge to fit the text, so you must scroll
down to read the complete description. Or, you can click the Description box, press CTRL+C
copy the text to the Clipboard, and paste the text into Notepad.

The file names for the processing workflows include the following descriptive text:
• Expected—The workflow runs a targeted analysis with the Generate Expected
Compounds and Find Expected Compounds nodes.

IMPORTANT You must customize the targeted workflows by selecting the targeted
compounds in the Generate Expected Compounds node. Before you can select the
compounds for the node, you must add the compounds to the Expected Compounds
library.

In the defined processing workflows for targeted analyses, the Generate Expected
Compounds node is set up to generate a mass list for the following adduct ions:
[M+H]+1 and [M–H]–1. For best results, make the appropriate selections for your
analysis from the Ions list in the Generate Expected Compounds node.

• Detect Unknowns, Unknown, or Untargeted—The workflow runs an untargeted analysis

with the Detect Compounds node.

Tip Mobile phase additives can have a significant effect on the base ions (adduct ions
with the highest intensity) in the full scan data for an LC/MS experiment. To avoid
misinterpreting the isotopic ion clusters, make sure that the Base Ions list in the
Detect Compounds node includes the predominant adduct ions. For example, if the
mobile phase contains a significant amount of ammonium acetate, consider adding
the ammonium adduct, [M+NH4]+1, to the list.

The processing workflows in the E and L folder include [M+NH4]+1 in the Base Ions
list.

• Online Databases—The workflow searches the mzCloud and ChemSpider databases.

Tip In the Search ChemSpider node, select the appropriate databases.

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• Local Database—The workflow searches your local mzVault and mass list files. For
metabolomics templates, the local databases include the local Metabolika pathways files.

Tip In the Search mzVault and Search Mass Lists nodes, select the appropriate files.
For LC studies, the application includes nine mzVault library files and nine mass lists.
• mzVault libraries:
– EpoxidizedSoybeanOil_Library_AN001586
– mzCloud Offline for mzVault_Endogenous_2021B
– mzCloud Offline for mzVault Autoprocessed_2021B
– mzCloud_Offline for mzVault_Endogenous_2021B
– mzCloud_Offline for mzVault_Endogenous-Autoprocessed_2021B
– Bamba Lab 34 Lipid Mediators Library Stepped NCE 10 30 45
– Bamba Lab 598 Polar Metabolites Stepped NCE 10 30 45
– LipidBlast-VS68-Neg
– LipidBlast-VS68-Pos
• Mass lists
– Arita Lab 6549 Flavonoid Structure Database
– Chemical List PFASSTRUCT-2022-04-20
– EFS HRAM Compound Database
– Endogenous Metabolites Database 4400 Compounds
– Extractables and Leachables HRAM Compound Database
– LipidMaps Structure Database 2021-09-13
– Natural Products Atlas_2020_06
– PFAS NEG
– PFAS NIST

• FISh Scoring—The workflow includes the FISh Scoring node, a structural confidence
scoring and annotation tool for comparing the predicted fragments of expected
compounds to the experimental fragmentation scans. This node adds a significant
amount of processing time.
• Stats or Statistics—The workflow includes the Differential Analysis node. If you submit
an analysis that does not include ratios, a warning message appears. If you do not want to
run a differential analysis, you can ignore the warning and submit the run.

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• Compound Class Scoring—The workflow includes the Compound Class Scoring node.

IMPORTANT Before you can select the compounds classes for the node, you must
add the fragment lists to the Compound Classes library.

• MMDF—The workflow includes the Filter By Mass Defect node.

• Background Removal—The targeted workflow includes the Mark Background
Compounds node for filtering out expected compounds that are also found in the blank
samples.

Note All the untargeted workflows include the Mark Background Compounds node
for filtering compounds detected in the blank samples.

• Pattern Scoring—The workflow includes the Pattern Scoring node.

Defined processing workflow templates

Tip To access these workflows from the Workflows page of an analysis, click Open
Common from the command bar, open the Workflow Templates folder, open the folder
for the applicable vertical market, and then select a template.

The following processing workflow templates are installed with the application:
• DegradantID folder
– Degradants Related and Unknown ID w Database Searches
– Degradants Unknown ID w Pattern Trace and Pattern Scoring
– Degradants w Stats Related and Unknown ID w Database Searches
• EandL folder
– E and L Expected w FISh Scoring
– E and L Unknown ID with Online and Local Database Searches
– E and L w Stats Unknown ID w Online and Local Database Searches
• Environmental folder
– Environmental Expected w Transformation and FISh Scoring
– Environmental Unknown ID w Online and Local Database Searches
– Environmental w Stats Unknown ID w Online and Local Database Searches
• Food Research folder
– Food Research Expected w FISh Scoring
– Food Research Unknown ID w Online and Local Database Searches
– Food Research w Stats Unknown ID w Online and Local Database Searches

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• Forensics folder
– Forensics Expected w FISh Scoring
– Forensics Unknown ID w Compound Class Scoring and Database Searches
– Forensics w Stats Unknown ID w Compound Class Scoring and Database Searches
• ImpurityID folder
– Impurity ID Related and Unknown
– Impurity ID w Stats Related and Unknown
• Lipidomics folder
– Untargeted Lipidomics using Local Databases, LipidBlast in-silico library and
LipidMaps database.cdProcessingWF
– Untargeted Lipidomics using Online Databases, LipidBlast in-silico library and
LipidMaps database.cdProcessingWF
• Metabolomics folder
– Max ID - Detect Unknowns with ID Using Online Database Searches Single Sample
– Untargeted Metabolomics Quick Detection Unknowns No ID
– Untargeted Metabolomics using Online Databases, mzLogic, and Molecular
Networks
– Untargeted Metabolomics with Statistics Detect Unknowns with ID using Local
Databases
– Untargeted Metabolomics with Statistics Detect Unknowns with ID using Online
Databases
– Untargeted Metabolomics with Statistics Detect Unknowns with ID using Online
Databases and mzLogic
• MetID folder
– MetID Generate Inclusion List For Acquisition Pos Mode
– MetID Generate Inclusion List For Acquisition Neg Mode
– MetID Pattern Scoring with Background Removal
– MetID w Stats Expected and Unknown w Background Removal
– MetID w Stats Expected and Unknown w MMDF and Background Removal
– MetID w Stats Expected w Background Removal
– MetID w Stats Expected w FISh Scoring and Background Removal
• NaturalProduct
– Natural Product Unknown ID w Online and Local Database Searches
– Natural Product Unknown ID w Stats Online and Local Database Searches

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• PFAS
– PFAS Unknown ID w Database Searches and Molecular Networks.cdProcessingWF
• PolymerID
– Unknown Polymer ID w Stats Online and Local Database Searches
– Unknown Polymer ID with Online and Local Database Searches
• Stable Isotope Labeling folder
– Stable Isotope Labeling w Metabolika Pathways and ID using Local Databases
– Stable Isotope Labeling w Metabolika Pathways and ID using Online Databases

Create a completely new processing workflow for LC studies

A processing workflow is part of an analysis, and you can perform analyses only from inside a
study. Therefore, to edit or create a processing workflow, you must open a study and start a
new analysis or open an analysis template.

A processing workflow always begins with the Input Files node. All processing workflows that
process MS data require the Select Spectra node. The only processing workflow that does not
require the Select Spectra node is limited to processing the data from an analog detector.

Y To create a completely new processing workflow from an empty Workflows page

1. Open the Workflows page. If the Workflows Tree area contains a processing workflow
that you do not want to edit, click Clear.
2. Drag the required Input Files node from the Workflow nodes pane to the Workflow Tree
pane.
The Input Files node reads the information in the raw data files.
3. To process the spectral data, drag the Select Spectra node to the Workflow Tree pane.
The Input Files node automatically connects to the Select Spectra node. The Select
Spectra node reads and filters the MS scan data in the raw data files. The default
parameter settings pass all the scan data to the next node.
4. To align multiple input files, drag the Align Retention Times (ChromAlign) node to the
Workflow Tree pane. Then, connect the Select Spectra node to the alignment node.

IMPORTANT The new Align Retention Times (ChromAlign) node is more rugged
than the original alignment node. So for most analyses, use the Align Retention
Times (ChromAlign) node instead of the Align Retention Times node. The original
alignment node is available for comparing the results from previous data sets to new
data sets of similar samples.

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Create a completely new processing workflow for LC studies

The alignment node chromatographically aligns the MS scan data in the input files. The
Align Retention Times (ChromAlign) node

IMPORTANT For analyses with multiple input files, always add one of the alignment
nodes to the processing workflow.

5. To find expected compounds, do the following:

a. Check whether your Expected Compounds library contains the compounds of
interest. To open the Expected Compounds library, choose Lists & Libraries >
Expected Compounds from the application menu bar.
b. Drag the Find Expected Compounds node to the Workflow Tree pane. Then,
connect the alignment node to it.

Note The Find Expected Compounds node accepts input from any of the
Spectrum Processing nodes.

c. Drag one or more Generate Expected Compounds nodes to the Workflow Tree
pane.
• To apply different transformation rules to multiple compounds, drag multiple
Generate Expected Compounds nodes to the Workflow Tree pane, one for each
set of rules.
• To apply the same transformation rules to one or more compounds, drag a single
Generate Expected Compounds node to the Workflow Tree pane.

IMPORTANT The Generate Expected Compounds node generates a list of

expected compounds by using one or more user-specified library compounds and
a set of user-specified chemical reactions.

The Compounds parameter is empty until you select the compounds of interest.
If you submit an analysis to the job queue without selecting the compounds of
interest, a Caution symbol appears.

d. For each Generate Expected Compounds node, select the compounds of interest. See
“Generate Expected Compounds node.”
e. Connect the Generate Expected Compounds node or nodes to the Find Expected
Compounds node.
f. Drag the Group Expected Compounds node to the Workflow Tree pane.
The Find Expected Compounds node automatically connects to it.
g. To add FISh scoring to the processing workflow for targeted compounds, drag the
FISh Scoring node to the Workflow Tree pane.
The Group Expected Compounds node automatically connects to it.

Note FISh scoring adds a significant amount of processing time to an analysis.

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Create a completely new processing workflow for LC studies

h. Do one of the following:

• To detect unknown compounds in addition to the expected compounds, go to
step 6.
• To merge the features found by the Expected Compounds node and detected by
the Unknown Compounds node, go to step 12.
6. To detect unknown compounds, do the following:
a. Drag the Detect Compounds node to the Workflow Tree pane. Then, connect the
alignment node to the Detect Compounds node.
b. Drag the Group Compounds node to the Workflow Tree pane.
The Detect Compounds node automatically connects to it.
7. For statistical analyses, drag the Fill Gaps node to the Workflow Tree pane.
The Group Compounds node automatically connects to it.

Note If the processing workflow does not include the Apply SERRF QC Correction
node, you can use the Apply Missing Value Imputation node instead of the Fill Gaps
node. Because the Group Compounds node does not automatically connect to the
Apply Missing Value Imputation node, you must manually connect the Group
Compounds node to the Apply Missing Value Imputation node.

8. To correct for batch effects, connect the Fill Gaps node to the Apply QC Corrections
node. Or, if the input files for the analysis are from more than one continuous batch,
connect the Fill Gaps node to the Apply SERRF QC Correction node.
If the analysis does not include quality control samples, the application ignores the QC
correction node.
9. To identify unknown compounds, add identification nodes to the processing workflow.
As you drag an identification node into the Workflow Tree pane, the Group Compounds
node automatically connects to it.
a. Drag the Predict Compositions node to the Workflow Tree pane.

IMPORTANT For best results, always include the Predict Compositions node in a
processing workflow for untargeted compounds. Without the Predict
Compositions node, the workflow does not report the elemental compositions of
the unknown compounds without a hit from the online search databases or the
local Metabolika database.

b. To assign a name, formula, and structure to the compounds in the Compounds table,
drag the Assign Compound Annotations node to the Workflow Tree pane.
c. (Optional) To search the online ChemSpider database, drag the Search ChemSpider
node to the Workflow Tree pane.

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 6 Create and edit processing workflows
Create a completely new processing workflow for LC studies

d. (Optional) To search mass lists, drag the Search Mass Lists node to the Workflow
Tree pane. In the Workflow Tree pane, select the Search Mass Lists node, and then,
in the parameters pane, select the appropriate mass lists.
e. (Optional) To search the online mzCloud database, drag the Search mzCloud node
to the Workflow Tree pane.
f. (Optional) To search your local mzVault database, drag the Search mzVault node to
the Workflow Tree pane. In the Workflow Tree pane, select the Search mzVault
node, and then, in the parameters pane, select libraries from the mzVault Library list.
10. To map detected compounds to a biochemical pathway, add pathway mapping nodes to
the processing workflow. As you drag a pathway mapping node into the Workflow Tree
pane, the Group Compounds node automatically connects to it.
• To search the local Metabolika pathways, drag the Map to Metabolika Pathways
node to the Workflow Tree pane.
• To search the KEGG database, drag the Map to KEGG Pathways node to the
Workflow Tree pane.
• To search the BioCyc database, drag the Map to BioCyc Pathways node to the
Workflow Tree pane.
11. To rank the hits from the Search ChemSpider node, Map to Metabolika Pathways node,
Search Mass Lists node, and Map to BioCyc Pathways node, drag the Apply mzLogic
node to the Workflow Tree pane.
When present, the Search ChemSpider node, Map to Metabolika Pathways node, Search
Mass Lists node, and Map to BioCyc Pathways node automatically connect to the Apply
mzLogic node.
12. To compare the features found by the Find Expected Compounds and Detect
Compounds nodes if applicable, drag the Merge Features node to the Workflow Tree
pane.
The Find Expected Compounds and Detect Compounds nodes automatically connect to
the Merge Features node.
13. To add Trace Creation nodes to the processing workflow, do the following:
• For each UV, PDA, or analog trace that you want to extract, drag a Create Analog
Trace node from the Workflow Nodes pane to the Workflow Tree pane.
The Input Files node automatically connects to the Create Analog Trace node.
• For each pattern trace that you want to extract, drag a Create Pattern Trace node to
the Workflow Tree pane. Then, connect the Align Retention Times (ChromAlign)
node to each Create Pattern Trace node.
• For each Fragment Ion Search (FISh) trace that you want to create, drag a Create
FISh Trace node to the Workflow Tree pane. Then, connect the Align Retention
Times (ChromAlign) node to each Create FISh Trace node.

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Connect the workflow nodes for an LC study

• For each mass trace that you want to extract, drag a Create Mass Trace node to the
Workflow Tree pane. Then, connect the Align Retention Times (ChromAlign) node
to each Create Mass Trace node.
14. In the Post-Processing Nodes pane, do the following:
• To add a differential analysis (volcano plot) to the workflow for the specified sample
groups and ratios, drag the Differential Analysis node to the Post-Processing Nodes
pane below the Workflow Tree pane.
• To add the descriptive statistics columns to the Compounds and Expected
Compounds tables in the result file, drag the Descriptive Statistics node to the
Post-Processing Nodes pane below the Workflow Tree pane. The descriptive statistics
columns provide information about the chromatographic peak areas (mean area,
median area, minimum area, quartile areas, standard deviation and relative standard
deviation of the areas) for each detected compound.

Note In a result file, the descriptive statistics columns are hidden by default.

15. To export the MS scan data in the raw data files to a common data format, drag an
Export Spectra node to the Workflow Tree pane. Then, connect one of these nodes to
the Export Spectra node:
• Select Spectra
• Align Retention Times

Note The Export Spectra node does not export analog data.

For details about each workflow node, see Chapter 7, “Workflow nodes.”

Connect the workflow nodes for an LC study

For details about the workflow node connections, see these topics:
• Manually connect the workflow nodes
• Peak area refinement node connections
• Input and output nodes for the workflow nodes

Manually connect the workflow nodes

For an LC study, most but not all the processing workflow nodes automatically connect to the
appropriate input and output nodes.

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 6 Create and edit processing workflows
Connect the workflow nodes for an LC study

When you add any of the following nodes to a processing workflow, you must connect them
manually:
• Any of the spectrum processing nodes (except for the Select Spectra node)
• Any of the trace creation nodes (except for the Create Analog Trace node)
• Generate Expected Compounds node (connects to the Find Expected Compounds node)
• Input spectrum processing node to the Detect Compounds node
• Any of the peak area refinement nodes

For LC studies, you can use the following nodes multiple times in a processing workflow: the
Generate Expected Compounds node, all the Trace Creation nodes, the Mark Background
Compounds node, and all the Spectrum Processing nodes, except for the Align Retention
Times node.

Y To connect the workflow nodes

1. Point to the input node of interest.

Five white boxes appear, with one box at the center of the node and the other boxes at the
center of each side.

2. Click one of the white boxes and hold down the mouse button until a red border and an
arrowhead appear.

3. Continue holding down the mouse button as you drag the arrowhead to the output node
of interest.

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 6 Create and edit processing workflows
Connect the workflow nodes for an LC study

Depending on the compatibility, one of the following occurs:

• If the selected input node is not compatible with the output node, a red border
appears around the output node.
• If the selected input node is compatible with the output node, a green border appears
around the output node. When you release the mouse button, a directional arrow
connects the input node to the output node.
Figure 80. Connecting the Select Spectra node to the Align Retention Times node (LC
study)

4. To automatically format the layout of the workflow nodes, click Auto Layout in the
Workflows command bar.

Peak area refinement node connections

(For LC studies) This topic describes how to make the appropriate node connections for an
untargeted processing workflow that includes the Fill Gaps node and any of the peak area
refinement workflow nodes: Apply QC Correction, Mark Background Compounds,
Normalize Areas, and Scale Areas.

Note None of the provided processing workflow templates include the Normalize Areas
node or the Scale Areas node. Thermo Fisher Scientific recommends using QC samples
and the appropriate QC correction node to correct for batch errors.

The Fill Gaps node takes input only from the Group Compounds node, and the Group
Compounds node automatically connects to it.

When you add any of the other peak area refinement nodes, you must make the appropriate
connections.

The processing workflow templates provided with the application use the following peak
refinement nodes in this connection order—Fill Gaps > Apply QC Correction or Apply
SERRF QC Correction > Mark Background Compounds.

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 6 Create and edit processing workflows
Connect the workflow nodes for an LC study

Figure 81. Suggested connection order for the peak area refinement nodes

If you add the Normalize Areas node to your processing workflow templates, the appropriate
input and output connections depend on whether your blank samples are solvent blanks or
matrix blanks:
• If the blanks are solvent blanks, connect the nodes in this order:
Group Compounds > Fill Gaps > Apply SERRF QC Correction or Apply QC Correction
> Mark Background > Normalize Areas

IMPORTANT Do not use the Apply Missing Value Imputation node with either of the
QC correction nodes. Use the Fill Gaps node instead.

The Apply Missing Value Imputation node only imputes the missing peak area
values—whereas, the Gap Filling node actually re-detects missing peaks by
performing peak detection at a very low threshold.

Because the Gap Filling node detects actual peaks, it provides more accurate results
than the Apply Missing Value Imputation node. More of the gap-filled compounds
will pass the RSD filter in the QC correction nodes and therefore have a QC
correction applied to them.

• If the blanks are matrix blanks, connect the nodes in this order:
Group Compounds > Fill Gaps > Apply SERRF QC Correction or Apply QC
Correction> Normalize Areas > Mark Background.

If you add the Scaling Factor node, add it to the end of the processing workflow template.

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 6 Create and edit processing workflows
Connect the workflow nodes for an LC study

Input and output nodes for the workflow nodes

Table 33 describes the node connections for the workflow nodes in an LC study.
Table 33. Input and output nodes for each workflow node in an LC study (Sheet 1 of 4)
Workflow node Input nodes Output nodes
1. Input/Output
Export Spectra node Select Spectra Filter Centroids
Input Files None • Select Spectra
(Begins every processing workflow) • Create Analog Trace
2. Spectrum Processing
Align Retention Times node Spectrum Processing • Spectrum Processing
• Trace Creation
• Find Expected Compounds
• Detect Compounds
Filter Centroids node • Spectrum Processing • Spectrum Processing
• Trace Creation
• Find Expected Compounds
• Detect Compounds
Filter By Mass Defect node • Spectrum Processing • Spectrum Processing
• Generate Expected Compounds • Trace Creation
• Find Expected Compounds
• Detect Compounds
Filter By Scan Event node Spectrum Processing • Spectrum Processing
• Trace Creation
• Find Expected Compounds
• Detect Compounds
Select Spectra node Input Files • Spectrum Processing
• Trace Creation
• Find Expected Compounds
• Detect Compounds
3. Trace creation
Create Analog Trace node (LC studies) Input Files None
Create Mass Trace node (LC studies) Spectrum Processing None
Create FISh Trace node (LC studies) Spectrum Processing None
Create Pattern Trace node (LC studies) Spectrum Processing None
4. Expected Compounds
FISh Scoring node (LC studies) Group Expected Compounds None

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Connect the workflow nodes for an LC study

Table 33. Input and output nodes for each workflow node in an LC study (Sheet 2 of 4)
Workflow node Input nodes Output nodes
Find Expected Compounds node • Generate Expected Compounds • Group Expected Compounds
• Spectrum Processing • Merge Features
Find Expected Compounds (Legacy) • Generate Expected Compounds • Group Expected Compounds
node • Spectrum Processing • Merge Features
Generate Expected Compounds node None • Find Expected Compounds
• Filter By Mass Defect
Group Expected Compounds node Find Expected Compounds • FISh Scoring
• Mark Background Compounds
Merge Features node • Find Expected Compounds None
• Detect Compounds
5. Compound Detection
Analyze Labeled Compounds node Assign Compound Annotations None
Detect Compounds node Spectrum Processing • Group Compounds
• Merge Features
Detect Compounds (Legacy) node Spectrum Processing • Group Compounds
• Merge Features
Fill Gaps node Group Compounds Any of the peak area refinements
nodes (except the Apply Missing
Value Imputation node)
Group Compounds node Detect Compounds • Compound Identification
• Pathway Mapping
• Fill Gaps
• Mark Background Compounds
6. Peak Area Refinement
IMPORTANT For information about connecting the peak area refinement nodes in the correct input–output order,
see “Peak area refinement node connections.”
Apply Missing Value Imputation node One of these: One of the other peak area
• Group Compounds refinement nodes.
• Normalize Areas
• Scale Areas The most common output nodes
• Apply QC Correction are either one of the QC correction
nodes or the Mark Background
Compounds node.
IMPORTANT Do not use the Apply
Missing Value Imputation node None of the provided processing
with the QC correction nodes. workflow templates for LC studies
include the Apply Missing Value
Imputation node.

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Connect the workflow nodes for an LC study

Table 33. Input and output nodes for each workflow node in an LC study (Sheet 3 of 4)
Workflow node Input nodes Output nodes
Apply QC Correction node Fill Gaps Normalize Areas or Scale Areas

(Connecting the Apply QC

Correction node to the Normalize
Areas node or the Scale Areas node
is not recommended.)
Apply SERRF QC Correction node Fill Gaps Normalize Areas or Scale Areas

(Connecting the Apply SERRF QC

Correction node to the Normalize
Areas node or the Scale Areas node
is not recommended.)
Mark Background Compounds node One of these: Typically the last node in the
• Group Expected Compounds processing workflow
• Group Compounds
• Peak refinement node
Normalize Areas node See “Peak area refinement node –
connections.”
Scale Areas node • Group Compounds None
• Fill Gaps
• Mark Background Compounds
• Apply QC Correction
• Apply SERRF QC Correction
Tip To use the Scales Areas node, the study must include assigned values
for a numeric study factor.
7. Compound Identification
Assign Compound Annotations node Group Compounds None
Predict Compositions node Group Compounds None
Search ChemSpider node • Group Expected Compounds None
• Group Compounds
Search Mass Lists node • Group Expected Compounds None
• Group Compounds
Search mzCloud node • Group Expected Compounds None
• Group Compounds
Search mzVault node • Group Expected Compounds None
• Group Compounds

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Connect the workflow nodes for an LC study

Table 33. Input and output nodes for each workflow node in an LC study (Sheet 4 of 4)
Workflow node Input nodes Output nodes
8. Pathway Mapping
All • Group Expected Compounds None
• Group Compounds
9. Compound Scoring
Apply Spectral Distance node • Search Mass Lists None
• Search ChemSpider
• Map to KEGG Pathways
• Map to Metabolika Pathways
• Map to BioCyc Pathways
Apply mzLogic node • Search Mass Lists None
• Search ChemSpider
• Map to Metabolika Pathways
• Map to BioCyc Pathways
Calculate Mass Defect node Group Compounds None
Compound Class Scoring node Group Compounds None
Generate Molecular Networks node Assign Compound Annotations None
Pattern Scoring node Group Compounds None
Search Neutral Mass Losses node Group Compounds None
10. Post-Processing (white nodes)
Descriptive Statistics node None None
Differential Analysis node None None
Export Xcalibur Inclusion or Exclusion None None
List node
Result Exporter None None
Scripting Node None None

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 6 Create and edit processing workflows
Save a custom processing workflow as a template

Save a custom processing workflow as a template

You can run an analysis without saving the processing workflow in the Workflow Tree pane;
however, you might want to save the processing workflow to a template for reuse. When you
save the processing workflow as a template, the application does not automatically store it in
the study folder. You can save a processing template to the Common Templates folder or a
folder of your choice.

Note When you run an analysis, the application automatically saves the processing
workflow to the result file. Selecting a result file on the Analysis Results page of a study
and clicking Reprocess opens the processing workflow saved with the result file.

Y To save a custom processing workflow as a template

1. Do one of the following:

• To save the template in the Common Templates folder, click Save Common.
The Save Workflow dialog box opens to the Common Templates folder.
• To save the template, click Save.
The Save Workflow dialog box opens to the last opened folder.
2. Select the folder where you want to store the template, name the template, and click Save.
If the processing workflow is valid, the application saves the template with the file name
extension.cdProcessingWF. If the processing workflow contains an error, an error message
box opens.
3. If the Exporting Template Workflow Failed message box opens, read the list of errors,
close the message box, fix the errors, and click Save.

Use the Workflows page (in any study) to create or edit processing workflows. The Workflows
page is a tabbed page to the right of the Grouping & Ratios page and is available only when
the Analysis view is open.

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 7

Workflow nodes
A processing workflow consists of a set of connected workflow nodes, and each workflow
node has a set of associated parameters. To create and edit processing workflows, see
Chapter 6, “Create and edit processing workflows.”

Note For information about the workflow nodes for GC studies, refer to the Compound
Discoverer User Guide for GC Studies or the Help system.
In the Compound Discoverer 3.3.x application, Thermo Fisher Scientific has improved
the functionality of the Detect Compounds and Find Expected Compounds nodes, which
now require fewer if any custom parameter settings.
To support legacy processing workflows, the Workflow Nodes pane still includes the
Detect Compounds (Legacy) and the Find Expected Compounds (Legacy) nodes.
The Align Retention Times (ChromAlign) and Result Exporter nodes were added in the
Compound Discoverer 3.3.0 application.
The processing workflow templates use the improved Detect Compounds and Find
Expected Compounds nodes and the new Align Retention Times (ChromAlign) node.

In the Workflow Nodes pane on the Workflows page, the workflow nodes are organized into
functional groups. For information about the workflow nodes, see the following topics:
• Input and Output nodes
• Spectrum Processing nodes
• Trace Creation nodes
• Expected Compounds nodes
• Compound Detection nodes
• Peak Area Refinement nodes
• Compound Identification nodes
• Pathway Mapping nodes
• Compound Scoring nodes
• Post-Processing nodes

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 7 Workflow nodes
Input and Output nodes

Input and Output nodes

For LC studies, the Input/Output area in the Workflow Nodes pane on the Workflows page
of an analysis includes these nodes:
• Export Spectra node
• Input Files node

Note All processing workflows begin with the Input Files node.

Export Spectra node

Use the Export Spectra node to export all or a subset of the mass spectrum scans in an
Xcalibur RAW file to an open-source format file. The Export Spectra node does not export
the data from analog detectors.

Note You can add multiple Export Spectra nodes to a processing workflow.

The Export Spectra node requires input from one of the data processing nodes. The
processing workflow shown in Figure 82 reads the input files, extracts the MS scans of
interest, and exports the data to an open source format file. Running this processing workflow
does not require an active software license.
Figure 82. Minimum processing workflow for the Export Spectra node

Table 34 describes the parameters for the Export Spectra node.

Table 34. Export Spectra node parameters (Sheet 1 of 2)
Parameter Description
1. Output Data
File Name Specifies the file name of the exported file. If you leave this box
empty, the node uses the result file name.
File Name Suffix Specifies the suffix that the application appends to the file name of
the exported file.

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Spectrum Processing nodes

Table 34. Export Spectra node parameters (Sheet 2 of 2)

Parameter Description
Export Format Specifies the data format of the exported file.

Selections:
• Mascot Generic Format (*.mgf )—Generates an MGF file,
which lists the MS scans by retention time. The scan data for
each time point consists of two columns: mass and intensity.
• mzDATA (*mzData)—Generates an XML-based file that
third-party mass spectrometry software packages can read.
• mzML (*mzML)—Generates an XML-based file that
third-party mass spectrometry software packages can read.

Input Files node

Every processing workflow must begin with the Input Files node. This node has no
parameters.

To view information about the input files for a result file, open its Input Files table.

Spectrum Processing nodes

The nodes under Spectrum Processing extract the mass spectral data from the input file set.

For an LC study, the following workflow nodes are available in the Spectrum Processing area
of the Workflow Nodes pane:
• Align Retention Times node
• Align Retention Times (ChromAlign)
• Filter By Mass Defect node
• Filter By Scan Event node
• Filter Centroids node
• Select Spectra node

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 7 Workflow nodes
Spectrum Processing nodes

Align Retention Times node

For LC studies, use the Align Retention Times node for chromatographic alignment of
multiple input files. The Align Retention Times node compensates for small differences in the
retention times of the components in a sequence of sample runs.

IMPORTANT In the spectrum processing node that supplies spectra to the Alignment, do
not apply a scan filter that excessively reduces the retention time window, as doing so
might cause an alignment failure. The Align Retention Times node requires a minimum
amount of representative scan data to chromatographically align the input files in an
analysis.

Note The Align Retention Times node generates the File Alignments result table. When
you open a result file from an analysis that included the Align Retention Times node, the
Retention Time Correction view is available.

For details, see these topics:

• Retention Time Corrections view
• File Alignments table

Table 35 describes the parameters for the Align Retention Times node.
Table 35. Align Retention Times node parameters (Sheet 1 of 2)
Parameter Description
1. General Settings
Alignment Model Specifies the curve-fitting algorithm for chromatographically
aligning the input files.

Default: Adaptive Curve

Selections:
• Adaptive Curve—Calculates a flexible curve for the retention
time shift for each retention time point for a compound.
• Linear—Uses a linear function to fit all the retention time
points for a compound.

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Spectrum Processing nodes

Table 35. Align Retention Times node parameters (Sheet 2 of 2)

Parameter Description
Alignment Fallback Specifies the alternate model to apply when the Adaptive Curve
regression model fails.

Default: Use Linear Model

Selections:
• None—There is no alternative. Continue to use the Adaptive
Curve model.
• Don’t Align—Do not chromatographically align the input
files.
• Use Linear Model—Use the Linear model instead of the
Adaptive Curve model.
Maximum Shift [min] Specifies the maximum retention time shift between the
alignment features (chromatographic peaks with the same
m/z × RT dimensions) in the input files.

Default: 2 (± 2 minutes for each feature); range: 0.01–4.0

Shift Reference File Specifies whether to shift the retention time of all the detected
features to eliminate any negative retention time values in the
input file set.

Default: True

Selections:
• True: If the data set includes features with negative retention
times, the algorithm shifts all of the features to avoid
cropping.
• False: Removes features with negative retention time values
from the analysis (crops the feature from the feature list passed
to the connected nodes).
Mass Tolerance Specifies the mass tolerance to be used for feature matching.

Default: 5.0 ppm; range: 0.1–50 ppm

Remove Outlier Specifies whether the retention time algorithm ignores outlier
landmark features.

Default: True

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 7 Workflow nodes
Spectrum Processing nodes

Align Retention Times (ChromAlign)

Table 36 describes the parameter for the Align Retention Times node.
Table 36. Align Retention Times node parameter
Parameter Description
1. General Settings
Reference File Specifies the input file that the analysis aligns all other input files
to.

When you leave this parameter setting empty, the application

automatically uses the first QC file as the reference file. If the
analysis does not include any QC files, the application
automatically uses the first sample file.

In the result file that the analysis generates, the Statistical Methods
table lists the reference file.

Filter By Mass Defect node

For LC studies, use the Filter By Mass Defect node to keep or remove mass spectral peaks
(centroids) in the full (MS1) scan data that fall within a set of specified mass tolerance and
mass defect windows.

You can add multiple Filter By Mass Defect nodes to a processing workflow.

To specify the elemental compositions for the node, you can enter the elemental compositions
in the Custom Compositions area of the node, or you can use the Generate Expected
Compounds node to provide the compositions.

Tip For more information about mass defects, see “Mass defect types and visualization
techniques.”

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Spectrum Processing nodes

Table 37 describes the parameters for the Filter By Mass Defect node.
Table 37. Filter By Mass Defect node parameters (Sheet 1 of 2)
Parameter Description
1. General Settings
Filter Direction Specifies whether the selected mass defect filter keeps or removes mass
spectral peaks (centroids) from further processing.

Default: Keep; Selections: Keep or Remove

Mass Defect Type Specifies the mass defect type.

Default: Standard Mass Defect

Selections:

Fractional Mass = exact mass – floor (exact mass)

Standard Mass Defect = exact mass – nominal mass

1e6 × (exact mass – nominal mass)

Relative Mass Defect = -----------------------------------------------------------------------------------------------------
-
(exact mass)

Kendrick Mass Defect = Kendrick mass – nominal Kendrick mass

Where:

Exact mass = Monoisotopic mass of the elemental composition

Nominal mass = Integer mass

Calculates the integer mass using the selected rounding function
(floor, ceiling, or round)

nominal mass of Kendrick formula

Kendrick Mass = exact mass × ------------------------------------------------------------------------------------------------------
exact mass of Kendrick formula
Kendrick Formula When you select the Kendrick Mass Defect type, this user-specified
elemental composition specifies the Kendrick formula.
Nominal Mass Specifies how the node calculates nominal masses.
Rounding
Default: Floor

Selections:
• Floor rounds down.
• Ceiling rounds up.
• Round rounds to the nearest integer value.

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Spectrum Processing nodes

Table 37. Filter By Mass Defect node parameters (Sheet 2 of 2)

Parameter Description
2. Tolerances

Using the calculated mass defect values calculated and the exact mass values calculated from
the elemental composition input, these mass tolerance values define the rectangular mass
defect filters.
Mass Tolerance The input from the data processing nodes is a table of m/z values and
intensities for each full (MS1) scan.

Specifies the mass tolerance for the ions that the filter removes or
passes through to the next node.

Default: 50 Da; Selection: 0 to 6000 Da

Mass Defect Specifies the mass defect tolerance for the ions that the filter removes
Tolerance or passes through to the next node.

Default: 0.025 (Da or unit-less for the Relative Mass Defect selection)

Range: 0–No limit

3. Custom Compositions
Composition Specify the elemental compositions that the node uses to create the
(5 entry boxes) mass defect filters.

Leave these boxes empty if you want to use one or more Generate
Expected Compounds nodes to generate the list of elemental
compositions.
Ions Specifies the ion definitions to be used with the custom compositions.
For each elemental composition, the node creates one mass defect filter
for each ion definition—that is, if you select five ion definitions, the
node creates five mass defect filters for each elemental composition.

Select the ion definitions from the dropdown list. Use the Ion
Definition Editor to create new ion definitions.

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Filter By Scan Event node

For LC studies, use the Filter By Scan Event node to filter the mass spectra by scan events.

Table 38 describes the parameters for the Filter By Scan Event node.
Table 38. Filter By Scan Event node parameters (Sheet 1 of 3)
Parameter Description
Filter Settings
Mass Analyzer Specifies the mass analyzer that the instrument used to acquire the
scan. A Thermo Scientific hybrid mass spectrometer, such as the
LTQ Orbitrap mass spectrometer, contains two mass analyzers
and can acquire both ITMS (low-resolution) and FTMS
(high-resolution) scans in one data file.

Filter selection: Any, Is, Is Not; default: (Not Specified)—The

application does not filter scan events by the mass analyzer that
was used to acquire the data.

Check box selections:

• Ion Trap (ITMS)
• Fourier Transform (FTMS))
• Time of Flight (TOFMS)
• Single Quad (SQMS)
• Triple Quad (TSMS)
• Sector Field (SectorMS)
MS Order Specifies the MS order (scan power that the instrument used) of
the scans that you want the node to filter.

Filter selection: Any, Is, Is Not; default: (Not Specified)—The

node does not filter the scans by MS order.

Check box selections: MS1–MS7

Note The Detect Compounds and Find Expected Compounds
nodes search the full (MS1) scans for mass peaks. If you filter
out the MS1 scans by selecting Is MS2 or higher for the MS
Order, the result tables for these nodes are empty.

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Table 38. Filter By Scan Event node parameters (Sheet 2 of 3)

Parameter Description
Activation Type Specifies the activation types that the instrument used to produce
the product ion spectra.

Filter selection: Any, Is, Is Not; default: (Not Specified)—The

node does not filter the scans by activation type.

Check box selections:

• CID (Collision Induced Dissociation)
• MPD (Multi Photon Dissociation)
• ECD (Electron Capture Dissociation)
• PQD (Pulsed Q Collision Induced Dissociation)
• ETD (Electron Transfer Dissociation)
• HCD (Higher Energy Collision Dissociation)
• EThcD (ETD With Supplemental HCD)
• UVPD (Ultra Violet Photo Dissociation)
• Any Activation Type
Min. Collision Energy Specifies the minimum Normalized Collision Energy™ for a
higher-order scan to pass through the filter.

Default: 0 (no filtering); Minimum value: 0; Maximum value:

unchecked
Max. Collision Energy Specifies the maximum Normalized Collision Energy for a
higher-order scan to pass through the filter.

Default: 1000; Minimum value: 0; Maximum value: 1000

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Table 38. Filter By Scan Event node parameters (Sheet 3 of 3)

Parameter Description
Scan Type Specifies the scan type for the scan event that the instrument used
to produce the product ion.

Filter selection: Any, Is, Is Not; default: (Not Specified)—The

node does not filter the scan events by scan type.

Check box selections:

• Full
• Single Ion Monitoring (SIM)
• Single Reaction Monitoring (SRM)
Polarity Mode Specifies the polarity mode for the scan.

Filter selection: Any, Is, Is Not

Default: (Not Specified)—The node does not filter the scan events
by polarity mode.

Check box selections:

• Positive
• Negative

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Filter Centroids node

Use the Filter Centroids node to remove mass spectral peaks (centroids) that are below a
user-specified intensity threshold from the mass scans, below a user-specified signal-to-noise
threshold for FTMS scans, or both.

Table 39 describes the parameters for the Filter Centroids node.

Table 39. Filter Centroids node parameters
Parameter Description
1. General
S/N Threshold Specifies the minimum signal-to-noise threshold for each centroid
(for FT-only) in an FTMS scan. The node excludes centroids from the analysis
that are below this intensity value.

The application uses the spectrum noise reported by an

instrument.

Default: 1.5
Minimum Intensity Specifies the minimum intensity threshold for the mass spectral
Threshold peaks (centroids). The node excludes centroids from the analysis
that are below this intensity value.

Default: 0 (no filtering)

Select Spectra node

The raw data file (Xcalibur RAW file) contains the mass spectral scans that the Thermo
Scientific mass spectrometer acquired and, for LC/MS data, any optional data acquired by a
PDA, UV-VIS, or analog detector during the acquisition run. The Select Spectra node can
read and filter the mass spectral scan data. The Select Spectra node cannot read the optional
data acquired by a PDA, UV-VIS, or analog detector.

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The mass spectral scans are numbered 1, 2, 3, and so on in single integer increments from the
beginning to the end of the acquisition run. Use the Select Spectra node to select the scans
that you want the application to process. Limiting processing to the scans of interest decreases
processing time and minimizes false positives. For example, if you know the retention time of
the compounds of interest, exclude scans that fall outside a specific retention time window.

IMPORTANT For LC studies, the default parameter settings for the Select Spectra node
are appropriate for most analyses. When using settings other than the defaults, follow
these guidelines:
• Because the application uses the full (MS1) scans to measure the accurate mass and
isotope patterns of the mass spectral peaks, do not filter out the full (MS1) scans when
the processing workflow includes any of these nodes:
– Find Expected Compounds
– Find Expected Compounds (Legacy)
– Detect Compounds
– Detect Compounds (Legacy)
• The following nodes require a representative amount of data to function properly:
– Align Retention Times
– Align Retention Times (ChromAlign)
– Find Expected Compounds
– Find Expected Compounds (Legacy)
If you excessively reduce the retention time window (for example, by using an RT or
scan number range), the chromatographic alignment algorithm (for the alignment
nodes) and the automatic peak width detection algorithm (for the find expected
compounds nodes) might fail to produce satisfactory results.

Table 40 describes the parameters in the Select Spectra node.

Table 40. Select Spectra node parameters (Sheet 1 of 9)
Parameter Description
1. Spectrum Properties Filter

The only basic parameters in this group are the lower and upper RT limits.
Note The retention time filter excludes scans outside the specified limits; however, the
application does not check the validity of the retention time settings against the actual
acquisition time for the raw data file. When both the lower and upper RT limits are set to
0 (default), the application does not use retention time to filter scans.
Lower RT Limit Excludes scans acquired before the user-specified retention time.

Default: 0; Minimum value: 0; Maximum value: Unchecked

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Table 40. Select Spectra node parameters (Sheet 2 of 9)

Parameter Description
Upper RT Limit With the exception of a setting of 0, excludes scans that were
acquired after the user-specified retention time.

Default: 0; Minimum value: 0; Maximum value: Unchecked

Note The scan number filter excludes scans outside the specified limits—however, the
application does not check the validity of the scan number settings against the actual scan
numbers in the raw data file. When both the first and last scan number are set to 0
(default), the application does not filter scans by scan number. When filtering by scan
number, verify the scan number range in Thermo Scientific application where you can
browse the mass spectra, such as FreeStyle.
First Scan Specifies the scan number of the first available scan that you want
the node to process.

When this parameter is set to 0, the node processes the first scan
that passes through the other filters.

When this parameter is set to a value that is greater than the last
available scan number, the node filters out all of the scans.

Default: 0 (no filtering)

Minimum value: 0; Maximum value: Unchecked

Last Scan Specifies the last available scan number that you want the node to
process.

When this parameter is set to 0 or a value that is greater than the

last available scan number, the node processes the last scan that
passes through the other filters.

Default: 0 (no filtering); Minimum value: 0; Maximum value:

Unchecked

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Table 40. Select Spectra node parameters (Sheet 3 of 9)

Parameter Description
Ignore Specified Scans Specifies the scan numbers that the analysis ignores. Placing the
cursor in the Ignore Specified Scans box and clicking the More
icon, , opens the Edit Parameter Text for Ignore Specified
Scans dialog box.

Use this dialog box to do any of the following:

• Manually enter the scan numbers to ignore.
• Load a text file that lists the scan numbers to ignore.
• Create and save a list of scan numbers to ignore.

Note The charge state filter excludes higher-order scans of precursor ions with a charge
state that is outside the specified limits. The charge state filter does not affect the MS1
scans.
Lowest Charge State Excludes higher-order scans of precursor ions with a lower charge
state than the specified charge state.

Default: 0; Minimum: 0
Highest Charge State Filters out scans from precursor ions with a higher charge state
than the specified charge state.

Default: 0 (specifies no upper limit)

Min. Precursor Mass Specifies the minimum precursor mass for a higher-order scan.

Default: 0 (no filtering); Minimum value: 0; Maximum value:

Unchecked
Max. Precursor Mass Specifies the maximum precursor mass for a higher-order scan.

Default: 0 (no filtering); Minimum value: 0; Maximum value:

Unchecked
Total Intensity Excludes scans that fall below the specified total intensity
Threshold threshold. The total intensity of a mass spectrum is the summed
intensity of its mass spectrum peaks (centroids).

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Table 40. Select Spectra node parameters (Sheet 4 of 9)

Parameter Description
Minimum Peak Count Specifies the minimum number of mass spectrum peaks
(centroids) that must be in the spectrum for the scan to pass
through the filter.

Minimum value: 1; Maximum value: Unchecked

2. Scan Event Filters

The only basic parameter in this group is Polarity Mode.

Mass Analyzer Specifies the mass analyzer that the instrument used to acquire the
scan. An LTQ Orbitrap hybrid mass spectrometer can acquire
both ITMS (low-resolution) and FTMS (high-resolution) scans in
one data file.

Filter selection: Any, Is, Is Not; default: (Not Specified)—The

node does not filter scan events by the mass analyzer used to
acquire the data.

Check box selections:

• Ion Trap (ITMS)
• Fourier Transform (FTMS))
• Time of Flight (TOFMS)
• Single Quad (SQMS)
• Triple Quad (TSMS)
• Sector Field (SectorMS)
MS Order Specifies the MS order of the scans that you want the node to
process.

Filter selection: Any, Is, Is Not; default: Any—The application

does not filter the scans by MS order.

Check box selections: MS1–MS7

IMPORTANT The Detect Compounds and Find Expected Compounds nodes search the
MS1 scans for mass peaks. If you filter out the MS1 scans by selecting Is MS2 or higher
for the MS Order, the result tables for these nodes are empty.

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Table 40. Select Spectra node parameters (Sheet 5 of 9)

Parameter Description
Activation Type Specifies the activation type that the instrument used to produce
the product ion spectra.

Filter selection: Any, Is, Is Not; default: (Not Specified)—The

node does not filter the scans by activation type.

Check box selections (as displayed in the drop-down list):

• CID (Collision Induced Dissociation)
• MPD (Multi Photon Dissociation)
• ECD (Electron Capture Dissociation)
• PQD (Pulsed Q Collision Induced Dissociation)
• ETD (Electron Transfer Dissociation)
• HCD (Higher Energy Collision Dissociation)
• EThcD (ETD With Supplemental HCD)
• UVPD (Ultra Violet Photon Dissociation)
• Any Activation Type
Min. Collision Energy Specifies the minimum Normalized Collision Energy for a
higher-order scan to pass through the filter.

Default: 0 (no filtering)

Minimum value: 0; Maximum value: Unchecked

Max. Collision Energy Specifies the maximum Normalized Collision Energy for a
higher-order scan to pass through the filter.

Default: 1000; Minimum value: 0; Maximum value: 1000

Scan Type Specifies the scan type for the scan event that the instrument used
to produce the product ion.

Filter selection: Any, Is, Is Not; default: Any—The application

does not filter the scan events by scan type.

Check box selections:

• Full
• Selected Ion Monitoring (SIM)
• Selected Reaction Monitoring (SRM)

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Table 40. Select Spectra node parameters (Sheet 6 of 9)

Parameter Description
Polarity Mode Specifies the polarity mode for the scan.

Filter selection: Any, Is, Is Not

Default: (Not Specified)—The node does not filter the scan events
by polarity mode.

Check box selections:

• Positive
• Negative
IMPORTANT When the input files for an analysis include mass range switching or CV
switching and the processing workflow includes a compound detection node, use the MS1
Mass Range filter or the FAMS CV filter, respectively, to specify the mass range or CV
value that you want to process.

The compound detection nodes can process spectra for only one mass range and one CV
value per input file.
MS1 Mass Range This filter applies only to MS1 scans. The format for this
parameter setting is [50.0000-1000.0000], where the dash is a
hyphen.

MS1 scans must match the specified mass range to pass the filter.

Default: Unspecified (Empty)

IMPORTANT Enter the masses in the mass range to four decimal
places, as the node checks the mass values to four decimal places.

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Table 40. Select Spectra node parameters (Sheet 7 of 9)

Parameter Description
FAIMS CV When the compensation voltage (FAIMS CV value) is unspecified
(empty), the analysis ignores CV values and all spectra pass the
filter.

When you specify a CV value, the analysis processes only the

spectra for the specified CV value.

Default: Unspecified (Empty)

IMPORTANT The compound detection nodes require MS1
spectra from each input file in an analysis, but they can process
spectra for only one CV value per input file.

To prevent an analysis that includes a compound detection node

from failing, do the following:
• When any of the input files include spectra for more than
one CV value (CV switching), specify the CV value that you
want to process, and make sure that every file in the Files for
Analysis list includes spectra for this CV value.
• When the input files include only one CV value per file but
not the same CV value for each file, do not specify the CV
value.
3. Peak Filters
S/N Threshold Specifies the signal-to-noise threshold for mass peaks in an FTMS
(FT-only) scan. Mass peaks below this threshold are filtered out.

Default: 1.5
4. Replacements for Unrecognized Properties
Unrecognized Charge Specifies the charge state or states to process when the charge state
Replacements of the precursor ion is indeterminate.

Default: 1

In the Qual Browser window, an indeterminate charge state is

specified with a question mark label (z=?) in a spectrum cell. In the
FreeStyle application, ions with indeterminate charge states are
labeled with a charge state of 0.

Default: 1; Selections: All, 1, 2, 3, 4, 5, 6, 7, or 8

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Table 40. Select Spectra node parameters (Sheet 8 of 9)

Parameter Description
Unrecognized Mass Specifies the mass analyzer used to acquire the data when the
Analyzer Replacements application cannot retrieve this information from the input file.

Default: ITMS
Selections:
• Ion Trap (ITMS)
• Fourier Transform (FTMS)
• Time of Flight (TOFMS)
• Single Quad (SQMS)
• Triple Quad (TSMS)
• Sector Field (SectorMS)
Unrecognized MS Specifies the MS order when the application cannot retrieve this
Order Replacements information from the input file.

Default: MS2; Selections: MS1–MS10

Unrecognized Specifies the activation type when the application cannot retrieve
Activation Type this information from the input file.
Replacements
Default: CID
Selections (as displayed in the drop-down list):
• CID (Collision Induced Dissociation)
• MPD (Multi Photon Dissociation)
• ECD (Electron Capture Dissociation)
• PQD (Pulsed Q Collision Induced Dissociation)
• ETD (Electron Transfer Dissociation)
• HCD (High Energy Collision Dissociation)
• EThcD (ETD With Supplemental HCD)
• UVPD (Ultra Violet Photon Dissociation)
Unrecognized Polarity Specifies the polarity mode when the application cannot retrieve
Replacement this information from the input file.

Default: (+); Selections: Positive (+) or Negative (–)

Unrecognized MS Specifies the resolution at m/z 200 for MS scans when the node
Resolution @ 200 cannot retrieve the resolution from the scan header.
Replacements
Default: 60 000
Unrecognized MSn Specifies the resolution at m/z 200 for MS/MS scans when the
Resolution @ 200 node cannot retrieve the resolution from the scan header.
Replacements
Default: 30 000

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Table 40. Select Spectra node parameters (Sheet 9 of 9)

Parameter Description
5. General Settings
Precursor Selection Specifies the MS order of the precursor scans for higher-order
MSn scans, such as MS3, MS4, and so on up to MS(n – 1).

Default: Use MS(n – 1) Precursor

Selections: Use MS1 Precursor or Use MS(n – 1) Precursor

Use Isotope Pattern in Determines whether the node considers the isotope pattern in
Precursor Reevaluation reevaluating precursors.

Default: True
Selections:
• True—The node considers the isotope pattern in reevaluating
precursors.
• False—The node does not consider the isotope pattern in
reevaluating precursors.
Provide Profile Spectra When set to True, the node stores the profile data for the scans.

When set to Automatic, the node checks whether any other nodes
in the processing workflow require profile data. If the profile data
is not required by any of the workflow nodes in the processing
workflow, the node only stores the centroid data.

Default: Automatic
Store Chromatograms Specifies whether the analysis stores the total ion current (TIC)
and base peak chromatograms in the result file.

Default: False

Trace Creation nodes

For LC studies, these nodes create specialized chromatographic traces:
• Create Analog Trace node
• Create FISh Trace node
• Create Mass Trace node
• Create Pattern Trace node

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Create Analog Trace node

For LC studies, use the Create Analog Trace node to view the chromatograms for these trace
types: ultraviolet-visible (UV), photo-diode array (PDA), or analog. Your Thermo Scientific
data system supports several brands of UV-Vis and PDA detectors. You can acquire UV traces
from a UV-Vis or a PDA detector and PDA traces from a PDA detector. If your analog
detector is not supported by a Thermo Scientific data system, you can acquire an analog trace
by connecting the detector to one of the analog channels on the communications panel of
your Thermo Scientific mass spectrometer.

You can access analog traces from the Specialized Traces table.

Note The Create Analog Trace node can also convert and display a pressure trace from an
LC pump and a temperature trace from a column heater or autosampler with temperature
control, when these instruments are controlled by the Xcalibur data system or equivalent
Thermo Scientific application.

Table 41 describes the parameters for the Analog Traces node.

Table 41. Create Analog Trace node parameters (Sheet 1 of 2)
Parameter Description
1. General Settings
Trace Type Specifies whether the application extracts a UV, PDA, or analog
trace from the raw data file.

Default: UV; Selections: UV, PDA, or Analog

RT Offset [min] Specifies the offset time, in minutes, between the UV, PDA, or
analog detector and the mass spectrometer traces.

A negative value shortens and a positive value lengthens the

apparent retention time of the peaks detected by the UV, PDA, or
analog detector.

Default: 0; range: –10 to 10

Custom Label Type text to identify the trace in the Specialized Traces table on
the result file page.
2. PDA Settings
Total Scan Specifies whether the node extracts a total scan trace for the
scanned wavelength range.

Total scan traces display the average absorbance for each time
point of all the wavelengths in the scan range.

Default: False

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Table 41. Create Analog Trace node parameters (Sheet 2 of 2)

Parameter Description
Spectrum Maximum Specifies whether the node extracts a spectrum maximum trace for
the scanned wavelength range.

Spectrum maximum traces display a plot of the maximum

absorbance values in the scan range for each time point.

Default: False
Note Use the Min. and Max. Wavelength boxes to specify a trace of average absorbance
versus time.
• To display the chromatogram for a specific scan wavelength, type the same
wavelength number in the Min. and Max. Wavelength boxes.
• To display a plot of the average absorbance values for a range of wavelengths, type the
beginning wavelength number in the Min. Wavelength box and the ending
wavelength number in the Max. Wavelength box.
Wavelength Range Specifies whether the node extracts the entire acquired scan or a
wavelength range.

Default: True—Uses a specified wavelength range.

Min. Wavelength Specifies the beginning wavelength, in nanometers, of the trace
that you want the node to extract.

Default: 190; range: 190–800 nm

Max. Wavelength Specifies the ending wavelength, in nanometers, of the trace that
you want the node to extract.

Default: 800; range: 190–800 nm

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Create FISh Trace node

For LC studies, use the Create (Fragment Ion Search) FISh Trace node to create FISh traces.
The Create FISh Trace node requires fragmentation scans and takes input from any of the
data processing nodes. The output from the FISh trace node is a summed FISh trace that is
accessible from the Specialized Traces Table, individual fragment traces that are accessible
from the FISh Trace Fragments result table, or both.

Table 42 describes the parameters for the Create FISh Trace node.
Table 42. Create FISh Trace node parameters (Sheet 1 of 3)
Parameter Description
1. Compound Selection
Compound Specifies the compound that the node uses to generate expected
fragment ions.

The selection list contains the compounds in the user-created Lists

& Libraries > Expected Compounds library. See “Expected
Compounds view.”
IMPORTANT To run an analysis that includes the Create FISh
Trace node, you must select a compound from this list. To add
compounds to the Expected Compounds library, see “Add and
edit expected compounds with the Compound Editor.”
2. Trace Settings
Mass Tolerance Specifies the mass tolerance that the node uses to create the FISh
trace.

Default: 2.5 mmu

Summed Trace Specifies whether the node generates a summed trace of all the
detected fragment ions. You can access the summed FISh trace
from the Specialized Traces result table.

Default: True
Individual Traces Specifies whether the node generates individual traces for each
generated fragment ion. You can access the individual traces from
the FISh Trace Fragments result table.

Default: True
Custom Label Type text that you can use to identify the chromatogram in a
report.

This box accepts alphanumeric and special characters.

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Table 42. Create FISh Trace node parameters (Sheet 2 of 3)

Parameter Description
3. Scan Filter Settings
Scan Polarity Specifies the polarity of the scan.

Default: + (Positive); Selections: Positive or Negative

Fragment Mode Specifies the fragmentation mode of the fragmentation scans that
you want the node to extract.

Default: Data-Dependent; Selections: Data-Dependent or Data

Independent

Select Data-Dependent for data-dependent fragmentation (DDF)

scans or Data Independent for all-ion fragmentation (AIF) scans.
4. Fragment Prediction Settings
Use General Rules Specifies whether the node uses the general fragmentation rules for
fragment prediction.
Use Libraries Specifies whether the node uses the fragmentation libraries for
fragment prediction.

Default: True
Max. Depth Specifies the maximum number of steps in the fragmentation
pathway.

Range: 1 to 20
Aromatic Cleavage Specifies whether the node includes a cleavage step in the
fragmentation pathway for highly aromatic structures—that is, for
aromatic structures where n in Huckel’s rule is 2 or higher.

4n + 2 = the number of electrons in the delocalized, conjugated

p-orbital cloud

For example, the following structure is aromatic with an n value

of 2, and the number of electrons in its delocalized, conjugated
p-orbital cloud is 10.

Default: True

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Table 42. Create FISh Trace node parameters (Sheet 3 of 3)

Parameter Description
Min. Fragment m/z Specifies the minimum m/z value of a fragment ion to be
generated by the prediction fragmentation pathway.

Default: 50; range: 0 or higher

Max. Fragment m/z Specifies the maximum m/z value of a fragment ion to be
generated by the prediction fragmentation pathway.

When the value is set to 0, the node ignores this parameter.

Default: 0

Create Mass Trace node

Use the Create Mass Trace node to extract a mass chromatogram that you can access from the
Specialized Traces Table of the result file. You can specify the type, the fragmentation order,
and the polarity of the trace. For an XIC trace, you must specify the mass range.

Table 43 describes the parameters for the Create Mass Trace node.
Table 43. Create Mass Trace node parameters (Sheet 1 of 2)
Parameter Description
1. General Settings
Trace Type Specifies the chromatogram type to be generated.

Default: BPC

Selections: TIC (total ion chromatogram), BPC (base peak

chromatogram), or XIC (extracted ion chromatogram)
MS Order Specifies the MS order of the mass spectra that make up the
chromatogram.

Default: MS1; Selections: MS1–MS10

Polarity Specifies the ionization polarity used to produce the mass spectra
that make up the chromatogram.

Default: + (Positive); Selections: + (Positive) or – (Negative)

Custom Label Use this box to type text that you can use to identify the
chromatogram.

This text appears in the Custom Label column of the Specialized

Traces result table.

This box accepts alphanumeric and special characters.

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Table 43. Create Mass Trace node parameters (Sheet 2 of 2)

Parameter Description
2. XIC Settings
Mass [Da] Defines the mass-to-charge (m/z) value of the extracted ion
chromatogram (XIC).

Default: 0
Mass Tolerance Specifies the mass tolerance for the spectral search.

(typed numeric value When you select Da or mmu (0.001 Da) in the units list, the mass
and selected units) tolerance is an absolute ± value for the mass specified in the Mass
box.

When you select ppm (parts per million) in the Units list, the
mass tolerance is a relative range:
Mass ± (Mass × User-specified ppm)/1e6

Default: 3 ppm

Range: 0 to no upper limit; units: Da, mmu, ppm

Create Pattern Trace node

Use the Create Pattern Trace node to draw a chromatogram from the mass peaks that match a
specific pattern within the filtered set of spectra. The pattern can be based on the elemental
composition of a target compound or on a user-specified pattern. To view the pattern trace in
the Chromatogram view for a result file, open the Specialized Traces Table and select the
pattern trace.

Tip For more information about working with isotope patterns, see these topics:
• Set up individual isotope patterns by using the Isotope Ratio Editor
• Specialized Traces table

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Table 44 describes the parameters for the Create Pattern Trace node.
Table 44. Create Pattern Trace node parameters (Sheet 1 of 2)
Parameter Description
1. General Settings
Isotope Ratios Displays either the elemental composition of the compound of
interest or the following text: [custom pattern].

You use the Isotope Ratio Editor to set up the isotope pattern for
the compound of interest.

The application can automatically set up the isotope pattern for a

non-isotopically labeled compound by using its elemental
composition. For isotopically-labeled compounds, you must enter
the expected mass shifts of the isotopic peaks as well as their
relative intensity to the A0 isotope.
IMPORTANT In the defined processing workflows, this
parameter is set to C15S with the following three isotope
selections:
• Monoisotopic ion (100% intensity)
• A2 ion with one sulfur-34 atom (peak with a +1.9958 Da
mass shift and a 4.52% relative intensity)
• A2 ion with two carbon-13 atoms (peak with a
+2.00669 Da mass shift and a 1.27% relative intensity)

When you create a new processing workflow, you must specify

the isotope ratios of interest to run an analysis.
Mass Tolerance Specifies the mass tolerance for the mass shifts between the mass
spectral peaks in the pattern.

Range: 0.0–1e6 ppm; default: 5 ppm

You set up the pattern with the Isotope Ratio Editor.

Intensity Tolerance [%] Specifies the relative intensity tolerance of the mass spectral peaks
in the pattern.

Range: 0.01–100.0

The A0 isotope is always the isotope with the lowest m/z value,
but it is not necessarily the isotope with the highest intensity. For
example, with more than one bromine atom, a bromine and a
chlorine atom, or more than four chlorine atoms, the M + 2 (A2)
isotope is the most intense isotope.

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Table 44. Create Pattern Trace node parameters (Sheet 2 of 2)

Parameter Description
MS Order Specifies the MS order of the mass spectrum.

Selections: MS1–MS10
Polarity Specifies the polarity of the mass spectrum.

Selections: Positive or Negative

Custom Label Use this box to enter a description of the trace.

Expected Compounds nodes

These nodes extract information about the compounds that you expect to find in the input
file set. The Find Expected Compounds and FISh Scoring nodes require structural
information about the targeted compounds. You supply this information by adding it to the
Expected Compounds library.
• FISh Scoring node
• Find Expected Compounds node
• Find Expected Compounds (Legacy) node
• Generate Expected Compounds node
• Group Expected Compounds node
• Merge Features node

FISh Scoring node

Use the FISh Scoring node to provide a confirmation score for compounds that the Find
Expected Compounds node detects and to annotate the fragmentation spectra for these
compounds. The FISh Scoring node requires data-dependent fragmentation (DDF) scans to
calculate the FISh coverage scores for related structures.

Note For information about how the node calculates the confirmation score, see “FISh
scoring for proposed structures.”

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Table 45 describes the parameters for the FISh Scoring node.

Table 45. FISh Scoring node parameters (Sheet 1 of 2)
Parameter Description
1. General Settings
Annotate Full Tree Specifies whether the node annotates the full spectrum tree or
only the MS2 scans in the Mass Spectrum view.

For information about viewing the FISh annotations in the Mass

Spectrum view, see “Mass Spectrum view.”

Default: True
Match Transformations Specifies whether the node matches fragments with
transformation shifts.

Default: True
S/N Threshold Specifies the signal-to-noise threshold for centroids. The node
ignores centroids below this threshold in the fragmentation
(MS/MS, MS3, and so on) spectra.

Default: 3
High Acc. Mass Specifies the mass tolerance for high-resolution mass spectra
Tolerance measured in the Orbitrap mass analyzer of a Thermo Scientific
mass spectrometer.

Default: 2.5 mmu; Minimum: 0.0; Maximum: Unchecked

Low Acc. Mass Specifies the mass tolerance for low-resolution mass spectra
Tolerance measured in the ion trap mass analyzer of a Thermo Scientific
mass spectrometer.

Default: 0.5 Da; Minimum: 0.0; Maximum: Unchecked

2. Fragment Prediction Settings
Use General Rules Specifies whether the node uses the general fragmentation rules.

Default: True
Use Libraries Specifies whether the node uses fragmentation libraries for
fragment prediction.

Default: True
Note Using fragmentation libraries to predict fragments adds
significant time to data processing; however, it also provides
significantly more predicted fragments.

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Table 45. FISh Scoring node parameters (Sheet 2 of 2)

Parameter Description
Max. Depth Specifies the maximum number of steps in the fragmentation
pathway.

Range: 1 to 20
Aromatic Cleavage Specifies whether the node includes a cleavage step in the
fragmentation pathway for highly aromatic structures—that is, for
aromatic structures where n in Huckel’s rule is 2 or higher.

4n + 2 = the number of electrons in the delocalized, conjugated

p-orbital cloud.

For example, the following structure is aromatic with an n value of

2. The number of electrons in the delocalized, conjugated
p-orbital cloud is 10.

Default: True
Min. Fragment m/z Specifies the minimum m/z value of a fragment ion to be
generated by the prediction fragmentation pathway.

Default: 50

Find Expected Compounds node

Use the Find Expected Compounds node to search for compounds in the compound ions list
provided by one or more Generate Expected Compounds nodes.

Using the input from one or more Generate Expected Compounds nodes, the Find Expected
Compounds node looks for expected compounds in the MS1 scans filtered through the data
processing nodes. The expected compounds are the parent compounds that the Generate
Expected Compounds nodes provide to the Find Expected Compounds node, and the
reaction products for these parent compounds. Each Generate Expected Compounds node
predicts the reaction products by using the user-specified Dealkylation step and the
user-specified transformation steps. The Dealkylation step can comprise multiple dealkylation
and dearylation reactions.

The processing results for the Find Expected Compounds node appear in these tables:
Expected Compounds Table, Expected Compounds per File Table, Expected Formulas Table,
and Expected Features Table.

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For more information about how the application finds expected compounds, see “Targeted
processing workflows for expected compounds.”

Table 46 describes the parameters for the Find Expected Compounds node.
Table 46. Find Expected Compounds node parameters (Sheet 1 of 3)
Parameter Description
1. General Settings
Mass Tolerance Specifies the mass tolerance that the node uses to create each
extracted ion chromatogram (XIC).

Default: 5 ppm; range: 0.1 to 20 ppm

Intensity Tolerance [%] Specifies the relative intensity tolerance that the node uses for
isotope pattern comparison.

Default: 30%; range: 0–100

Intensity Threshold Specifies the minimum intensity relative to the base peak for an
[%] isotopic peak in an isotope pattern simulation. The application
does not search for isotopic peaks below the specified intensity
threshold.

Default: 0.1; range 0.01–10.0

Min. # Isotopes Specifies the minimum number of isotopes (mass spectrum peaks
in a centroided mass spectrum) that must match the theoretical
isotope pattern of the expected elemental composition.

Default: 2; range: 1 to no limit

Use Most Intense Specifies whether the node reports the chromatographic peak area
Isotope Only for the most intense isotope peak within an isotope pattern or for
all the detected isotope peaks in the isotope pattern.

When set to True, the analysis reports the area of the

chromatographic peak for the most intense m/z value in the
isotope pattern and reports this m/z value as the reference peak.
The analysis result displays the XIC trace for the most intense
isotope peak in the Chromatogram view.

When set to false, the analysis reports the summed areas for all the
isotope peaks in the isotope pattern. The analysis result displays
the TIC for all the detected isotopes.

Default: True

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Table 46. Find Expected Compounds node parameters (Sheet 2 of 3)

Parameter Description
Minimum Peak Specifies the minimum apex intensity, in ion counts, of the
Intensity detected chromatographic peak. The node discards
chromatographic peaks below this intensity threshold.

Default: 1000; Minimum: 0.0

Average Peak Width Specifies the average chromatographic peak width (FWHM) in
the filtered time range.

Default: 0 (automatic peak width detection); range: unchecked

When this value is set to 0, the node automatically determines the

average peak width.
IMPORTANT The node detects no chromatographic peaks in
the following cases:
• The filtered retention time is too small compared to the
determined or user-specified average peak width value. For
information about filtering the scan data, see “Select Spectra
node.”
• The determined or user-specified average peak width value
is too small compared to the scan rate of the instrument.
For example, if the instrument acquires a full (MS1) scan
every 0.01 minutes, do not enter an Average Peak Width
value of less than 0.02 (2 × 0.01 minutes), as the peak
detection algorithm requires a minimum of three data
points to detect a chromatographic peak.

For best results, keep the default setting of 0, which turns on

automatic peak width detection. Enter a nonzero value only
when the automatically detected peak width is not suitable or
fails for your chromatographic method.
2. Peak Detection
Chromatographic S/N Filters out all chromatographic peaks below the specified
Threshold threshold.

Default: 1.5; range: 0.0 to unchecked

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Table 46. Find Expected Compounds node parameters (Sheet 3 of 3)

Parameter Description
Remove Baseline Specifies whether the node applies a baseline correction to the
XIC traces.

When set to False, the node drops perpendicular tangent lines

from the start and end points of each chromatographic peak and
includes this additional area in the reported area for each
compound.

Default: False
Gap Ratio Threshold Does not store (ignores) chromatographic peaks from XIC traces
(advanced) that have a gap ratio exceeding the specified threshold. The gap
ratio for an XIC trace is the number of missing data points (gaps)
to the total number of data points for the XIC trace.

Default: 0.35; range 0 to 1

Max. Peak Width Specifies the maximum allowed peak width at half height in
[min] (advanced) minutes for a chromatographic peak. Ignores chromatographic
peaks that are wider than this limit.

Default: 1 minute; minimum value: 0.05 minutes

Min. Relative Valley Specifies the minimum valley depth between two
Depth (advanced) chromatographic peaks to consider them resolved—that is, to
report them as two separate peaks.

The specified value is the minimum ratio of the height of the

shorter peak to the valley height.

Default: 0.1; range: 0.05 to 0.5

Min. #Scans per Peak Specifies the minimum number of scans required to define a
(advanced) chromatographic peak.

Default: 5; range: 3 to 20

Find Expected Compounds (Legacy) node

Use the Find Expected Compounds node to search for compounds in the compound ions list
provided by one or more Generate Expected Compounds nodes.

Using the input from one or more Generate Expected Compounds nodes, the Find Expected
Compounds node looks for expected compounds in the MS1 scans filtered through the data
processing nodes. The expected compounds are the parent compounds that the Generate
Expected Compounds nodes provide to the Find Expected Compounds node, and the

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reaction products for these parent compounds. Each Generate Expected Compounds node
predicts the reaction products by using the user-specified Dealkylation step and the
user-specified transformation steps. The Dealkylation step can comprise multiple dealkylation
and dearylation reactions.

The processing results for the Find Expected Compounds node appear in these tables:
Expected Compounds Table, Expected Compounds per File Table, Expected Formulas Table,
and Expected Features Table.

For more information about how the application finds expected compounds, see “Targeted
processing workflows for expected compounds.”

Table 46 describes the parameters for the Find Expected Compounds node.
Table 47. Find Expected Compounds (Legacy) node parameters (Sheet 1 of 3)
Parameter Description
1. General Settings
Mass Tolerance Specifies the mass tolerance that the node uses to create each
extracted ion chromatogram (XIC).

Default: 5 ppm; range: 0.1 to 20 ppm

Intensity Tolerance [%] Specifies the relative intensity tolerance that the node uses for
isotope pattern comparison.

Default: 30%; range: 0–100

Intensity Threshold Specifies the minimum intensity relative to the base peak for an
[%] isotopic peak in an isotope pattern simulation. The application
does not search for isotopic peaks below the specified intensity
threshold.

Default: 0.1; range 0.01–10.0

Min. # Isotopes Specifies the minimum number of isotopes (mass spectrum peaks
in a centroided mass spectrum) that must match the theoretical
isotope pattern of the expected elemental composition.

Default: 2; range: 1 to no limit

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Table 47. Find Expected Compounds (Legacy) node parameters (Sheet 2 of 3)

Parameter Description
Use Most Intense Specifies whether the node reports the chromatographic peak area
Isotope Only for the most intense isotope peak within an isotope pattern or for
all the detected isotope peaks in the isotope pattern.

When set to True, the analysis reports the area of the

chromatographic peak for the most intense m/z value in the
isotope pattern and reports this m/z value as the reference peak.
The analysis result displays the XIC trace for the most intense
isotope peak in the Chromatogram view.

When set to false, the analysis reports the summed areas for all the
isotope peaks in the isotope pattern. The analysis result displays
the TIC for all the detected isotopes.

Default: True
Minimum Peak Specifies the minimum apex intensity, in counts, of the detected
Intensity chromatographic peak. The node discards chromatographic peaks
below this intensity threshold.

Default: 1000; Minimum: 0.0

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Table 47. Find Expected Compounds (Legacy) node parameters (Sheet 3 of 3)

Parameter Description
Average Peak Width Specifies the average chromatographic peak width (FWHM) in
[min] the filtered time range.

Default: 0 (automatic peak width detection); range: unchecked

When this value is set to 0, the node automatically determines the

average peak width.
IMPORTANT The node detects no chromatographic peaks in
the following cases:
• The filtered retention time is too small compared to the
determined or user-specified average peak width value. For
information about filtering the scan data, see “Select Spectra
node.”
• The determined or user-specified average peak width value
is too small compared to the scan rate of the instrument.
For example, if the instrument acquires a full (MS1) scan
every 0.01 minutes, do not enter an Average Peak Width
value of less than 0.02 (2 × 0.01 minutes), as the peak
detection algorithm requires a minimum of three data
points to detect a chromatographic peak.

For best results, keep the default setting of 0, which turns on

automatic peak width detection. Enter a nonzero value only
when the automatically detected peak width is not suitable or
fails for your chromatographic method.

Generate Expected Compounds node

Use the Generate Expected Compounds node to generate a list of m/z values for the ionized
compounds that you expect to find in a sample. The list includes the parent compounds and
their possible dealkylation, dearylation, and transformation products. The application
generates the list by using the structures of the parent compounds, the user-specified
transformation lists and number of combinatory steps, and the user-specified ionic species.

The default transformations library contains common Phase 1 and Phase 2 metabolic
transformations. If the transformation list does not include the possible transformations for
your compound, add them to the transformations library as described in “Add or edit
transformations with the Transformation Editor.”

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When you add transformations to the library, you can assign them to one of the following
groups: Phase I, Phase II, or Others. The Generate Expected Compounds node treats
transformations assigned to the Others group as Phase I transformations; that is, it applies
Phase I and Others transformations before it applies Phase II transformations.

To predict the transformation products for the selected parent compounds, the Generate
Expected Compounds node follows these rules:
1. When the user enables Dealkylation, apply the dealkylation steps first. If a subsequent
transformation reverses the dealkylation step, reject the subsequent transformation. When
the user enables both Dealkylation and Dearylation, apply both of these steps first, and
then determine two separate reaction pathways for the remaining transformation steps.
Consider all steps under Dealkylation together as one step. For example, consider the
selections shown in Figure 83 as one step in the total set of reaction pathways and create
separate reaction pathways. Apply the transformation steps on the parent compound and
the reaction products from the dealkylation pathways.
Figure 83. Dealkylation step example

Parent compounds

Products of Products of Products of Parent compounds Products of Products of

one dealkylation two dealkylation one dealkylation step one dearylation two dearylation
step steps and step steps
one dearylation step

2. When more than one reaction pathway produces the same elemental composition, use the
pathway with the lowest number of transformation steps.
3. Reject transformations that remove elements that are not present. For example, do not
apply an oxidative dechlorination step if the compound does not contain chlorine.

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4. For Phase I and Others transformations, limit the maximum number of times to apply
the transformation on a single compound to the lower of these two values:
– Max Occurrence setting for the transformation in the Transformations library
For example, for the oxidation transformation, the default value for Max Occurrence
is 3.

– Maximum number of steps specified by the node’s Max. # All Steps parameter minus
any previously applied Dealkylation step.
5. For Phase II transformations, limit the maximum number of times to apply the
transformation on a single compound to the lowest of these three values:
– Max Occurrence setting for the transformation in the Transformations library
– Maximum number of steps for all reactions (setting for node’s Max. # All Steps
parameter) minus any previously applied Dealkylation or Transformation step
– Maximum number of steps for a Phase II transformation (setting for node’s Max. #
Phase II parameter)

You can connect one or more Generate Expected Compounds nodes to the Find Expected
Compounds node and the Filter By Mass Defect node.

Table 48 describes the parameters for the Generate Expected Compounds node. The
application cannot use the processing workflow until you select a compound from the
Compound list.

If you want to generate expected compounds for more than one parent compound, do the
following:
• To target multiple compounds with a different set of transformation rules for each
compound, add multiple Generate Expected Compounds nodes to the processing
workflow.

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• To target multiple compounds with the same set of transformation rules, add one
Generate Expected Compounds node to the processing workflow and select multiple
compounds in the node’s Compound list.

Table 48. Generate Expected Compounds node parameters (Sheet 1 of 3)

Parameter Description
1. Compound Selection
Compound Specifies the parent compounds that the node uses to build a list
of possible product compounds.
Show Checked Displays only the selected compounds.
Items Only
Check All Selects all compounds in the list.
Uncheck All Undoes all selections.
Note Before you can use the Generate Expected Compounds node to predict the
transformation products of specific compounds, you must first add the compounds to the
Expected Compounds library.
2. Dealkylation
Apply Dealkylation When you select True, the node applies the dealkylation
transformations for the specified compound before applying other
transformations.

Default: True
Apply Dearylation When you select True, the node applies the dearylation
transformations for the specified compound before applying other
transformations.

Default: False

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Table 48. Generate Expected Compounds node parameters (Sheet 2 of 3)

Parameter Description
Max. # Steps Specifies the maximum number of Dealkylation steps.

For example, if you select True for Dealkylation, True for

Dearylation, and 1 for the Max. # Steps, the node applies up to
one dealkylation step and up to one dearylation step as the initial
Dealkylation step in the set of reaction pathways. For another
example, see Figure 83 on page 262.

Parent compound

Products of Products of
one dearylation one dearylation
Parent compound
step step

Default: 1; Selection: 1–10

Min. Mass [Da] Specifies the minimum mass of the dealkylation product.

Default: 200
3. Transformations
Phase I Specifies the set of possible Phase 1 transformations.

Default: All check boxes are clear.

Phase II Specifies the set of possible Phase II transformations.

Default: All check boxes are clear.

Others Specifies other possible transformations.

The node treats Others transformations as Phase I

transformations.
Max. # Phase II Specifies the maximum number of Phase II steps to be applied.

Default: 1; range: 1–10

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Table 48. Generate Expected Compounds node parameters (Sheet 3 of 3)

Parameter Description
Max. # All Steps Specifies the maximum number of all steps to be applied.

All steps that occur as a result of the selections in the Dealkylation

area equal one step in the maximum number of all steps—that is,
after the node applies the steps in the Dealkylation area, the
remaining number of possible steps is equal to the
Max. # All Steps – 1.

Default: 3; range: 1–10

4. Ionization
Ions Specifies the possible ionic species.

Default: [M+H]+1 (protonated species for the positive mode)

Note The ion definitions library that the application provides
contains the common ionic species associated with the positive
and negative modes for the electrospray ionization-mass
spectrometry (ESI-MS) technique. If the Ions list does not
include the possible ionic species for your analysis, add the ion
definition to the Ion Definition library as described in “Ion
Definitions view.”

Group Expected Compounds node

Use the Group Expected Compounds node to combine similar components
(chromatographic peaks with the same MW × RT dimensions) that the Find Expected
Compounds node finds across the input file set. This node combines chromatographic peaks
by using their chemical formula (resulting from the dealkylations and dearylations and
transformations of a parent compound) and retention time. This node also selects the best
representative MS1 scan and fragmentation tree, which other nodes, such as Predict
Compositions, Search mzCloud, Search mzVault, and so on use for identification.

Table 49 describes the parameters for the Group Expected Compounds node.
Table 49. Group Expected Compounds node parameters (Sheet 1 of 3)
Parameter Description
1. General Settings
RT Tolerance [min] Specifies the retention time tolerance, in minutes, that the node
uses to group mass peaks generated from the same parent
compound through the same reaction pathway.

Default: 0.1; range: 0 to 1.0

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Table 49. Group Expected Compounds node parameters (Sheet 2 of 3)

Parameter Description
Align Peaks Specifies whether the node aligns the chromatographic peaks for a
specific compound across all the input files.

Default: False
Preferred Ions Select the preferred ions (adducts) from the list. The application
uses the list to select the best fragmentation data for each
compound to submit to an mzCloud or mzVault search.

Selection: The selection list includes all the ion definitions in the
Ion Definitions list under Lists & Libraries.
Area Integration Specifies which ions the node uses to determine the
chromatographic peak areas.

For the Most Common Ion selection, the node uses the
chromatographic peak area of the most common adduct ion
detected across the input file set.

For the All Ions selection, the node sums the areas of all the
adduct ions detected in a particular input file.

Default: Most Common Ion; selections: Most Common Ion and

All Ions
2. Peak Rating Contributions

These parameter settings determine how the node calculates the peak rating values for
chromatographic peaks. See “Chromatographic peak rating filter.”

The maximum value for each contributing parameter is unlimited.

The contribution of each individual parameter is as follows:

(Contribution value for the individual parameter/Divided by the sum of all the contribution
values)×10.
Area Contribution Specifies the chromatographic peak area contribution to the peak
rating.

Default: 3
CV Contribution Specifies the contribution of the coefficient of variation for the
peak areas across replicate samples to the peak rating. If an analysis
includes no replicates, the node sets the CV contribution to 0
during processing.

Default: 10

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Table 49. Group Expected Compounds node parameters (Sheet 3 of 3)

Parameter Description
FWHM to Base Specifies the FWHM (full width at half the maximum peak
Contribution height) to base contribution to the peak rating.

Default: 5
Jaggedness Specifies the jaggedness contribution to the peak rating.
Contribution
Default: 5
Modality Contribution Specifies the modality contribution to the peak rating.

Default: 5
Zig-Zag Index Specifies the zig-zag index contribution to the peak rating.
Contribution
Default: 5
3. Peak Rating Filter

The node does not store chromatographic peaks that have a peak rating below the threshold
value in the specified number of files.

When either or both of the peak rating parameters are set to 0, this filter is not enabled.

By default, this filter is not enabled.

Peak Rating Threshold Specifies the minimum peak rating for the chromatographic
peaks.

The node ignores this parameter setting unless you specify a

nonzero value for the number of files.

Default: 0; range: 0 to 10
Number of Files Specifies the minimum number of files across the input set where
the chromatographic peak for a compound must meet the peak
rating threshold to be stored in the result file.

The optimum value depends on the number of files in the data set
and the probability of similar compounds in these files.

When there is a very low probability that the samples contain the
same compounds, set this value to 0. For replicate samples that
probably contain the same compounds, set this value to the
number of replicates or one less than the number of replicates.

The node ignores this value unless you specify a nonzero peak
rating threshold.

Default: 0

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Compound Detection nodes

Merge Features node

Use the Merge Features node to do the following:
• Combine the expected compounds found by the Find Expected Compounds node and
the unknown compounds found by the Detect Compounds node by using their
chromatographic retention time and m/z values.
• Create the Merged Features table that includes four status columns: Ion Conflict Status,
Detect Compounds, Find Expected Compounds, and Custom Explanations.
• Link the manual peaks table to the related Compounds table.

Table 50 describes the parameters for the Merge Features node.

Table 50. Merge Features node parameters
Parameter Description
1. General Settings
Mass Tolerance Specifies the mass tolerance for chromatographic peak grouping.

Default: 5 ppm; range: 0.1–20 ppm

RT Tolerance [min] Specifies the retention time tolerance, in minutes, for
chromatographic peak grouping.

Default: 0.05; range: 0.0–1.0

Compound Detection nodes

Use these nodes to detect unknown compounds:
• Analyze Labeled Compounds node
• Detect Compounds (Legacy) node
• Detect Compounds node
• Fill Gaps node
• Group Compounds node

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Analyze Labeled Compounds node

Use the Analyze Labeled Compounds node to detect labeled compounds and their labeling
rates. For more information about reviewing the results for stable isotope labeling
experiments, see “Isotopologues Distribution Chart view.”
Table 51. Analyze Labeled Compounds node (Sheet 1 of 2)
Parameter Description
1. Label Settings
Label Element Specifies the labeled element and its isotope in this format:

[mass number]element symbol

Where element symbol is the symbol in the periodic table

Max. Exchange Specifies the maximum number of exchangeable atoms for any
of the compounds. If the number of exchangeable atoms for a
compound is below this number, the application uses the lower
number.

If set to zero, the compound’s elemental composition determines

the maximum number of exchangeable atoms.

Default: 25
Source Efficiency [%] Specifies the isotopic purity of the labeled compound introduced
into the biological system.

Most commercially available stable isotope labeled compounds

have an isotopic purity of 98 to 99%. Keeping the setting at
100% is appropriate for these compounds.

Default: 100
2. Pattern Analysis
Mass Tolerance [ppm] Specifies the mass tolerance for the isotope search and XIC trace
generation.

Default: 5 ppm
Intensity Tolerance [%] Specifies the relative intensity tolerance for isotope pattern
matching.

Default: 30
Intensity Threshold [%] Specifies the isotope intensity threshold, relative to the pattern’s
base peak, for the theoretical isotope pattern.

Default: 0.1

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Table 51. Analyze Labeled Compounds node (Sheet 2 of 2)

Parameter Description
S/N Threshold Specifies the signal-to-noise threshold for isotope pattern
matching.

Default: 3
3. General Settings
Mark Irregular Exchange Adds the Irregular Exchange status to the following result table
columns: Labeling Status column of the Compounds Table and
the Status column of the Compounds per File Table.

The Irregular Exchange status applies to compounds where the

exchange rate for the mid-mass isotopologues is less than 5% of
the exchange rate for the isotopologues.

Default: True
Exclude Blanks Specifies whether to exclude blank samples (Sample Type:
Blank) from the main Compounds table.

Default: True
Hide Unprocessed Specifies whether to hide compounds with unassigned formulas
in the Compounds table. The node does not process compounds
without formulas.

Default: True

Detect Compounds (Legacy) node

Use the Detect Compounds node to detect unknown compounds for studies where you want
to compare new analyses with analyses performed in earlier versions of the Compound
Discoverer application.

The processing results for the Detect Compounds node appear in the Compounds per File
table and the Features per File table.

For information about an untargeted processing workflow, see “Untargeted processing

workflows for identifying unknown compounds.”

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Table 52 describes the parameters for the Detect Compounds (Legacy) node.
Table 52. Detect Compounds (Legacy) node parameters (Sheet 1 of 4)
Parameter Description
1. General Settings
Mass Tolerance [ppm] Specifies the mass tolerance for the XIC traces.

Default: 5.0 ppm; range: 1–20.0 ppm

Intensity Tolerance [%] Specifies the intensity tolerance for the isotope pattern search.

Default: 30%; range: 0 to 100%

Min. Peak Intensity Specifies the minimum base peak height to detect peaks in the
XIC traces. The analysis does not report chromatographic peaks
below this minimum peak intensity (peak height at the apex).

The optimal minimum peak intensity setting depends upon the

instrument (see Table 53).

Default: 10 000
Ions Specifies the adduct ions that might be in your samples.

Default: [M+H]+1, [M+K]+1, [M+Na]+1

Selection: The list includes the ion definitions in your Ion

Definitions library.
Base Ions Specifies the adduct ions that you expect to have the highest
intensity in your samples.

Default: [M+H]+1 and [M–H]–1

Note The processing workflows (in the Common Workflows > Workflow Templates > E
and L, MetID, folder) specify the following base ions:
• [M+H]+1
• [M+NH4]+1
• [M–H]–1.

The selection of base ions includes the ammonium adduct because extractable and
leachable compounds tend to be nonpolar compounds that require ammonium acetate as
a mobile phase modifier for optimal chromatography.
Min Element Counts Specifies the minimum number of each possible element. The
node uses these values for the isotope pattern search.

Default: C H

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Table 52. Detect Compounds (Legacy) node parameters (Sheet 2 of 4)

Parameter Description
Max Element Counts Specifies the maximum number of each possible element. The
node uses these values for the isotope pattern search.

Default: C90 H190 Br3 Cl4 K2 N10 Na2 O15 P2 S5

Min. #Scans per Peak Specifies the minimum number of scans (data points) required to
define a chromatographic peak.

Default: 5; range: 3 to 20
Use Most Intense Specifies whether the node reports the chromatographic peak area
Isotope Only for the most intense isotope peak within an isotope pattern or for
all the detected isotope peaks in the isotope pattern.

When set to True, the analysis reports the area of the

chromatographic peak for the most intense m/z value in the
isotope pattern and reports this m/z value as the reference peak.
The analysis result displays the XIC trace for the most intense
isotope peak in the Chromatogram view.

When set to false, the analysis reports the summed areas for all the
isotope peaks in the isotope pattern. The Chromatograms view in
the analysis result displays the TIC for all the detected isotopes.

Default: True
2. Trace Detection (advanced parameters)
Max. Number of Gaps Specifies the maximum number of contiguous missing values in
to Correct the XIC trace for the compound. You can set the maximum
number of allowed contiguous missing values from 0 to 3.

When the XIC trace includes more than the maximum number of
allowed contiguous missing values (gaps), the node does not store
the trace in the analysis result.

Default: 2; range: 0 to 3
Min. Number of Specifies the minimum number of non-zero values adjacent to a
Adjacent Non-Zeroes gap before the node fixes the gap.

Default: 2; range: 1 to 3
3. Peak Detection (advanced parameters)
Filter Peaks Specify whether you want to turn on the chromatographic peak
filtering parameters.

Default: True

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Table 52. Detect Compounds (Legacy) node parameters (Sheet 3 of 4)

Parameter Description
Max. Peak Width When Filter Peaks is set to True, specifies the maximum peak
[min] width at half height, in minutes, for detected chromatographic
peaks.

Default: 0.3; range: 0.05 to no upper limit

Remove Singlets If set to True, does not report a component if the
chromatographic peak for the component contains only A0
centroids.

Default: True
4. Isotope Pattern Detection (advanced parameters)
Min. #Isotopes Specifies the minimum number of isotopes in the isotope pattern
are required in the mass spectrum scans that define the
chromatographic peak.

Default: 2
Use Peak Quality for Specifies whether the node filters out low-quality
Isotope Grouping chromatographic peaks before it groups the XIC traces for ions in
an isotope pattern.

When set to True, the node uses a two-stage approach for isotope
grouping. In the first stage, the node groups only high-quality
peaks that pass the peak quality thresholds. In the second stage,
the node groups the remaining chromatographic peaks.

When set to False, the node does not consider the peak quality
thresholds for isotope grouping.

Default: False
Filter out Features with Specifies whether to remove a feature when all the
Bad Peaks Only chromatographic peaks for the feature across the input file set are
low-quality chromatographic peaks that do not pass the peak
quality thresholds.

Default: True
See “Chromatographic peak rating filter.”
Zig-Zag Index Specifies the zig-zag index threshold for the chromatographic
Threshold peaks.

Default: 0.2; range 0 to 1

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Table 52. Detect Compounds (Legacy) node parameters (Sheet 4 of 4)

Parameter Description
Jaggedness Threshold Specifies the jaggedness threshold for the chromatographic peaks.

Default: 0.4; range 0 to 1

Modality Threshold Specifies the modality threshold for the chromatographic peaks.

Default: 0.9; range 0 to 1

Min. Spectral Distance Specifies the minimum spectral distance score for grouping
Score features together as part of one isotope pattern. Increasing this
score filters out compounds with low-scoring isotope patterns,
potentially decreasing the number of detected compounds.

Default: 0; range: 0 to 100%

Remove Potentially Specifies whether to filter out an isotope in a spectrum if there is a
False Positive Isotopes gap of four missing isotopes between this isotope and the isotopes
to its left (on the m/z axis).

For example, if the analysis detects only one A0 and one A5

isotope in the isotope pattern, and you specify that it must find a
minimum of two isotopes to detect a compound, it does not
detect the compound.

Default: True
5. Skipped
6. AcquireX Settings (advanced)
Detect Persistent When set to True, this parameter generates a related Background
Background Ions Ions table for each input file. This parameter is not relevant for
typical operation of the Compound Discoverer application. Its use
is currently limited to the AcquireX™ data acquisition workflow.

Default: False

Table 53 lists the recommended range for the minimum peak intensity parameter. The
optimal setting depends on the sensitivity of the mass spectrometer.
Table 53. Recommended minimum peak intensity range
Minimum peak intensity
Mass spectrometer
(chromatographic peak height)
Q Exactive, Q Exactive Plus, and Q Exactive HF 500 000 to 1 000 000
Orbitrap Fusion, Orbitrap Lumos, and Orbitrap ID-X 50 000 to 100 000

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Table 53. Recommended minimum peak intensity range

Minimum peak intensity
Mass spectrometer
(chromatographic peak height)
Exactive, Exactive Plus, Orbitrap Elite, and Orbitrap 100 000 to 500 000
Velos Pro
LTQ Orbitrap XL and LTQ Orbitrap Velos 25 000 to 100 000

Detect Compounds node

The new Detect Compounds node includes peak quality thresholds for filtering out XIC
traces with low-quality chromatographic peaks. Use this node for most untargeted analyses.
Only use the Detect Compounds (Legacy) node when you want peak detection to mimic a
legacy analysis.
Table 54. Detect Compounds node parameters (Sheet 1 of 5)
Parameter Description
1. General Settings
Mass Tolerance Specifies the mass tolerance for the XIC traces.

Default: 5.0 ppm; range: 1–20.0 ppm

Min. Peak Intensity Specifies the minimum base peak height to detect peaks in the
XIC traces. The analysis does not report chromatographic peaks
below this minimum peak intensity (peak height at the apex).

The optimal minimum peak intensity setting depends upon the

instrument (see Table 53).

Default: 10 000
Min. #Scans per Peak Specifies the minimum number of scans (data points) required to
(advanced) define a chromatographic peak.

Default: 5; range: 3 to 20

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Table 54. Detect Compounds node parameters (Sheet 2 of 5)

Parameter Description
Use Most Intense Specifies whether the node reports the chromatographic peak area
Isotope Only for the most intense isotope peak within an isotope pattern or for
all the detected isotope peaks in the isotope pattern.

When set to True, the analysis reports the area of the

chromatographic peak for the most intense m/z value in the
isotope pattern and reports this m/z value as the reference peak.
The analysis result displays the XIC trace for the most intense
isotope peak in the Chromatogram view.

When set to false, the analysis reports the summed areas for all the
isotope peaks in the isotope pattern. The analysis result displays
the TIC for all the detected isotopes.

Default: True
2. Trace Detection (advanced parameters)

A gap is a missing data point in the XIC trace for a compound. If the XIC trace for a
compound contains more than the specified number of contiguous gaps, the node ignores
the chromatographic peaks for this XIC trace.
Max. Number of Gaps Specifies the maximum number of contiguous missing values in
to Correct the XIC trace for the compound. You can set the maximum
number of allowed contiguous missing values from 0 to 3.

When an XIC trace includes with more than the maximum

number of allowed contiguous missing values (gaps), the node
does not store the chromatographic peaks for this trace in the
analysis result.

Default: 2; range: 0 to 3
Min. Number of Specifies the minimum number of non-zero values adjacent to a
Adjacent Non-Zeroes gap before the node fixes the gap.

Default: 2; range: 1 to 3
3. Peak Detection
Chromatographic S/N Filters out all chromatographic peaks below the specified
Threshold threshold.

Default: 1.5; range: 0.0 to unchecked

Remove Baselines Specifies whether the node applies baseline correction to the XIC
traces.

Default: False

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Table 54. Detect Compounds node parameters (Sheet 3 of 5)

Parameter Description
Gap Ratio Threshold Does not store (ignores) chromatographic peaks from XIC traces
(advanced) that have a gap ratio exceeding the specified threshold. The gap
ratio for an XIC trace is the number of missing data points (gaps)
to the total number of data points for the XIC trace.

Default: 0.35; range 0 to 1

Max. Peak Width Specifies the maximum allowed peak width at half height in
[min] (advanced) minutes for a chromatographic peak. Ignores chromatographic
peaks that are wider than this limit.

Default: 1 minute; minimum value: 0.05 minutes

Min. Relative Valley Specifies the minimum valley depth between two
Depth (advanced) chromatographic peaks to consider them resolved—that is, to
report them as two separate peaks.

The specified value is the minimum ratio of the height of the

shorter peak to the height of the valley between the peaks.

Default: 0.1; range: 0.05 to 0.5

4. Isotope Pattern Detection
Group Isotopes For Specifies whether the node also groups the isotopic ions for
chlorine and bromine. For example, when you select Cl, the node
groups the isotopic ions for 35CI and 37CI.

The node automatically groups the various isotopic ions for the
elements C, H, N, O, and S.

Default: The check boxes for Cl and Br are selected.

Use Peak Quality for Specifies whether the node filters out low-quality
Isotope Grouping chromatographic peaks before it groups the XIC traces for ions in
(advanced) an isotope pattern.

When set to True, the node uses a two-stage approach for isotope
grouping. In the first stage, the node groups only high-quality
peaks that pass the peak quality thresholds. In the second stage,
the node groups the remaining chromatographic peaks.

When set to False, the node does not consider the peak quality
thresholds for isotope grouping.

Default: True

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Table 54. Detect Compounds node parameters (Sheet 4 of 5)

Parameter Description
Filter Out Features Specifies whether to remove a feature when all the
with Bad Peaks Only chromatographic peaks for the feature across the input file set are
(advanced) low-quality chromatographic peaks that do not pass the peak
quality thresholds.

Default: True
See “Chromatographic peak rating filter.”
Zig-Zag Index Specifies the zig-zag index threshold for the chromatographic
Threshold peaks.

Default: 0.2; range 0 to 1

Jaggedness Threshold Specifies the jaggedness threshold for the chromatographic peaks.

Default: 0.4; range 0 to 1

Modality Threshold Specifies the modality threshold for the chromatographic peaks.

Default: 0.9; range 0 to 1

Remove Potentially When set to True, the node runs an additional check for false
False Positive Isotopes positive isotopes.
(advanced)
Default: True
5. Compound Detection
Ions Specifies the adduct ions that might be in your samples.

Default: [M+H]+1, [M+K]+1, [M+Na]+1

Selection: The ion definitions in your Ion Definitions library

Base Ions (advanced) Specifies the adduct ions that you expect to have the highest
intensity in your samples.

Default: [M+H]+1 and [M–H]–1

Note The processing workflows (in the Common Workflows > Workflow Templates > E
and L, MetID, folder) specify the following base ions: [M+H]+1, [M+NH4]+1, and [M–
H]–1.

The selection of base ions includes the ammonium adduct because extractable and
leachable compounds tend to be nonpolar compounds that require ammonium acetate as
a mobile phase modifier for optimal chromatography.

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Table 54. Detect Compounds node parameters (Sheet 5 of 5)

Parameter Description
Remove Singlets If set to True, does not report a component if the
(advanced) chromatographic peak for the component contains only A0
centroids.

Default: True
6. AquireX Settings (advanced)
Detect Persistent When set to True, the node detects and stores persistent
Background Ions background ions.

Default: False

Fill Gaps node

Use the Fill Gaps node to find chromatographic peaks that were detected by the Detect
Compounds node in one of the input files but were missing from other input files in the file
set.

For information about adding the Fill Gaps node to a processing workflow, see “Peak area
refinement node connections.”

The Fill Gaps node adds the (hidden) Gap Status column to the Compounds Table and
creates the related (hidden) Filled Gaps Table.

The Filled Gaps table describes how the node calculated the missing chromatographic peak
areas. Clicking a row in the Filled Gaps table displays the gap-filled trace and the integrated
peak area.

Table 55 describes the parameters for the Fill Gaps node.

Table 55. Fill Gaps node parameters (Sheet 1 of 2)
Parameter Description
1. General Settings
Mass Tolerance Specifies the mass tolerance that the node uses to search for
matching mass peaks.

Search range = expected mass ± mass tolerance/1e6

Default: 5 ppm; range: 0.1 to 20 ppm

S/N Threshold Specifies the minimum signal-to-noise threshold for centroids.

Default: 1.5; minimum: 1

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Table 55. Fill Gaps node parameters (Sheet 2 of 2)

Parameter Description
Use Real Peak Specifies whether the analysis fills gaps in the chromatogram by
Detection using a peak detection algorithm or only a peak simulation
algorithm.

True—The node uses the Parameterless Peak Detection (PPD)

algorithm to fill the gaps with redetected low-intensity peaks.
Using PPD can significantly increase the processing time.

False—The node uses only a peak simulation algorithm to fill the

gaps with simulated chromatographic peaks.
Apply Restrictive Gap Specifies whether the node uses a more restrictive retention time
Filling tolerance for filling individual gaps than the retention time
tolerance that the Group Compound node uses for compound
grouping.

True—The node uses a more restrictive retention time tolerance

to avoid grouping peaks for other compounds. Thermo Scientific
recommends this setting.

False—The node uses the retention time tolerance that you

specified in the Group Compounds node, except when a gap is
due to missing ions. For gaps due to missing ions, the node sets
the RT tolerance to the expected FWHM of the missing peak,
because the expected RT of the missing peak is known.
Note This parameter is new in Compound Discoverer 3.3 SP1.
In previous versions of the Compound Discoverer application,
the Fill Gaps node automatically used a more restrictive time
tolerance than the Group Compounds node to avoid grouping
peaks for other compounds.

The default RT Tolerance [min] for the Group Compounds

node is 0.2 min, and the available range is 0 to 1.0 min. See
“Group Compounds node.”

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Group Compounds node

Use the Group Compounds node to combine unknown compounds across the input file set
by their molecular weight and retention time. This node also selects the best representative
MS1scan and fragmentation tree, which the Predict Compositions node and search nodes use
for identification.

Table 56 describes the parameters for the Group Compounds node.

Table 56. Group Compounds node parameters (Sheet 1 of 3)
Parameter Description
1. Compound Consolidation
Mass Tolerance Specifies the mass tolerance that the node uses to search for
matching mass peaks.

Default: 5 ppm; range: 0.1 to 20 ppm

RT Tolerance [min] Specifies the retention time tolerance, in minutes, that the node
searches for mass peaks within the specified mass tolerance.

Default: 0.05; range: 1.0

Align Peaks Specifies whether the node aligns the chromatographic peaks for a
compound across all the input files.

Default: False
Preferred Ions Select the preferred ions (adducts) from the list. The application
uses the list to select the best fragmentation data for each
compound to submit to an mzCloud or mzVault search.

Selections: One or more of the ions in your Ion Definitions library

Default: [M+H]+1 and [M–H]–1

Area Integration Specifies what ions the node uses to determine the
chromatographic peak areas.

For the Most Common Ion selection, the node uses the
chromatographic peak area of the most common adduct ion
detected across the input file set.

For the All Ions selection, the node sums the areas of all the
adduct ions detected in a particular input file.

Default: Most Common Ion; selections: Most Common Ion and

All Ions

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Table 56. Group Compounds node parameters (Sheet 2 of 3)

Parameter Description
2. Peak Rating Contributions

These parameter settings determine how the node calculates the peak rating values for
chromatographic peaks. See “Chromatographic peak rating filter.”

The maximum value for each contributing parameter is unlimited.

The contribution of each individual parameter is as follows:

(Contribution value for the individual parameter/Divided by the sum of all the contribution
values)×10.
Area Contribution Specifies the chromatographic peak area contribution to the peak
rating.

Default: 3
CV contribution Specifies the contribution of the coefficient of variation for the
peak areas across replicate samples to the peak rating. If an analysis
includes no replicates, the node sets the CV contribution to 0
during processing.

Default: 10
FWHM to Base Specifies the FWHM to base contribution to the peak rating.
Contribution
Default: 5
Jaggedness Specifies the jaggedness contribution to the peak rating.
Contribution
Default: 5
Modality Contribution Specifies the modality contribution to the peak rating.
Zig-Zag Index Specifies the zig-zag index contribution to the peak rating.
Contribution
Default: 5
3. Peak Rating Filter

The node does not store chromatographic peaks that have a peak rating below the threshold
value in the specified number of files.

When either or both of the peak rating parameters are set to 0, this filter is not enabled.

By default, this filter is not enabled.

For more information about the peak rating filter, see “Chromatographic peak rating filter.”

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Table 56. Group Compounds node parameters (Sheet 3 of 3)

Parameter Description
Peak Rating Threshold Specifies the minimum peak rating for the chromatographic
peaks.

The node ignores this parameter setting unless you specify a

nonzero value for the number of files.

Default: 0; range: 0 to 10
Number of Files Specifies the minimum number of files across the input set where
the chromatographic peak for a compound must meet the peak
rating threshold to be stored in the result file.

The optimum value depends on the number of files in the data set
and the probability of similar compounds in these files.

When there is a very low probability that the samples contain the
same compounds, set this value to 0. For replicate samples that
probably contain the same compounds, set this value to the
number of replicates or one less than the number of replicates.

The node ignores this value unless you specify a nonzero peak
rating threshold.

Default: 0

Peak Area Refinement nodes

These nodes modify the chromatographic peak areas for compounds or mark the background
compounds:
• Apply Missing Value Imputation node
• Apply QC Correction node
• Apply SERRF QC Correction node
• Mark Background Compounds node
• Normalize Areas node
• Scale Areas node

Apply Missing Value Imputation node

For LC studies, try using the Missing Value Imputation node if the Fill Gaps node does not
yield the expected results.

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The Apply Missing Value Imputation node provides two methods for imputing missing
chromatographic peak areas for compounds: Random Forest and Median + Small Value.
• The Random Forest imputation method consists of a self-trained machine learning
system.
• The Median + Small Value imputation method is a mixed method:
– (Partially missing values) For study groups where a compound is detected in at least
one of the samples, but not all the samples, the node imputes an area value for each
value by using the mean of the values that are present in the same study group.
– (Full gap) If the compound is not present in any of the samples in a study group, the
node imputes area values for the compound in each sample by dividing the smallest
detected peak area for any compound in a sample by 2.
Table 57. Missing Value Imputation node parameters (Sheet 1 of 2)
Parameter Description
1. General Settings
Imputation Method Specifies the imputation method for missing chromatographic
peaks across a set of input files.

Selections:
• (Default) Automatic Selection—The application
automatically uses the Median + Small Value with Variability
imputation method when the analysis includes three or more
study groups and the deconvolution node detects 50 or more
compounds. If these conditions are not met, the application
uses the Random Forest imputation method. For information
about defining the study groups, see “Set up the sample
groups and ratios for a new analysis.”
• Median + Small Value with Variability
• Random Forest Imputation
Fill Blanks with Min Specifies whether the node fills the chromatographic peak for a
Value compound with a minimum value in blank samples.

When your processing workflow includes a QC correction node,

select True for this parameter. The QC correction node requires
area values for each detected compound across all the input files,
including the blanks (samples with the Blank sample type
assignment).

Default: False
2. Random Forest Settings

These parameters apply only to the Random Forest Imputation method.

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Table 57. Missing Value Imputation node parameters (Sheet 2 of 2)

Parameter Description
Number of Trees Specifies the number of decision trees.

Default: 100; range: 20 to 1000

Max Number of Specifies the maximum number of iterations.
Iterations
Default: 10; range: 2 to 50

Apply QC Correction node

When acquiring raw data files for a large sample set, you can use pooled quality control (QC)
samples to compensate for time-dependent batch effects.

When the processing workflow includes the Apply QC Correction node and the input file set
includes QC samples, an analysis uses the QC samples to create a linear regression or cubic
spline curve of area versus acquisition time for each detected compound. For more
information, see Using quality control samples to compensate for batch effects.

The Apply QC Correction node adds the QC columns and the Norm. Area column to the
compounds table (Compounds table). You can view the correction curves in the Compound
Area Corrections view and the QC corrected areas for the compounds in the Normalized Area
column. For more information, see “Compound Area Corrections view.”

Table 58 describes the parameters for the Apply QC Correction node.

Table 58. Apply QC Correction node parameters (Sheet 1 of 3)
Parameter Description
1. General Settings

The analysis uses the QC samples to create a regression curve for each detected compound.
Unless all three of the following conditions are met, the analysis does not create a regression
curve for a particular compound or does not correct the areas in the non-QC samples:
• It detects the compound in the specified minimum percentage of QC samples.
• The relative standard deviation of the detected peak areas for the compound in the QC
samples does not exceed the specified threshold.
• The number of samples acquired between the QC samples does not exceed the specified
number.

If the analysis does not create a regression curve for a compound, it does not perform a
batch normalization of the peak areas for the compound in the non-QC samples (Sample
type: Sample, Control, or Standard).

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Table 58. Apply QC Correction node parameters (Sheet 2 of 3)

Parameter Description
Regression Model Specifies the regression model as Linear or Cubic Spline.

Default: Linear
The Min. QC Coverage Max. [%], QC Area RSD [%], and Max. Corrected QC Area RSD
[%] parameters act as display filters for the compounds table.

When the compounds table includes compounds that the analysis was unable to normalize,
a filter icon appears on the table’s tab. Pointing to the tab displays the number of
compounds displayed, the total number of compounds detected, and the number of
compounds filtered out.
Min. QC Coverage [%] Specifies the minimum percentage of the QC samples where the
analysis must detect a particular compound before it creates a
regression curve for the compound. If the coverage falls below
this value, the analysis does NOT perform a batch normalization
of the peak areas for the compound in the non-QC samples.

Default: 50%; range: 25 to 100%

Max. QC Area RSD [%] Specifies the maximum relative standard deviation (RSD%) for
the areas for a particular compound across the QC samples. If
the RSD% exceeds this maximum percentage, the analysis does
not create a regression curve for the compound, calculate the
normalized areas for the compound, or report normalized areas
in the compounds table.

Default: 30%; range: 10 to 50%

Max. Corrected QC Area Specifies the maximum allowed relative standard deviation for a
RSD (%) particular compound area within the QC samples after
correction. If the RSD% exceeds this maximum percentage, the
analysis does not create a regression curve for the compound,
calculate the normalized areas for the compound, or report
normalized areas in the compounds table.

Default: 25; range: 5 to 50%

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Table 58. Apply QC Correction node parameters (Sheet 3 of 3)

Parameter Description
Max. #Files Between QC The application checks the acquisition time stamp for each
Files input file in an analysis and orders the samples within an analysis
set by acquisition time.

Specifies the maximum number of non-QC samples that you

can acquire between the QC samples. If the application detects
more non-QC samples between the QC samples than the
maximum allowable number, it does not correct the
chromatographic peak areas in the non-QC samples—that is, it
does not perform a batch normalization on these samples.

Default: 15; range: 1 to unchecked value

Apply SERRF QC Correction node

For LC studies, use the Apply SERRF QC Correction node if you are processing input files
from batches acquired on noncontiguous days. SERRF stands for systematic error removal
with random forests.

The Apply SERRF QC Correction node takes input from the Group Compounds node or the
Fill Gaps node. It creates the QC correction columns in the Compounds table and the Batch
column in the Input Files table.

For information about how the Apply SERRF QC Correction node creates the time-based
normalization curve for the chromatographic peak areas, see “Batch normalization for
multiple sequence runs (LC studies).”
Table 59. Apply SERRF QC Correction node parameter descriptions
Parameter Description
1. General Settings
Min. QC Coverage [%] Specifies the minimum percentage of the QC samples where
the analysis must detect a particular compound before it
creates a regression curve for the compound. If the coverage
falls below this value, the analysis does NOT perform a batch
normalization of the peak areas for the compound in the
non-QC samples.

Default: 50%; range: 25 to 100%

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Table 59. Apply SERRF QC Correction node parameter descriptions

Parameter Description
Max. QC Area RSD [%] Specifies the maximum relative standard deviation (RSD%)
for the areas for a particular compound across the QC
samples.

If the RSD% exceeds this maximum percentage, the analysis

does not create a regression curve for the compound,
calculate the normalized areas for the compound, or report
normalized areas in the compounds table.

Default: 30%; range: 10 to 50%

Max. Corrected QC Area Specifies the maximum allowed relative standard deviation
RSD [%] for a particular compound area within the QC samples after
correction.

If the RSD% exceeds this maximum percentage, the analysis

does not create a regression curve for the compound,
calculate the normalized areas for the compound, or report
normalized areas in the compounds table.

Default: 25; range: 5 to 50

Max. #Files Between QC The application checks the acquisition time stamp for each
Files input file in an analysis and orders the samples within an
analysis set by acquisition time.

Specifies the maximum number of non-QC samples that you

can acquire between the QC samples. If the application
detects more non-QC samples between the QC samples than
the maximum allowable number, it does not correct the
chromatographic peak areas in the non-QC samples—that is,
it does not perform a batch normalization on these samples.

Default: 15; range: 1 to unchecked value

# Batches Specifies the maximum number of batches used to acquire
the set of input files for the analysis. The node does not
exceed this number when it determines the number of
batches for the input file set.

Default: 2; range 1 to 50
Interpolate Gap-filled QC When set to True, the node discards the gap-filled areas for
Areas the QC samples and instead uses the mean of the
non-gap-filled areas for these compounds.

Default: False

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Table 59. Apply SERRF QC Correction node parameter descriptions

Parameter Description
Correct Blank Files Specifies whether the correction process adjusts the
chromatographic peak area values for samples with the Blank
sample type assignment.

Typically, there are two types of blank samples—solvent

blanks and matrix blanks.

True: The node adjusts the chromatographic peak area values

for blank samples.

False: The node does not adjust the chromatographic peak

area values for blank samples.
IMPORTANT When using a QC correction node, the
processing workflow must include the Fill Gaps node.
2. Random Forest Settings
#Trees Specifies the number of decision trees that the Random
Forest algorithm uses.

Default: 200; minimum: 10

Mark Background Compounds node

Use the Mark Background Compounds node to flag compounds that are also found in the
sample blanks (Sample Type—Set to Blank). For information about editing the assigned
sample types, see “Edit the sample type and study factor values.”

IMPORTANT As you drag the Fill Gaps and the Normalize Areas nodes into the Workflow
Tree pane, the application automatically connects the Group Compounds node to the Fill
Gaps node, and the Fill Gaps node to the Normalize Areas node. The application does not
connect the Mark Background Compounds node to other nodes, so you must manually
make the appropriate connections.

For more information about the node connections, see “Peak area refinement node
connections.”

Table 60 describes the parameters for the Mark Background Compounds node.

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Table 60. Mark Background Compounds node parameters

Parameter Description
1. General Settings
Max. Below this ratio threshold, the node labels the expected compound as a
Sample/Blank background compound in the compounds table. If the input file set
includes more than one blank sample, the node uses the largest peak area
for the compound in the blank input files as the peak area of the blank.
Peak Area Sample
----------------------------------- < Specified value
Peak Area Blank

Default: 5

When this setting is 0, the node ignores this parameter.

Max. Below this ratio threshold, the node labels the compound as a
Blank/Sample background compound in the compounds table. If the input file set
includes more than one blank sample, the node uses the largest peak area
for the compound in the blank input files as the peak area of the blank.
Peak Area Blank
----------------------------------- < Specified value
Peak Area Sample

If the compound is found in a blank sample but not in a non-blank

sample, (ratio X/0), the node marks the compound as a background
compound.

Default: 0 (The node does not use this parameter to mark background
compounds.)
Hide When the Hide Background parameter is set to True, the tab for the
Background compounds table includes a filter icon ( ), and the compounds that fall
below the threshold are hidden. Clicking the filter icon displays the
filtered compounds.

When the Hide Background parameter is set to False, the background

compounds appear in the result table.

The Background column is a hidden column in the compounds table.

When a compound is flagged as a background compound, its
Background check box is selected.

Default: True

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Normalize Areas node

Use the Normalize Areas node to normalize the chromatographic peak areas for each
compound across the input file set.

Thermo Fisher Scientific does not recommend using this node. To compensate for batch
effects, add quality control samples to the batch and a QC correction workflow node to the
processing workflow.

When the Normalize Areas node is part of a processing workflow, the Use Normalized Areas
check box is available in the Descriptive Statistics view and the Principal Component Analysis
view. The Normalize Areas node adds the Norm. Area column to the compounds table.

IMPORTANT When both the Normalize Areas and Mark Background Compounds nodes
are part of a processing workflow, do the following:
• If the analysis includes solvent blanks (Blank sample type), connect the Mark
Background Compounds node to the Normalize Areas node.
• If the analysis includes matrix blanks (Blank sample type), connect the Normalize
Areas node to the Mark Background Compounds node.

Table 61 describes the parameters for the Normalize Areas node.

Table 61. Normalize Areas node parameters (Sheet 1 of 2)
Parameter Description
1. General Settings
Normalization Type Specifies the algorithm for normalizing the peak areas for each
compound across the input files.

Selections:
• Constant Sum
• Constant Mean
• Constant Median
• Median Absolute Deviation (MAD)
Tip For best results, select Constant Mean for input file sets
that include matrix blanks.

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Table 61. Normalize Areas node parameters (Sheet 2 of 2)

Parameter Description
Exclude Blanks Specifies whether to exclude Blank sample types from
normalization.

Default: True
Tip For best results, follow these guidelines:
• Select True for solvent blanks to exclude them from the
normalization process. If you do not exclude the solvent
blanks from the normalization process, the Fill Gaps node
adds small “noise” peaks to the solvent blanks for each
detected compound in the input file set. The Normalize
Areas node magnifies these small peaks, causing the
sample-to-blank ratio to fall below the user-specified value
in the Mark Background Compounds node. The Mark
Background Compounds node then hides most of the
detected compounds across the input file set (marks them
as background compounds).
• Select False for matrix blanks, such as plasma and urine, as
these blanks typically contain a large number of
compounds that you might want to hide.

Scale Areas node

Use the Scale Areas node to scale the chromatographic peak areas on the basis of the numeric
study factor values that you assigned to each sample file.

Table 62 describes the parameters for the Scale Areas node. If your processing workflow
includes both of the grouping nodes, and you want to scale the output from both of these
nodes, you must connect each grouping node to a separate Scale Areas node.
Figure 84. Connections to Scale Areas node

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Table 62. Scale Areas node parameters

Parameter Description
1. General Settings
Study Factor Name Specifies the study factor to use as the scaling factor for the
chromatographic peak areas when you select Scaling Factor in
the Normalization Type list.

Multiplies the peak area for a compound by the value for the
selected numerical study factor.

Selections: Defined numerical study factors; default: Empty

Exclude Blanks Specifies whether to exclude blank samples (where the sample
type is set to Blank) from the scaling process.

Default: True
Tip For best results, follow these guidelines:
• Select True for solvent blanks to exclude them from the
scaling process.
• Select False for matrix blanks, such as plasma and urine, as
these blanks typically contain a large number of
compounds that you might want to scale.

Compound Identification nodes

Use these nodes to identify unknown compounds:
• Assign Compound Annotations node (LC studies)
• Predict Compositions node
• Search ChemSpider node
• Search Mass Lists node
• Search mzCloud node
• Search mzVault node

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Assign Compound Annotations node (LC studies)

Use the Assign Compound Annotations node to select the preferred data sources for the
following annotations: name, formula, and structure. The application attempts to assign the
annotations provided by the first data source. If the first source does not provide the
annotation, the application uses the second data source, and so on until it goes through all the
specified sources. If the processing workflow does not include the Assign Compound
Annotations node, the application does not populate the Name, Formula, or Structure
columns of the Compounds table for an LC study.

Table 63 describes the parameters for the Assign Compound Annotations node.
Table 63. Assign Compound Annotation node parameters (Sheet 1 of 2)
Parameter Description
1. General Settings
Mass Tolerance Specifies the mass tolerance for validating the annotations.

Default: 5 ppm; range: 0.1–20 ppm

2. Data Sources

Available sources: mzCloud Search, mzVault Search, BioCyc Search, Mass List Match,
Metabolika Search, ChemSpider Search, and Predicted Compositions
Data Source #1 Specifies the primary source for the compound annotations.

Default: mzCloud Search

Tip If a stable isotope analysis misidentifies known compounds,
consider reprocessing the analysis after selecting your custom
mass list as the first data source.
Data Source #2 Specifies the secondary source for compound annotations if the
primary source is unavailable.

Default: Predicted Compositions

Data Source #3 Specifies the source for compound annotations if the primary and
secondary sources are unavailable.

Default: Mass List Search

Data Source #4 Specifies the source for compound annotations if all the previous
sources are unavailable.

Default: ChemSpider Search

Data Source #5–7 Use to specify additional annotation sources in the list.

Default: Empty

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Table 63. Assign Compound Annotation node parameters (Sheet 2 of 2)

Parameter Description
3. Scoring Rules
Use mzLogic When set to True, uses the score from the Apply mzLogic node to
select the best candidate.

Default: True
Use Spectral Distance When set to True, uses the SFit score from the Apply Spectral
Distance node to select the best candidate.

Uses the SFit Threshold and SFit Range values to limit the
number of valid candidates.

Default: True
SFit Threshold Specifies the minimum SFit score for a candidate.

Default: 20; range: 0 to 100

SFit Range Specifies the maximum allowed difference between the SFit scores
for the best and worst candidates.

Default: 20; range: 0 to 100

4. Reprocessing
Clear Names When set to True, the node clears the assigned annotations (name,
formula, and structure) for the detected compounds when you
reprocess the analysis.

When set to False, the node does not remove the assigned
annotations when you reprocess the analysis. If you modify the
identification workflow nodes, these nodes can overwrite the
existing annotations. If you remove the identification nodes
responsible for the initial annotations, these annotations remain in
the final analysis result.

This parameter is new in the Compound Discoverer 3.3

application. In previous versions, the application always cleared
the assigned annotations when you partially reprocessed an
analysis result.

Default: False

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Predict Compositions node

Use the Predict Compositions node to predict the chemical formulas of the unknown
compounds. This node creates the Predicted Compositions Table and populates the Formula
column of the Compounds table for LC studies when the processing workflow also includes
the Assign Compound Annotations node.

Table 64 describes the parameters for the Predict Compositions node.

Table 64. Predict Compositions node parameters (Sheet 1 of 4)
Parameter Description
1. Prediction Settings
Mass Tolerance Specifies the mass tolerance for the XIC traces.

Default: 5.0 ppm; range: 1–20.0 ppm

Min. Element Counts Specifies the minimum count for each element in the
hypothetical compound. If an element is not listed, its minimum
count is zero.

Default: C H
Max. Element Counts Specifies the maximum count for each element in the
hypothetical compound. If an element is not listed, its maximum
count is the same as its minimum count.

Default: C90 H190 Br3 Cl4 K2 N10 O18 P3 S5

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Table 64. Predict Compositions node parameters (Sheet 2 of 4)

Parameter Description
Min. RDBE and Specifies a range of values for ring and double-bond equivalents.
Max. RDBE The RDBE value is a measure of the number of unsaturated
bonds in a compound. The specified value limits the calculated
formulas to only those that make sense chemically.

The following formula determines the RDBE value for an

elemental composition:

imax

 Ni ( Vi – 2 )
i
D = 1 + ------------------------------------------
2

where:
• D is the value for the RDB equivalents
• imax is the total number of different elements in the
composition
• Ni is the number of atoms of element i
• Vi is the valence of atom i
Min. H/C Specifies the minimum hydrogen-to-carbon ratio.

Default: 0.1

The value of 0 means no limit. The application does not accept

negative values.
Max. H/C Specifies the maximum hydrogen-to-carbon ratio.

Default: 3.5

The value of 0 means no limit. The application does not accept

negative values.

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Table 64. Predict Compositions node parameters (Sheet 3 of 4)

Parameter Description
Note For most compounds, the hydrogen-to-carbon ratio falls within the range from 0.5
to 2.0.
• Long chain alkanes have an H/C ratio of approximately 2.
• Polycyclic aromatics have an H/C ratio of approximately 0.5.
Max. #Candidates Specifies the maximum number of compositions to store for each
compound in the result file.

Default: 10; range: 1–50

Max # Internal Specifies the maximum number of compositions to calculate for
Candidates each detected component.

Default: 200; range: 1 to unchecked

Tip To optimize the processing time, the maximum number of
internal candidates is limited to 200 by default and sorted by
the mass error. Normally, this works well for masses below
500 Da. However, as a component’s mass or the number of
elements increases, the number of possible elemental
compositions also increases. This increase means that the
chance of rejecting the correct formula, when it has a higher
mass error than the first 200 candidates, also increases.

For samples with components that have a relatively large

number of elements or a mass above 500 Da, consider
increasing the limit to 500.
2. Pattern Matching
Intensity Tolerance [%] Specifies the intensity tolerance for the isotope pattern search.

Default: 30%; range: 0 to 100%

Intensity Threshold [%] Specifies the intensity threshold, relative to the base peak (most
intense ion) in the isotope pattern, for the isotope pattern search.
The analysis ignores isotopes below this threshold.

Default: 0.1%; range: 0.1 to 10%

S/N Threshold Specifies the signal-to-noise threshold for the isotope search.
Isotopes with a theoretical intensity below the threshold are not
required.
Min. Spectral Fit [%] Specifies the minimum spectral fit for reporting a predicted
composition in the Predicted Compositions result table.

Default: 30%; range: 0 to 100%

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Table 64. Predict Compositions node parameters (Sheet 4 of 4)

Parameter Description
Min. Pattern Cov. [%] Specifies the minimum percentage for the summed intensity of
the matching isotope peaks in the measured MS1 spectrum
relative to the summed intensity of the theoretical isotope
pattern.

 Im
------------- × 100 = Min. Pattern Cov. [%]
 It
where:
Im = the matching isotope peaks
It = the theoretical isotope peaks

Default: 90%; range: 0 to 100%

Use Dynamic Specifies whether the application uses the dynamic recalibration
Recalibration algorithm to shift the theoretical pattern for the candidate
formula by the difference in the observed m/z value of the
leftmost (A0) isotopic peak in the measured spectrum.

Use dynamic recalibration when there is a systematic error (due

to calibration) in the measured spectrum.

Default: True
3. Fragments Matching
Use Fragments Specifies whether the application uses the fragment matching
Matching algorithm, which ranks the identified candidates (chemical
formulas) by the number of matching centroids (with an
m/z value that matches a subset of the elemental composition for
a particular candidate) in the fragmentation scan for the
precursor ion.

Default: True
Mass Tolerance Specifies the mass tolerance for matching the centroids in the
fragmentation scans to the m/z values for the expected fragments.

Default: 5 ppm; range: 0 to unchecked

S/N Threshold Specifies the signal-to-noise threshold for the centroids in the
fragmentation scans. The node ignores centroids with an
intensity below this threshold.

Default: 3; range: 0 to unchecked

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Search ChemSpider node

Use the Search ChemSpider node to search mass spectral databases for matching compounds
within a specified mass tolerance range or with a certain elemental composition. This node
requires input from the Group Compounds node. It adds the #ChemSpider Results column
to the Compounds Table and creates the ChemSpider Results Table.

When the processing workflow includes a ChemSpider search, the processing computer must
have Internet access. To verify whether the processing computer can access the ChemSpider
database, run the Communication test. See Chapter 17, “Test communication to the online
databases.”

Table 65 describes the parameters for the Search ChemSpider node.

Table 65. Search ChemSpider node parameters (Sheet 1 of 2)
Parameter Description
1. Search Settings
Database(s) Specifies the databases for the ChemSpider search. For more
information about the ChemSpider databases, go to the Resources
page on the My Compound Discoverer website.

Default: KEGG
Search Mode Default: By Formula or Mass

Selections: By Formula or Mass, By Formula Only, By Mass Only

Mass Tolerance Specifies the mass tolerance that the node uses to search for
matching mass peaks.

Default: 5 ppm; range: 0.1 to 20 ppm or 0.0 to 0.1 Da

Max# of Results Per Specifies the maximum number of hits (matches) to return (store
Compound in the result file).

Default: 100; range: 1 to 2000

Max # of Predicted Specifies the maximum number of predicted compositions to
Compositions to be search for in the ChemSpider database.
Searched per
Compound Default: 3; range: 1 to 100

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Table 65. Search ChemSpider node parameters (Sheet 2 of 2)

Parameter Description
Result Order (for Max# Specifies the sort order in the ChemSpider Results table.
of Results per
Compound) Selections:
• Order By Reference Count (DESC)—Sorts the search results
by the number of references for each compound.
• Order By Data Source Count (DESC)—Sorts the search
results by the number of data sources.
• Order By Mass Deviation (ASQ)—Sorts the search results by
mass deviation from the expected mass.
• Order By PubMed Count (DESC)—Sorts the search results
by the number of PubMed references.
• Order By RSC Count (DESC)—Sorts the search results by
the number of RSC references.
• Order By CSID (ASQ)—Sorts the search results by the
ChemSpider ID.
2. Predicted Composition Annotation
Check All Predicted Specifies whether to add a flag to the Predicted Compositions
Compositions table. When set to True, the Search ChemSpider node adds the In
ChemSpider column to the Predicted Compositions table and
marks the matched Predicted Compositions with an X.

Default: False

Search Mass Lists node

Use the Search Mass Lists node to search mass lists for masses that match the detected
compounds. This node adds the #Matched Masses to the Compounds Table and creates the
Mass List Search Results Table.

Table 66 describes the parameters for the Mass List Search node.

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Table 66. Search Mass List node parameters

Parameter Description
1. Search Settings
Mass Lists Specifies the mass list files that the node searches for matching
masses.

The mass list must have the following columns—Mass, Retention

Time, and Name. The mass list can also contain the following
additional columns—Molecular Structure and Text Annotation.

Y To select input files for the mass list search

1. In the Mass box, click the browse icon, .

The Select Input Files dialog box opens.
2. Select the check boxes for the files that you want to use for the
mass list search.
3. Click OK.
Use Retention Time Specifies whether to search for compounds by retention time in
addition to mass.

Default: True
RT Tolerance [min] Specifies the retention time tolerance, in minutes, for the search.
The node searches for matching peaks in a retention time window
equal to the expected retention time plus or minus the specified
RT tolerance.

Default: 2; range: 0 to 10
Mass Tolerance Specifies the mass tolerance that the node uses to search for
matching compounds.

Default: 5 ppm; range: 0.1 to 20 ppm or 0.0 to 0.1 Da

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Table 67 describes the table columns in the Select Input Files dialog box.
Table 67. Select Input File(s) dialog box parameters
Table column Description
Selected Selecting the check box for a mass list adds the list to the search.
Filename Displays the file name of the imported file.
Description Editable text field.

Clicking the table cell displays a text entry field for typing a name
or a description of the mass list. Use this column to name and sort
your mass lists.
File Size Displays the file size of the imported file.
Uploaded Displays the date (month/day/year) and time (hour/minute) when
you added the file to the library in the following format:
MM/DD/yyyy HH:mm
Updated Displays the date and time when the file was updated.
Context Displays the source of the mass list—for example, Import from
CSV or Import from XML.
State Specifies whether the mass list is available, corrupted, or missing.

If you remove a mass list file from the ServerFiles folder and restart
the computer, the state of the file changes to Missing. If you edit a
mass list file in the ServerFiles Folder and restart the application,
the state of the file changes to Corrupted.

Search mzCloud node

Use the Search mzCloud node to search the mzCloud database for matching fragmentation
spectra. This node creates the mzCloud Results table and adds the #mzCloud Results,
mzCloud Best Match, and mzCloud Best Match Confidence columns to the compounds
table.

For LC studies, the Search mzCloud node requires input from the Group Compounds node
or the Group Expected Compounds table.

Note In addition to running an automated search with an analysis, you can manually
submit a fragmentation scan to the mzCloud database from the Mass Spectrum view for
an active result file.

When the processing workflow includes an mzCloud search, the processing computer must
have Internet access. To verify whether the processing computer can access the mzCloud
database, run the Communication tests.

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Table 68 describes the parameters for the Search mzCloud node.

Table 68. Search mzCloud node parameters (Sheet 1 of 5)
Parameter Description
1. General Settings
Compound Classes Specifies the compound classes for the search. Select All
or select specific classes.

Default: All
Precursor Mass Tolerance Specifies the tolerance for the precursor mass.

Default: 10 ppm; range: 0–0.1 Da or 0–20 ppm

FT Fragment Mass Tolerance Specifies the mass tolerance for high-resolution
fragmentation scans performed in the Orbitrap analyzer
(FTMS).

Default: 10 ppm; range: 0–0.5 Da or 0–100 ppm

IT Fragment Mass Tolerance Specifies the mass tolerance for low-resolution
fragmentation scans performed in the ion trap analyzer
(ITMS).

Default: 0.4 Da; range: 0–0.1 Da or 0–20 ppm

Library Specifies the mzCloud library for the search:
Autoprocessed, Reference, or both.
• Reference library—Contains only spectra that have
been manually curated by mass spectrometry experts.
• Autoprocessed library—Contains spectra curated
with an automated process. As time permits, spectra
in the Autoprocessed library are manually curated
and transferred to the Reference library.
Post Processing Specifies whether to search the library for filtered or
recalibrated spectra.

Selections:
• Filtered—Removes extraneous mass peaks that do
not match the theoretical mass spectrum.
• Recalibrated (Default)—The mass peaks for the
known ion fragments are recalibrated to match the
theoretical mass spectrum by a series of manually
supervised ion calibration steps.

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Table 68. Search mzCloud node parameters (Sheet 2 of 5)

Parameter Description
Max. # Results Specifies the maximum number of hits for each
compound, for each fragmentation spectrum in the
spectrum tree for the compound, and for each search
library to store in the result file.

Displays the hits with the highest match score above the
cutoff storage number in the result file.

For example, if you specify 2 as the maximum number of

results per compound and select two libraries to search,
the search returns up to four results for a compound that
has one fragmentation scan in its spectrum tree and up to
eight results for a compound that has two fragmentation
scans in its spectrum tree.

Default: 10; range: 1 to 50

Annotate Matching Fragments Specifies whether the processing workflow annotates the
matching fragments with structures that you can review
in the Spectrum view of the result page.

Default: False
Search MSn Tree Specifies whether the analysis submits the full MSn
spectral tree for the database search.

Default: False

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Table 68. Search mzCloud node parameters (Sheet 3 of 5)

Parameter Description
2. DDA Search
Identity Search Specifies the identity search algorithm.

Selections:
• HighChem DP—Alternative score using a modified
dot product algorithm that includes a “hard penalty”
function for spectra with a low number of fragment
ions.
• HighChem HighRes—Use for high-resolution data.
Correlation algorithm that uses the geometric mean
of a modified Spearman’s rank order correlation to
separately determine the intensity and m/z accuracy
of the fragment ions.
• NIST
• Cosine—Dot product algorithm with fragment
intensities weighted by 0.75 and no weighting on
fragment m/z values.

Default: HighChem HighRes

Match Activation Type Specifies whether to only search for fragmentation spectra
with the same activation type.

Default: True
Match Activation Energy Specifies whether to search for fragmentation spectra
generated by the same ion activation energy within a
tolerance or by any ion activation energy.

Default: Match with Tolerance

Activation Energy Tolerance Specifies the tolerance as an absolute value for the ion
activation energy used to generate the fragmentation
spectrum.

For example, if the ion activation energy used to generate

your spectrum was a normalized collision energy of 35%
and you specify an ion activation energy tolerance of ±20,
the search looks for spectra with an ion activation energy
from 15 to 55.

Default: 20; range: 0 to 200

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Table 68. Search mzCloud node parameters (Sheet 4 of 5)

Parameter Description
Apply Intensity Threshold Specifies whether to apply an automatic intensity
threshold that sets the threshold intensity by calculating
the spectrum noise level.

Default: True
Similarity Search Specifies the similarity search algorithm.

Selections:
• None (Default)—Does not run a similarity search.
• Confidence Forward— Uses the dot product of the
forward search match and distribution of peaks, and
the ratio of the most intensive matching peaks as part
of the similarity score. A higher similarity score
indicates the extent to which the unknown
component resembles the library compound.
• Confidence Reverse—Uses the dot product of the
reverse search match and distribution of peaks, and
the ratio of the most intensive matching peaks as part
of the similarity score. A higher similarity score
indicates the extent to which the library compound
resembles the unknown component.
• Similarity Forward—Searches for a match between
the best fragmentation scan for a compound (across
the input file set) and a fragmentation scan in the
mzCloud database. Unlike the Identity Search, this
search ignores the m/z value of the precursor ion.
• Similarity Reverse—Searches for a match between the
fragmentation scans in the mzCloud database and the
best fragmentation scan for a compound (across the
input file set).
Match Factor Threshold Specifies the minimum match factor for reporting a
spectrum match.

Default: 60; range: 0 to 100%

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Table 68. Search mzCloud node parameters (Sheet 5 of 5)

Parameter Description
3. DIA Search
Use DIA Scans for Search Specifies whether to submit data independent scans to the
mzCloud database for a spectral search.

Default: False
Note Keep the default setting of False for GC CI data.
Max. Isolation Width [Da] Specifies the maximum MS2 isolation width. The
isolation width for a scan is listed in its scan header.

Default: 500 Da; minimum width: 10 Da

Match Activation Type See Match Activation Type under DDA Search.

Default: False
Match Activation Energy See Match Activation Energy under DDA Search.

Default: Any
Activation Energy Tolerance See Activation Energy Tolerance under DDA Search.

Default: 100
Apply Intensity Threshold See Apply Intensity Threshold under DDA Search.

Default: False
Match Factor Threshold See Match Factor Threshold under DDA Search.

Default: 20

Search mzVault node

Use the Search mzVault node to search a local mass spectra database for compounds of
interest.

For LC studies, this node requires input from the Group Compounds node or the Group
Expected Compounds node. And it can process compounds from both of these nodes in one
processing workflow.

For GC studies, this node requires input from the GC CI Deconvolution node.

The node creates the mzVault Results table. See “mzVault Results table.”

Y To use mzVault libraries created with the mzVault 1.1 or earlier application

Change the following settings:

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• For the Match Ion Activation Type, select False.

• For the Match Ion Activation Energy, select Any.
• For the Match Ionization Method, select False.

Table 69 describes the parameters for the Search mzVault node.

Table 69. Search mzVault node parameters (Sheet 1 of 4)
Parameter Description
1. Search Settings
mzVault Library Specifies the mzVault libraries to search. You can select
one or more of the mzVault libraries in your Spectral
Libraries list. See “Spectral Libraries view.”
Compound Classes Specifies the compound classes for the search. Select All
or select specific classes.

Default: All
Match Ion Activation Type Specifies whether to only search for library scans that
match the ion activation type of the query spectrum.

Default: True
Match Ion Activation Energy Specifies whether to search for library scans generated by
the same ion activation energy within a tolerance of the
query spectrum or by any ion activation energy.

Default: Match with Tolerance

Ion Activation Energy Specifies the tolerance as an absolute value for the ion
Tolerance activation energy used to generate the fragmentation
spectrum.

For example, if the ion activation energy used to generate

your spectrum was a normalized collision energy of 35%
and you specify an ion activation energy tolerance of ±20,
the search looks for spectra with an ion activation energy
from 15 to 55.

Default: 20; range: 0 to 200

Match Ionization Method Specifies whether to only search for library spectra from
the same ionization method (for example, HESI, APCI,
and so on) as the query spectrum.

Default: True

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Table 69. Search mzVault node parameters (Sheet 2 of 4)

Parameter Description
Apply Intensity Threshold Specifies whether to apply an automatic intensity
threshold that sets the threshold intensity by calculating
the spectrum noise level.

Default: True
Remove Precursor Ion When set to True, the search ignores (removes from
consideration) mass peaks within 2.2 Da of the precursor
ion’s m/z value in the query spectrum—that is, the match
score is not negatively affected if the library spectrum
does not include a mass peak within 2.2 Da of the
m/z value for the precursor ion.

Default: True
Precursor Mass Tolerance Specifies the tolerance for the precursor mass.

Default: 10 ppm; range: 0 to 0.1 Da or 0 to 20 ppm

FT Fragment Mass Tolerance Specifies the mass tolerance for high-resolution
fragmentation scans performed in the Orbitrap analyzer
(FTMS).

Default: 10 ppm; range: 0 to 0.5 Da or 0 to 100 ppm

IT Fragment Mass Tolerance Specifies the mass tolerance for low-resolution
fragmentation scans performed in the ion trap analyzer
(ITMS).

Default: 0.4 Da; range: 0 to 0.1 Da or 0 to 20 ppm

Match Analyzer Type Specifies whether to only search for library spectra from
the same mass analyzer type as the query spectrum.

Default: True

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Table 69. Search mzVault node parameters (Sheet 3 of 4)

Parameter Description
Search Algorithm Specifies the identity search algorithm.

Selections:
• HighChem DP—Alternative score using a modified
dot product algorithm that includes a “hard penalty”
function for spectra with a low number of fragment
ions.
• HighChem HighRes—Use for high-resolution data.
Correlation algorithm that uses the geometric mean
of a modified Spearman’s rank order correlation to
separately determine the intensity and m/z accuracy
of the fragment ions.
• NIST

Default: HighChem HighRes

Match Factor Threshold Specifies the minimum match factor for reporting a
spectrum match.

Default: 50; range: 0 to 100%

Max. # Results Specifies the maximum number of hits for each
compound, for each fragmentation spectrum in the
spectrum tree for the compound, and for each search
library to store in the result file.

Displays the hits with the highest match score above the
cutoff storage number in the result file.

For example, if you specify 2 as the maximum number of

results per compound and select two libraries to search,
the search returns up to four results for a compound that
has one fragmentation scan in its spectrum tree and up to
eight results for a compound that has two fragmentation
scans in its spectrum tree.

Default: 10

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Table 69. Search mzVault node parameters (Sheet 4 of 4)

Parameter Description
RT Tolerance [min] Specifies the retention time tolerance for the library
search.

Default: 2; range: 0 to 10 minutes

Use Retention Time Specifies whether to filter the database hits by their
retention time. Filters out scans without retention time
information.

Default: False

Pathway Mapping nodes

Use these nodes to map detected compounds to a biochemical pathway:
• Map to BioCyc Pathways node
• Map to KEGG Pathways node
• Map to Metabolika Pathways node

Map to BioCyc Pathways node

Use the Map to BioCyc Pathways node to map the BioCyc pathways for each compound. The
input to this node is a list of molecular weights, chemical formulas, or both. For LC studies,
the Group Compounds node and the Group Expected Compounds node provide this input.

The Map to BioCyc Pathways node adds the following items to the result file:
• The BioCyc Pathways and BioCyc Results main tables
• The #BioCyc Pathways and BioCyc Pathways columns in the main compounds table
• The BioCyc Compound IDs, BioCyc Compound Names, and BioCyc Compound
Formula columns in the related compounds table and the related BioCyc Pathways table.

Table 71 describes the parameters for the Map to BioCyc Pathways node.
Table 70. Map to BioCyc Pathways node parameters (Sheet 1 of 2)
Parameter Description
1. Search Settings
BioCyc Database/Organism Specifies the databases for the search.
to be Searched

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Table 70. Map to BioCyc Pathways node parameters (Sheet 2 of 2)

Parameter Description
Search Mode Default: By Formula or Mass

Selections: By Formula or Mass, By Formula Only, By Mass

Only
2. By Mass Search Settings
Mass Tolerance Specifies the mass tolerance that the node uses to search for
matching compounds.

Default: 5 ppm; range: 0.1 to 20 ppm

3. By Formula Search Settings
Max. # of Predicted Specifies the maximum number of predicted compositions to
Compositions to be search for per compound.
Searched per Compound
Default: 3; range: 1 to 100
4. Display Settings
Maximum # of Pathways in Specifies the maximum number (n) of pathways to display by
“Pathways” Column name in the Pathways column of the Compounds result
table. The Pathways column displays the names of the first
n – 1 pathways that include the compound. The other
pathways that include the compound are grouped in the
Other category.

Default: 20; range: 1 to 30

Map to KEGG Pathways node

The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database contains
connection diagrams of molecular interactions, reactions, and relations.

Use the Map to KEGG Pathways node to add explanations to the result file about the reaction
pathways for each detected compound.

The node requires the following input— a list of molecular weights or chemical formulas. For
LC studies, the KEGG node requires input from the Group Compounds node, the Group
Expected Compounds node, or both of these nodes.

The Map to KEGG Pathways node adds the following items (output) to the result file:
• The KEGG Pathways table
• The KEGG Compound IDs, KEGG Compound Names, and KEGG Compound
Formula columns in the related compounds table
• The #Pathways and Pathways columns in the main compounds table

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When the processing workflow includes the Map to KEGG Pathways node, the processing
computer must have Internet access. To verify whether the processing computer can access the
KEGG Pathways database, run the communication test as described in Chapter 17, “Test
communication to the online databases.”

Table 71 describes the parameters for the Map to KEGG Pathways node.
Table 71. Map to KEGG Pathways node parameters
Parameter Description
1. Search Settings
Search Mode Specifies the search mode.

Default: By Formula or Mass

Selections: By Formula or Mass, By Formula Only, By Mass

Only
2. By Mass Search Settings
Mass Tolerance Specifies the mass tolerance that the node uses to search for
matching compounds.

Default: 5 ppm; range: 0.1 to 20 ppm

3. By Formula Search Settings
Max. # of Predicted Specifies the maximum number of predicted compositions to
Compositions to be search for per compound.
Searched per Compound
Default: 3; range: 1.0
4. Display Settings
Maximum # of Pathways in Specifies the maximum number (n) of pathways to display by
“Pathways” Column name in the Pathways column of the Compounds result
table. The Pathways column displays the names of the first
n – 1 pathways that include the compound. The other
pathways that include the compound are grouped in the
Other category.

Default: 20; range: 1–30

Map to Metabolika Pathways node

To search your local database of Metabolika pathways for pathways that include matching
structures for the unknown compounds in your data set (by formula, mass, or both), add the
Metabolika Pathways node to the processing workflow and select the pathways to search.

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Note 378 Metabolika pathway files are automatically installed with the application. You
can edit these pathways or create your own pathways by using the Metabolika pathway
editor. For details, see “Metabolika Pathways view.”

Table 72 describes the parameters for the Map to Metabolika Pathways node.
Table 72. Map to Metabolika Pathways node parameters
Parameter Description
1. Search Settings
Metabolika Pathways Specifies the Metabolika pathways to search.

Default: All
Search Mode Specifies whether to search by formula, mass, or both.

Default: By Formula or Mass

Selections: By Formula or Mass, By Formula Only, By Mass

Only
2. By Mass Search Settings
Mass Tolerance Specifies the mass tolerance that the node uses to search for
matching compounds.

Default: 5 ppm; range: 0.1 to 20 ppm

3. By Formula Search Settings
Max. # of Predicted Specifies the maximum number of predicted compositions to
Compositions to be search for per compound.
Searched per Compound
Default: 3; range: 1 to 100
4. Display Settings
Maximum # of Pathways in Specifies the maximum number (n) of pathways to display by
“Pathways” Column name in the Pathways column of the Compounds result
table. The Pathways column displays the names of the first
n – 1 pathways that include the compound. The other
pathways that include the compound are grouped in the
Other category.

Default: 20; range: 1 to 30

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Compound Scoring nodes

Compound Scoring nodes

Use the nodes under Compound Scoring to score the explanations for each detected
compound.

The Calculate Mass Defect, Compound Class Scoring, Pattern Scoring, and Search Neutral
Losses nodes require input from the Group Compounds node. The Generate Molecular
Networks node requires input from the Assign Compound Annotations node, and the Apply
mzLogic and Apply Spectral Distance nodes take input from the Search ChemSpider node.

See these topics:

• Apply Spectral Distance node
• Apply mzLogic node
• Calculate Mass Defect node
• Compound Class Scoring node
• Generate Molecular Networks node
• Pattern Scoring node
• Search Neutral Losses node

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Apply Spectral Distance node

Use the Apply Spectral Distance node to calculate a spectral similarity score (SFit[%]) for the
compound annotations. The SFit[%] column appears in the related “compound annotations”
tables for the compound selected in the Compounds table. Depending on the processing
workflow, the related “compound annotations” tables can include any of these tables:
ChemSpider Results, Mass List Search Results, Metabolika Results, and BioCyc Results. In
addition to providing an SFit score for you to review in the related “compound annotations”
tables, the node sends the scores to the Assign Compound Annotation node.

Table 73 describes the parameters for the Apply Spectral Distance node.
Table 73. Apply Spectral Distance node parameters
Parameter Description
1. General Settings
Mass Tolerance Specifies the mass tolerance that the node uses to search for
matching mass peaks.

Search range = expected mass ± mass tolerance/1e6

Default: 5 ppm; range: 0.1 to 20 ppm

Intensity Tolerance [%] Specifies the relative intensity tolerance of the mass spectral peaks
in the isotope pattern.

Default: 30; range: 0 to 100%

Intensity Threshold Specifies the isotope intensity threshold, relative to the base peak
[%] of the isotope pattern, that the node uses for pattern simulation.
The node does not add isotopes below this threshold to the
simulated pattern.

Default: 0.1
S/N Threshold Specifies the signal-to-noise threshold for the isotope search. The
node does not include isotopes that are expected to be below this
threshold in the SFit score—that is, these isotopes are not required
in the measured isotope pattern.

Default: 3
Use Dynamic Specifies whether to shift the theoretical isotope pattern if the
Recalibration pattern base peak in the query spectrum is shifted.

Default: True

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Apply mzLogic node

Use the Apply mzLogic node to score explanations from the ChemSpider node, Search Mass
List node, Map to BioCyc Pathways node, and Map to Metabolika Pathways node.
Table 74. Apply mzLogic node parameters
Parameter Description
1. Search Settings
Max # Compounds Specifies the maximum number of compounds to display and
score in the result table.

Default: 0 (no maximum limit)

Max # mzCloud Similar Specifies the maximum number of compounds to consider from
Results to Consider per an mzCloud similarity search. Increasing the number of
Compound compounds to consider increases the processing time.

Range: 5 to 100
Match Factor Threshold Specifies the minimum match score returned for a compound by
an mzCloud similarity search. The analysis ignores compounds
with match scores below this threshold.

Default: 30
Advanced parameters
FT Fragment Mass Specifies the mass tolerance for the mass peaks in
Tolerance high-resolution fragmentation spectra when searching the
mzCloud spectral database.

Default: 10 ppm; range: 0 to 0.5 Da or 0 to 100 ppm

IT Fragment Mass Specifies the mass tolerance for the mass peaks in low-resolution
Tolerance fragmentation spectra when searching the mzCloud spectral
database.

Default: 0.4 Da; range: 0 to 1 Da or 0 to 1500 ppm

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Calculate Mass Defect node

Use this node to calculate the mass defect for each detected compound. You can specify up to
four calculation methods and up to five Kendrick formulas. This node adds the Mass Defect
column to the Compounds table for reviewing the result of the specified calculations.

Table 37 describes the parameters for the Filter By Mass Defect node.
Table 75. Filter By Mass Defect node parameters
Parameter Description
1. Mass Defect
Fractional Mass Fractional Mass = exact mass – floor (exact mass)
Standard Mass Standard Mass Defect = exact mass – nominal mass
Defect
Relative Mass Relative Mass Defect = 1e6 × (exact mass – nominal mass)/exact mass
Defect
Kendrick Mass Kendrick Mass Defect = Kendrick mass –nominal Kendrick mass
Defect
Kendrick mass – nominal Kendrick mass

where:
Kendrick mass = a × (b/c)
a = exact mass of the elemental composition
b = nominal mass of the Kendrick formula
c = exact mass of the Kendrick formula

Nominal Mass Specifies how the node calculates nominal masses.

Rounding
Default: Round

Selections:
• Floor rounds down.
• Ceiling rounds up.
• Round rounds to the nearest integer value.
2. Kendrick Formulas

When you select Kendrick Mass Defect as the Mass Defect Type, this user-specified
elemental composition specifies the Kendrick formula.
Formula 1–5 Use to add Kendrick formulas.

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Compound Scoring nodes

Compound Class Scoring node

Use the Compound Class Scoring node to score detected compounds against a set of fragment
ions commonly present in the fragmentation scans for a compound class. The node compares
the ions (m/z values) detected in the fragmentation scans to the fragments in the selected
compound class libraries.

In a processing workflow, connect the Group Compounds node to the Compound Class
Scoring node.

The Compound Class Scoring node does the following:

• Annotates the centroids in the fragmentation scans for a compound with the matching
fragment structures from the selected compound class libraries.
• Provides a Class Coverage score in the Mass Spectrum view legend.
• Adds the Class Coverage column with the percent coverage to the Compounds table.
• Creates the Compound Class Matches Table—a table related to the Compounds table.

When you add the Compound Class Scoring node to a processing workflow, you must select
the compound class fragment lists.

For information about adding compound class fragment lists to the Compound Classes
library, see “Compound Classes view.”

Table 76 describes the parameters for the Compound Class Scoring node.
Table 76. Compound Class Scoring node parameters (Sheet 1 of 2)
Parameter Description
1. General Settings
Compound Classes Select the compound classes that you want to use for the fragment
search.

Compound classes contain a list of fragment structures and

m/z values that the application compares to the fragmentation
scans for each detected compound. For details, see “Compound
Classes view.”
S/N Threshold Specifies the signal-to-noise threshold for the centroids in the
fragmentation spectra. The application ignores centroids below
the signal-to-noise threshold. The application attempts to match
centroids with m/z values above the threshold to the fragment
structures in the selected compound classes.

Default: 50

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Table 76. Compound Class Scoring node parameters (Sheet 2 of 2)

Parameter Description
High Acc. Mass Specifies the mass tolerance for high-resolution mass spectra
Tolerance measured in the Orbitrap mass analyzer of a Thermo Scientific
mass spectrometer.

Default: 2.5 mmu; Minimum: 0.0; Maximum: Unchecked

Low Acc. Mass Specifies the mass tolerance for low-resolution mass spectra
Tolerance measured in the ion trap mass analyzer of a Thermo Scientific
mass spectrometer.

Default: 0.5 Da; Minimum: 0.0; Maximum: Unchecked

Use Full MS Tree Specifies whether scoring is applied on the full spectrum tree or
only the MS2 scans.
Allow DIA Scoring Specifies whether the node uses DIA scans for scoring when there
are no available data-dependent scans. If set to false, the node
annotates DIA scans, but it does not use them for scoring.

Default: True

Generate Molecular Networks node

Use the Generate Molecular Networks node to determine and visualize the similarity between
various compounds in the Compounds table for LC studies.

Note For LC studies, the Assign Compound Annotations node connects to the Generate
Molecular Networks node.

Table 77 describes the parameters for the Generate Molecular Networks node.
Table 77. Generate Molecular Networks node parameters (Sheet 1 of 4)
Parameter Description
1. Spectral Similarity

These parameters define how fragmentation spectra are compared to determine the
similarity score between two compounds.
Use Full MSn Tree Specifies whether the node determines the spectral similarity from
the full MSn tree or only from the MS2 spectra.

Default: True (uses the full MSn tree)

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Table 77. Generate Molecular Networks node parameters (Sheet 2 of 4)

Parameter Description
Match Mass Shift For fragments that are not a direct match by mass, specifies
whether the shift to the fragment mass must match the mass shift
between the two compounds.

Default: True
Match Transformations For fragments that are not a direct match by mass, specifies
whether the shift to the fragment’s mass must match the mass of
the assigned transformation between the two compounds.

Default: True
Variate For fragments that are not a direct match by mass, specifies
Transformations whether the masses of all the variations of the individual steps of
the assigned transformation between the two compounds are used
as the expected fragments shifts. Fragments shifted by these masses
are considered as matching.

Default: False
S/N Threshold Specifies the signal-to-noise threshold for the centroids in the
fragmentation spectra. The node ignores centroids below the
signal-to-noise threshold—that is, the node attempts to match
only centroids with m/z values above the threshold.

Default: 3
Mass Tolerance Specifies the mass tolerance to use for fragments matching.

Default: 2.5 mmu

Min. Fragment m/z Specifies the minimum m/z values of the centroids to consider.

Default: 50
2. Transformations
Phase I Specifies the set of possible single-step Phase 1 transformations.

Default: All check boxes are clear.

Phase II Specifies the set of possible single-step Phase II transformations.

Default: All check boxes are clear.

Others Specifies other possible single-step transformations.

The node treats Others transformations as Phase I

transformations.

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Table 77. Generate Molecular Networks node parameters (Sheet 3 of 4)

Parameter Description
Max. # Phase II Specifies the maximum number of Phase II steps to be applied.

Default: 1; range: 1 to 10
Max. # All Steps Specifies the maximum number of all steps to be applied.

All steps that occur as a result of the selections in the Dealkylation

area equal one step in the maximum number of all steps—that is,
after the node applies the steps in the Dealkylation area, the
remaining number of possible steps is equal to the
Max. # All Steps – 1.

Default: 3; range: 1 to 10
3. Applied View Filters

These parameters filter out (hide) connections with lower confidence in the Similar
Compounds table for a compound. This filtering has no effect on the stored data—that is,
you can click the filter icon on the Similar Compounds tab to undo all of these filters.
Require When set to True, similar compounds without assigned
Transformation transformations are hidden.

Default: True
Require MSn When set to True, similar compounds without a spectral similarity
score are hidden.
Min. MSn Score Specifies the minimum MSn Score value for a similar compound.
If a similar compound has no fragmentation data, the application
does not apply this filter.
Min. MSn Coverage Specifies the minimum Forward or Reverse Coverage value for a
connection. The connection is hidden only if both values are
below this threshold. If a similar compound has no fragmentation
data, the application does not apply this filter.
Min. # Fragments Specifies the minimum Forward or Reverse Matches value for a
connection. The connection is hidden only if both values are
below this threshold. If a similar compound has no fragmentation
data, the application does not apply this filter.

Default: 3

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Table 77. Generate Molecular Networks node parameters (Sheet 4 of 4)

Parameter Description
4. Applied Thresholds

These parameters define the filtering rules for storing connections. The application does not
store connection that fall below these thresholds. The main purpose of these filters is to
reduces the amount of stored data by removing low confidence connections.
Require If set to True, removes connections without assigned
Transformation transformations.

Default: False
Require MSn If set to True, removes connections without a spectral similarity
score.

Default: False
Min MSn Score Specifies the minimum MSn Score value for a stored connection.
If the connection has no fragmentation data, the application does
not apply this filter and stores the connection if it passes the other
filters.

Default: 20; range 0 to 100

Min MSn Coverage Specifies the minimum Forward or Reverse Coverage value for
storing a connection. The application removes the connection
only if both values are below this threshold. If the connection has
no fragmentation data, the application does not apply this filter
and stores the connection if it passes the other filters.

Default 20; range 0 to 100

Min. # Fragments Specifies the minimum number of matched fragments for storing
a connection; that is, if both of these match scores are below the
user-specified threshold, the application does not store the
connection. If the connection has no fragmentation data, the
application does not apply this filter and stores the connection if it
passes the other filters.

Default: 0

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Pattern Scoring node

Use the Pattern Scoring node to provide a spectrum fit score (SFit%) for each detected
compound in the Compounds table (LC studies). The Pattern Scoring node compares the
measured isotope pattern for each detected compound to a defined isotope pattern—that is, it
compares the mass shifts and intensities of the centroids in the isotope pattern for the detected
compound to set of defined mass shifts and relative intensities. Use the Pattern List Editor
dialog box to store defined isotope patterns for your analyses.

The Pattern Scoring node adds the Pattern Matches column to the compounds table and
creates the related Matched Patterns Table.

Table 78 describes the parameters for the Pattern Scoring node.

Table 78. Pattern Scoring node parameters (Sheet 1 of 2)

Parameter Description
1. General Settings
Isotope Patterns Specifies the isotope patterns to be used for scoring.

For information about setting up the isotope patterns, see Set

up individual isotope patterns by using the Isotope Ratio
Editor and Create an isotope patterns list by using the
Pattern List Editor.
Mass Tolerance Specifies the mass tolerance for calculated elemental
compositions and pattern matching.

Default: 5 ppm; range: 0.0 to no limit

Intensity Tolerance [%] Specifies the relative intensity tolerance of the mass spectral
peaks in the isotope pattern.

Default: 30; range: 0.01 to 100.0

S/N Threshold Specifies the signal-to-noise threshold for the search. The
application ignores isotopes with a theoretical intensity value
below this threshold.
Min. Spectral Fit [%] Specifies the minimum required spectral fit value as a
percentage.

Range: 0 to 100%

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Table 78. Pattern Scoring node parameters (Sheet 2 of 2)

Parameter Description
Preferred Ions Specifies the preferred adduct ions for matching the isotope
patterns for compounds.

When this selection is empty, the node evaluates all the

adduct ions present across the input files.

An empty selection for this parameter generates a validation

prompt when you submit the analysis to the run queue.

Search Neutral Losses node

Table 79 describes the parameters for the Search Neutral Losses node. This node generates the
Neutral Losses column in the Compounds table and the Neutral Losses table.

Table 79. Search Neutral Losses node parameters

Parameter Description
1. General Settings
Neutral Losses Specifies the neutral losses for the search. The dropdown list
includes all the neutral losses in the Lists & Libraries >
Neutral Losses view. See “Neutral Losses view.”
High Accuracy Mass Specifies the mass tolerance to be used for searching
Tolerance fragments within high-accuracy MS2 scans such as those
from the Thermo Scientific Orbitrap MS.
Low Accuracy Mass Specifies the mass tolerance to be used for searching
Tolerance fragments within low-accuracy MS2 scans such as those from
an ion trap mass analyzer.
S/N Threshold Specifies the signal-to-noise threshold for the search. The
application ignores spectral peaks (centroids) with an
intensity value below this threshold.
Use DIA Scans for Search Specifies whether to search data-independent scans such AIF
scans for fragments in addition to searching the data
dependent (DDF) scans.

Post-Processing nodes
These nodes provide additional information about the detected or found compounds.
• Descriptive Statistics node
• Differential Analysis node

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• Export Xcalibur Inclusion or Exclusion List node

• Result Exporter node
• Scripting Node

Descriptive Statistics node

Use the Descriptive Statistics node to store descriptive statistics for each expected or unknown
compound in the result file and add the following hidden columns to the Compounds and
Expected Compounds tables: Mean Area, Median Area, Minimum Area, Q1 Area, and Q3
Area.

To store the descriptive statistics in the result file, the processing workflow must include the
Group Expected Compounds node for targeted workflows and the Group Compounds node
for untargeted workflows.

The Descriptive Statistics node has no parameters.

Note The Descriptive Statistics node generates the descriptive statistics for individual
compounds; it has no effect on the Descriptive Statistics view that is available for a result
file.

Differential Analysis node

Use the Differential Analysis node to calculate the statistics for a differential analysis (fold
change, ratio, p-values, and so on), store this data in the result file, and create a volcano plot in
the Differential Analysis view by using the data stored in the compounds table (Compounds
table or Expected Compounds table). A volcano plot is a type of scatter plot for replicate data
where the x axis represents the log2 of the fold change between two sample groups (generated
ratio), and the y axis represents the negative log10 of the p-value (test of significance) of the
fold change.

This node requires input from a compounds node for a sample set with replicate data points
and generated ratios. If the Grouping & Ratios page of an analysis does not contain generated
ratios, the following confirmation message appears:
No quan ratios defined in ‘Grouping & Ratios’ tab

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Table 80 describes the parameter for the Differential Analysis node.

Table 80. Differential Analysis node parameters
Parameter Description
1. General Settings
Log10 Transform Values Specifies whether to calculate log10 values of the
chromatographic peak areas before storing the data in the
result file.

Default: True
2. Peak Rating Contributions

These parameter settings determine how the node calculates the peak rating values for
chromatographic peaks. See “Chromatographic peak rating filter.”

The maximum value for each contributing parameter is unlimited.

The contribution of each individual parameter is as follows:

(Contribution value for the individual parameter/Divided by the sum of all the contribution
values)×10.
Area Contribution Specifies the chromatographic peak area contribution to the
peak rating.

Default: 3
CV contribution Specifies the contribution of the coefficient of variation for
the peak areas across replicate samples to the peak rating. If
an analysis includes no replicates, the node sets the CV
contribution to 0 during processing.

Default: 10
FWHM to Base Specifies the FWHM to base contribution to the peak rating.
Contribution
Default: 5
Jaggedness Contribution Specifies the jaggedness contribution to the peak rating.

Default: 5
Modality Contribution Specifies the modality contribution to the peak rating.
Zig-Zag Index Contribution Specifies the zig-zag index contribution to the peak rating.

Default: 5

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Export Xcalibur Inclusion or Exclusion List node

Use the Export Xcalibur Inclusion/Exclusion List node to create an Inclusion/Exclusion mass
list for a Thermo Scientific mass spectrometer.

Table 81 describes the parameters for the Export Xcalibur Inclusion or Exclusion List node.
Table 81. Export to Xcalibur Inclusion/Exclusion List node parameters
Parameter Description
1. General Settings
File Name Specifies the file name for the inclusion/exclusion list.
Selected Instrument Bases the format of the inclusion/exclusion list on the selected
MS.

Selections: LTQ Orbitrap, Orbitrap Fusion, Q Exactive

2. Use Filter Set
Add Filter Set Specifies the filters sets (FILTERSET file type) that you want to
apply to the generated inclusion list or exclusion list.
3. Advanced Settings
Left RT [min] Specifies the window to the left of the specified retention time for
a mass.

Default: 1 min; range: 0.001 to 1000 min

Right RT [min] Specifies the window to the right of the specified retention time
for a mass.

Default: 1 min; range: 0.001 to 1000 min

Include Isotopic Peaks Specifies whether to include isotopic peaks in the list.

Default: False
4. LTQ Orbitrap Settings
Maximum Concurrent Specifies the maximum number of entries with overlapping time
Entries windows.

Default: 500; range: 1 to 2000

Mass Precision Specifies the required number of decimal places for the mass
Decimals values.

Default: 5

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Result Exporter node

Use the Result Exporter node to export the data in each result table to a spreadsheet or text
file. The application exports separate files for each result table.

Table 82 describes the parameters for the Result Exporter node.

Table 82. Result Exporter node parameters
Parameter Description
1. Output Data
File Name Specifies the base file name for the exported TXT or XLS files.

When the file name is not specified, the application uses the name
of the result file for the exported TXT or XLS files.

Default: Empty—The application uses the name of the result file.

Export Format Specifies the file format for the exported data.

Default: No selection; selections: Excel or Text

Exports All Columns Specifies whether all the columns in the result file tables are
exported to the selected file type.

Default: False—The application exports only the visible columns

in the result file to the user-selected file format.
2. Text Export Options
R-Friendly Columns Specifies whether the column names are R-Friendly. Applies only
to TXT files.

Default: False

Scripting Node
Use the Scripting Node to perform custom post-processing actions on the data in the result
tables.

Tip For information about using the Scripting node, go to the Resources page of the
following web site: https://mycompounddiscoverer.com/.

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Table 83 describes the parameters for the Scripting node.

Table 83. Scripting node parameters
Parameter Description
Executable and Parameters
Path to Executable Specifies the path to the executable file, for example,
c:\Python37\python.exe.
Command Line Specifies command line arguments provided to the executable, for
Arguments example, "d:\My Scripts\script.py \" %NODEARGS%.
Requested Tables and Specifies the requested result table columns for the executable.
Columns
If you specify a table without specifying specific columns in the
table, the node exports the entire table.

Use a colon to separate the table name from the table columns, a
comma to separate the table columns, and a semicolon to separate
tables.

Format:

TableName1: Column1, Column2; TableName2: Column3, Column4

To enter this list, do the following:

1. Click the browse icon.
The Edit Parameter Text for Requested Tables and Columns
dialog box opens.
2. Do one of the following:
• Enter the tables and columns requested. Use a new line
for each table.
• Click Load File, select a text file that contains the table
and column information, and click Open.
3. Click OK.
Use R-Friendly Specifies whether the column names are R-Friendly.
Columns
Default: True
Archive Datafiles Specifies whether the node creates an archive containing the
JSON files and the text (.txt) files.

Default: False

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Review the analysis results

The Compound Discoverer application stores the results of an analysis in a result file
(CDRESULT).
The following topics describe how to open result files, filter the result tables, edit the
compound annotations, propose custom structures, modify the layout of a result page, and
export mass lists and spectral data.
• Open, close, and update result files
• Factory default layout for a result page
• Modify the result page layout for ease of use
• Custom color-coded tags for result table entries
• Save, restore, and manage layouts
• Edit compound annotations
• Add or delete proposed structures for a compound
• Replace an annotation with a structure proposal
• Apply FISh scoring
• Filter the data for data reduction
• View the result summaries
• Shortcut menu commands for the result tables
• Export the tabular data in a result file to an external file
• Export spectral data to a new or existing mzVault library
• Export compounds to a new or existing mass list
• Copy or save graphical views for publication
• Copy structures to the Clipboard for use in other applications

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Open, close, and update result files

For details about each of the graphical views and result tables, see these chapters:
• Chapter 9, “Graphical views for a result file.”
• Chapter 10, “Descriptive information for the result tables.”

Open, close, and update result files

During an analysis, the Compound Discoverer application processes a set of input files
(Xcalibur RAW files) by using a processing workflow and stores the processing results in a
result file (CDRESULT).

Note Result files are also known as analysis results, as you can open them from the
Analysis Results page of a Compound Discoverer study.

When you open a result file for the first time, you see a tabbed document with the default
layout in the application window. You can modify the layout and save these changes with the
result file. The next time you open the result file, it will open with your custom layout.

To open a result file from a previous version of the application, you must update the file to the
current version.

For instructions on how to open, close, and update result files, see these topics:
• Open result files created in the current version of the application
• Open result files created in previous versions of the application
• Update modes for legacy result files
• Close a result file

Open result files created in the current version of the application

You can open a result file from the application window, the Start Page, the Job Queue page, or
the Analysis Results page. A result file opens as a tabbed document. The tab displays the file
name of the result file ( File Name X).

Y To open a result file created in the current version of the application

• From the application window, do one of the following:

– From the menu bar, choose File > Open Result. In the Open dialog box, browse to
the appropriate folder, select the result file of interest, and click Open.
– From the menu bar, choose File > Recent Results > recent result file.
• From the Start Page, do one of the following:
– Under Recent Results, click the blue link for the result file of interest.

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– Under What Would You Like to Do?, click Open Result.

• From the Job Queue page, do one of the following:
– Double-click the table row for a completed job.
– Select the table row of a completed job and click Open Results.
• From the Analysis Results page, do one of the following:
– Double-click the table row for a completed analysis.
– Select the file of interest and click Open Results.

Tip You can also drag and drop result files (CDRESULT) from Windows Explorer into
the application window.

You can open as many result files as you want. To view a particular result file, click its tab.

Open result files created in previous versions of the application

Y To open a result file from a previous version of the application

1. From the menu bar, choose File > Open Result. In the Open dialog box, browse to the
appropriate folder, select the result file of interest, and click Open.
The File Update Required dialog box opens.
Figure 85. File Update Required dialog box

2. Select one of the following update processes:

• To retain the original result file, select the Keep Original File check box.
The application then automatically selects the Failsafe Update check box.
• To automatically delete the original file after the update process ends, select only the
Failsafe Update check box.
When the Failsafe Update check box is selected, the application automatically backs
out of the update process if an error occurs.
–or–
• To minimize the processing time, clear both check boxes.

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The application immediately processes the file without first creating a temporary file.
Errors that occur during the update process can corrupt the file.

IMPORTANT To prevent loss of data when not using the fail-safe mode to update
legacy result files, Thermo Fisher Scientific recommends that you manually store
copies of these files in another directory.

3. To start the update process, click Update.

Update modes for legacy result files

When you attempt to open a legacy result file, the application prompts you to select an
update process:
• Selecting the Keep Original File check box runs the update process in the fail-safe mode
and renames the original result file with an appended version number. This option takes
the most processing time, but it prevents data corruption of the original file.
• Selecting the Failsafe Update check box runs the update process in the fail-safe mode, but
it does not save the original result file. If the update process fails, the application retains
the original result file. You can make another attempt to update the file or you can open
the file in a previous version of the application.

Note You can install multiple versions of the Compound Discoverer application on
the same data system computer.

• Clearing both check boxes turns off the fail-safe mode. This option takes the least amount
of processing time, but it risks the possibility of corrupting the original file and making it
unrecoverable.

In the fail-safe mode, the application does the following:

1. Creates a temporary file.
2. Runs the updates on the temporary file.
3. After completing the update process successfully, it does the following:
a. Appends the application version to the file name of the original file. Because the
application does not reprocess the original file, the file retains its original time stamp.
b. Changes the file name extension of the temporary file to CDRESULT. The time
stamp for the updated file corresponds to the completion of the update process.
If the update process fails, the application does not rename the original file.

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Factory default layout for a result page

Close a result file

You can close a result file (CDRESULT) in one of two ways.

Y To close a result file

• Right-click the tab and choose Close.

–or–
• Click the close icon on the document’s tab ( ).
If the tab is not visible, click the Current Tabs icon, , and select the result file from the
list. For details, see “Show, hide, and rearrange the tabbed pages of the application.”

Factory default layout for a result page

When you open a result file, it appears as a tabbed page in the application window. See
“Open, close, and update result files.”

The factory default layout for a result page includes the following items:
• A tab with the result file name
• For LC studies, the Chromatograms view on the top left is populated with XIC traces for
the component with the largest chromatographic peak area across the input files—that is,
the view is populated with the XIC traces for the compound listed in the first row of the
Compounds table or the Expected Compounds table. The view is zoomed to the start and
end points of the chromatographic peak.
• For LC studies, the Mass Spectrum view on the top right is populated with the MS1 scan
with the highest resolution and highest intensity related to the preferred ions across the
input files. The spectrum tree to the left includes the MS1 scans and the available
fragmentation scans within the following time range for a compound:
– Peak apex (RT) ± the peak’s full width at half maximum (FWHM)
–or–
– Start and end points of the chromatographic peak, as determined by the peak
detection algorithm
–
• A set of tabbed main tables below the two graphical views
• A collapsed area for the related tables below the main tables

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Factory default layout for a result page

Figure 86 shows a result page for a result file generated with an untargeted processing
workflow.
Figure 86. Default layout for a result page from an untargeted workflow (LC studies), numbered at
the top left from 1 to 3 and from the bottom left from 4 to 7
1 2 3

4 5 6 7

No. Description No. Description

1 Result file tab 5 Opens the Field Chooser dialog box for the
current table
2 Chromatograms view with a collapsible pane at 6 Opens the related tables pane for the item that is
the left currently selected in the active main table
3 Mass Spectrum view with a spectrum tree at the 7 Main result tables
left
4 Opens the Select Visible Tables dialog box

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Modify the result page layout for ease of use

You can change the layout of a result file as follows:

• The views that you want to display and their location. See Chapter 9, “Graphical views
for a result file.”
• The main and related tables and table columns that you want to display and the order of
the table columns from left to right. See Chapter 8, “Review the analysis results,” “Show
or hide result tables,” and “Show or hide table columns.”
• The data (table rows) displayed or hidden in the result tables. See “Filter the data for data
reduction.”

For more information, see “Modify the result page layout for ease of use.”

Modify the result page layout for ease of use

The result file layout includes the relative positions of the graphical views, the visible result
tables, the column arrangement and column fixing if it is enabled, and the applied result
filters.

Tip For information about modifying the layout of the table columns and rows, see
Chapter 15, “Common operations for manipulating data tables.” This chapter describes
how to hide or display specific table columns by using the Field Chooser dialog box,
reorder or stack the table columns by using the mouse, and pin rows to the top of the
tables.

These topics describe some of the ways that you can change the layout of a tabbed result page:
• Float a result page view
• Enlarge a result page view
• Use the collapsible pane options for filtering, grouping, coloring, and discriminating by
• Show or hide result tables

Float a result page view

Y To change a docked view on a result page to a floating view

Do one of the following:

• Right-click the title bar of the view and choose Floating.
• Double-click the title bar of the view.
–or–
• Drag the view away from its docked position.

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Enlarge a result page view

Y To enlarge a floating view for a result page to fill the screen

Double-click the title bar of the view.

To restore the previous size of a floating window, double-click the title bar again.

Use the collapsible pane options for filtering, grouping, coloring, and
discriminating by
These four views on a result page include a collapsible pane of filtering, grouping, coloring, or
discriminating by options:
• Chromatograms view. See “Chromatograms view.”
• Trend Chart view. See “Trend Chart view.”
• Principal Component Analysis view. See “Principal Component Analysis view.”
• Partial Least Squares Discriminant Analysis. See “Partial Least Squares Discriminant
Analysis view.”
• Descriptive Statistics view. See “Descriptive Statistics view.”

Note If the analysis does not include samples with different study factor values or sample
types, the application cannot group the samples, and only the Files check box appears in
the Group By list.

Table 84 describes the effect of clearing and selecting the check boxes in the collapsible pane
at the left of a view.

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Table 84. Effect of clearing or selecting the check boxes in the collapsible pane
Objective Selection
Remove or display data Use the check boxes under Filter By to remove or display data
points points by sample type, study factor value, or individual file.

By default, the application selects all the check boxes under Filter
By for the Chromatograms view.

By default, the application does not select the Blank sample type
or the Quality Control sample type check boxes for the statistics
views, and the Identification Only sample type does not appear
in the Sample Type list.
Visually distinguish data For the Chromatograms view, use the check boxes under Group
points by grouping them By to colorize the traces by group. The application duplicates the
check boxes in the Study Variables area of the Grouping and
Ratios page of the analysis.

For the Trend Chart view, use the check boxes under Group By
to change how the data points for the selected compound are
grouped across the input files.
Distinguishing data For the Principal Component Analysis view, use the Color By
point by color check boxes to distinguish the principal components by color.
For the Descriptive Statistics view, use the Color By check boxes
to visually group the box plots by color.
Discriminate by specific For the Principal Least Squares–Discriminant Analysis view, use
study variables the Discriminate By check boxes to select the study variables for
the supervised analysis.

Table 85 describes the Group By and Filter By options in the collapsible pane.
Table 85. Options in the collapsible left pane (Sheet 1 of 2)
Feature Description
(X/Y) The left integer is the number of samples that are selected under
Filter By (and that also contain the selected compound). The right
integer is the number of samples that contain the selected
compound.
ON/OFF toggle for ON—The check boxes are available.
the Filter By items
OFF—The check boxes are unavailable and the items are not
filtered out.

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Table 85. Options in the collapsible left pane (Sheet 2 of 2)

Feature Description
Check boxes
Group By Study Selecting one or more of these check boxes groups the samples
Variable with the same value or values for the selected study variable or
variables and displays the groups in different colors.

By default, the application duplicates the selection in the Study

Variables pane on the Grouping and Ratios page of the analysis.
Study variables include the study factor values and the sample
types.
Group By Sample Selecting this check box displays the data points for the selected
samples in the Filter By area in different colors.

Default: Clear
Filter By Study Factor Select these check boxes to display data for one or more study
factors.

By default, the application selects all the study factors.

Filter By Sample Type Select these check boxes to display data for one or more sample
types.

For the Chromatograms view, the Filter By:

application selects all sample types ON Sample Type
by default.  Quality Control
 Sample
 Blank
 Identification Only

For the statistical views, the Filter By:

application excludes the ON Sample Type
Identification Only sample type  Sample
and clears the Blank sample type Quality Control
check box. Blank

Filter By File Select these check boxes to display data from one or more of the
files.

By default, the application selects all of the files.

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For more information about using the options on the collapsible pane, see these topics:
• Filter the result data by the study variable values
• Filter the result data by input file
• Group the result data by the study variables or by individual files

Filter the result data by the study variable values

You can filter the data points displayed in a result page view by selecting or clearing the check
boxes for the study variable values in the collapsible pane.

Y To filter data points by the study variable values

1. If the collapsible pane is closed, click the icon, , in the upper-left corner of the view.
2. Under Filter By, click the expand icon to the left of the study variable name to open the
values list.
3. Clear the check boxes for the items that you want to hide or values that you want to
remove from the statistical calculations.

Filter the result data by input file

You can filter the data points displayed in a result page view by selecting or clearing the check
boxes for the input files in the collapsible pane.

Y To filter the data by selected files

1. Under Filter By, click the expand icon to the left of File to open the File list.
2. Clear the check boxes for the files that you want to exclude from the display or the
statistical calculations.

Note By default, for the statistical views, the check box for the Blank sample type under
Filter By is clear.

Group the result data by the study variables or by individual files

You can group the data points displayed in a result page view by selecting or clearing the check
boxes under Group By in the collapsible pane.

Y To group the data points in a view

1. To group the data by the study variables or by the individual files, select a row in the
active result table. Then, select one or more check boxes under Group By.
2. To view a color legend of the sample groups, right-click the Chromatograms view and
choose Display Options > Show Legend.

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Show or hide result tables

The set of result tables in a result file depends on the processing workflow. By default, some of
the result tables are hidden.

Y To show or hide result tables

1. Open a result file. See “Open, close, and update result files.”
2. Click the Select Table Visibility icon, , to the left of the result table tabs.
The Select Visible Tables dialog box opens.
3. Select the check box that corresponds to the table that you want to show, or clear the
check box that corresponds to the table that you want to hide.
4. Click OK to accept the changes.

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Custom color-coded tags for result table entries

Custom color-coded tags for result table entries

In the result file tables that include the Tags column, you can label entries with color-coded
name tags, and then use these tags to sort and filter the tables. You can customize the number
of tags displayed (number of subcolumns in the Tags column), the tag names, and the tag
colors.
Figure 87. Tags column showing selected tags with the standard colors and text labels

For details, see the following topics:

• Define custom tags by using the Custom Tags Editor
• Add or remove custom tags
• Filter a result table by the custom tags
• Import or export custom tags

Define custom tags by using the Custom Tags Editor

Use the Custom Tags Editor to customize the number of available tags and the colors and text
labels for these color-coded tags in the Tags column of a result table.

By default, the Tags column contains five tags. From left to right, the subcolumn headings for
the tags are labeled A, B, C, D, and E, and the tag colors are set to blue, red, yellow, green, and
purple. You can change the number of tags to 0 or any integer value from 1 to 15 by selecting
or clearing the check boxes in the Custom Tags Editor.

Y To create a set of named and color-coded tags

1. Open a result file.

2. From the menu bar, choose View > Custom Tags Editor.

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Figure 88. Custom Tags Editor with the default settings

Default tags

3. (Optional) If you have created a stored custom tags file (.tags) and you want to edit it, do
the following:
a. Click Import and select the file that you want to edit.
b. In the Custom Tags Editor, select the number of tags that you want to display in the
Tags columns of the result tables in the current result file by selecting the check boxes.
4. To modify the colors and text labels for the tags, follow the instructions in Table 86.
You use the Color dialog box to modify the colors.
Figure 89. Color dialog box

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Table 86. Defining the tags for a result file

Task Procedure
Change the color of a tag 1. In the editor, click the color circle to the left of the
to a different standard name box.
color.
2. In the Color dialog box, select a color from the set of
basic colors and click OK.

Change the color of a tag 1. In the editor, click the color circle to the left of the
to a custom color. name box.
2. In the Color dialog box, click Define Custom Colors.
3. Define a custom color by using the color gradient or
entering the Red, Green, and Blue (RGB) values or the
Hue, Saturation, and Luminosity (HSL) values, and
then and click Add to Custom Colors.
4. Select the custom color and click OK.

The color of the selected tag in the Custom Tag Editor

changes to the selected color.
Change the text label for In the editor, select the current text in the text box, and
a tag. then enter your custom text label.

5. To apply the custom settings in the Custom Tags Editor dialog box to the tags in the
current result file, click Apply.
The Custom Tags Editor dialog box remains open until you close it.

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6. (Optional) To export the defined tags to an external file that you can use with any result
file, do the following:
a. Click Export.
The Save Custom Tags Editor Settings dialog box opens.
b. Name the file, select its storage location, and click Save.

Add or remove custom tags

The Tags column is available for most of the result tables in a result file. When the Tags
column is available, the shortcut menu (also known as a context or right-click menu) includes
the following commands: Add Tag, Remove Tag, Set Tags, Remove All Tags in All Tables.

Note For more information about the shortcut menus for result tables, see “Shortcut
menu commands for the result tables.”

Before you add tags to the result tables, define the names and colors of the tags. See “Define
custom tags by using the Custom Tags Editor.”
Table 87. Adding tags to and removing tags from items (Sheet 1 of 3)
Task Procedure
Add a tag to an item in the Click the circle for the tag in the Tags column for the
current result table. item.

Or, right-click the item in the result table, choose Add

Tag, and then select the tag that you want to add.
Remove a specific tag from an Click the circle for the tag in the Tags column.
item in the current result table.
Or, right-click the entry, choose Remove Tag, and then,
select the tag that you want to remove.
Remove all the tags from all the Right-click any result table that has a Tags column and
entries in all the result tables. choose Remove All Tags in All Tables. Then, click OK at
the prompt.
Note Use the Set Tags shortcut menu to remove selected tags from the following:
• Selected items in the current result table.
• Selected items in the current result table and all its subtables.
• All items in the current table.
• All items in the current result table and all its subtables.

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Table 87. Adding tags to and removing tags from items (Sheet 2 of 3)
Task Procedure
Remove specific tags from 1. Select the items (rows) of interest by using the
selected items in the current SHIFT key or the CTRL key.
result table.
2. Right-click a selected table row and choose Set Tags.
The Set Tags dialog box opens.
3. Double-click the tags that you want to remove.
The center of the selected tags turn gray.
4. Select the Selected Items option and the In This
Table option.
The following figure shows the settings for removing
tags 1 and 5 from the selected items (rows) in the
current result table.

5. Click Apply.
Remove specific tags from 1. Select the items (rows) of interest by using the
selected items in the current SHIFT key or the CTRL key.
result table and all the subtables
2. Right-click a selected table row and choose Set Tags.
for the selected items.
The Set Tags dialog box opens.
3. Select the tags that you want to remove.
The color of the selected tags turns to gray.
4. Select the Selected Items option and the In This and
All Subtables option.
5. Click Apply.

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Table 87. Adding tags to and removing tags from items (Sheet 3 of 3)
Task Procedure
Remove specific tags from all 1. Right-click a selected table row and choose Set Tags.
items in the current result table.
The Set Tags dialog box opens.
2. Select the tags that you want to remove.
The color of the selected tags turns to gray.
3. Select the All Items option and the In This Table
option.
4. Click Apply.
Remove specific tags from all 1. Right-click a selected table row and choose Set Tags.
items in the current result table
and all items in the subtables for The Set Tags dialog box opens.
the current result table. 2. Select the tags that you want to remove.
The color of the selected tags turns to gray.
3. Select the All Items option and the In This and all
Subtables option.
4. Click Apply.

Filter a result table by the custom tags

Use the Result Filters view to filter the result tables by the custom tags. For general
information about using the Result Filters view, see “Filter the data for data reduction.”
Figure 90. Result Filters view (right side) showing the filters for the Tags column

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Y To filter the result tables in a result file by the custom tags

1. Open the result file of interest.

2. If you have not already defined and applied custom tags, follow the instructions in these
topics:
• Define custom tags by using the Custom Tags Editor
• Add or remove custom tags
3. From the application menu bar, choose View > Result Filters.
4. On the left side of the Result Filters view, select the tables that you want to filter.
5. On the right side of the view, set up the filters for each table one-by-one.
6. To set up a single custom tags filter, select Tags, and then select the remaining filters as
follows:
• Is True or Has No Value > In Tag > Tag Name
• Is True or Has No Value > In Any Tag
• Is True or Has No Value > In Every Tag
7. To filter by multiple conditions, use the AND and OR conjunctions.
8. Click Apply Filters.

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Import or export custom tags

When you create a set of custom tags, you can export the tag definitions to a TAGS file or
import the tag definitions from a TAGS file to the current result file.

The Custom Tags Editor is not available until you open a result file.
Table 88. Importing or exporting custom tags
Task Procedure
Export custom tags to a TAGS 1. Open the result file that includes the definitions that
file you want to export. Or, open any result file.
2. From the application menu bar, choose View >
Custom Tags Editor.
The Custom Tags Editor opens.
3. Define the tags if you have not already done so.
4. Click Export.
The Save Custom Tags Editor Settings dialog box
opens.
5. Name the file, select where you want to store the file,
and click Save.
Import custom tags from a 1. Open the result file of interest.
TAGS file
2. From the application menu bar, choose View >
Custom Tags Editor.
The Custom Tags Editor opens.
3. Click Import.
The Load Custom Tags Editor Settings dialog box
opens.
4. Browse to and select the TAGS file of interest. Then,
click Open.

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Save, restore, and manage layouts

Save, restore, and manage layouts

The layout of the result file includes the location of the graphical views, the result tables that
you want to display, the columns and rows that you want to display in the result tables, the
filter set, the custom annotations, and the Group By and Filter By settings.

In addition to the factory default layout, the application comes with the following custom
layouts for LC studies:
• Stable Isotope Labeling—Opens the Isotopologues Distribution Chart, the Trend Chart,
and the Metabolika Pathways view in the bottom right of the result page. In the
Compounds table, hides the following columns: #Metabolika Pathways, Avg. Exchange,
FISh Coverage, and Metabolika Pathways. Opens the Labeled Compounds per File table
that is related to the currently selected compound in the main Compounds table.
• Statistics—Opens the Differential Analysis and Trend Chart views on the bottom left and
the Principal Component Analysis, Partial Least Squares Discriminant Analysis, and
Hierarchical Cluster Analysis views on the bottom right. Closes the Chromatograms and
Mass Spectrum views. Closes the search and pathway result tables if they are visible.

For details about working with layouts, see the following topics:
• Save the current layout of a result file
• Reset the layout to the factory defaults
• Create a custom layout
• Apply a layout
• Manage the layouts

Save the current layout of a result file

After you modify the layout of a result file, you can save the current layout so that when you
reopen the result file, it opens to the current layout.

Y To save the current layout of a result file

With the result file selected as the active page, do one of the following:
• In the toolbar, click the Save the Currently Active Item icon, .
• From the menu bar, choose File > Save.

Reset the layout to the factory defaults

After you modify the layout of a result file, you can quickly restore the default layout.

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Y To reset the layout to the factory default settings

With the result file selected as the active page, choose Window > Reset Layout from the
menu bar.
The application closes the result file, and then reopens the result file to the factory default
layout.

Create a custom layout

If you frequently modify the layout of your result files, you might want to create a custom
layout with the result tables, result table columns, and views that you prefer to display.

Y To create a custom layout for a result file

1. Open a result file and modify its layout.

For details, see these topics:
• Open, close, and update result files
• Modify the result page layout for ease of use
2. From the menu bar, choose Window > Save Layout.
The Save Result Layout dialog box opens.

3. Name the layout and click OK.

Apply a layout
A layout determines which of the available result tables and graphical views appear as well as
where they appear in the application window when you open a result file.

Y To apply a layout

1. With the result file selected as the active page, choose Window > Apply Layout from the
menu bar.
2. Select a layout from the list or use the hot keys.

IMPORTANT The custom layouts—Statistics and Stable Isotope Labeling—are designed

for LC studies that include statistical analysis results or stable isotope labeling results,
respectively.

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Edit compound annotations

Manage the layouts

Use the Manage Result File Layouts dialog box to specify manage the list of layouts that
appear in the Window > Apply Layouts list. From this dialog box, you can delete or rename
each layout or specify the default layout.

Y To manage the layouts

1. From the menu bar, choose Window > Manage Layouts.

The Manage Result File Layouts dialog box opens. The list order corresponds to the hot
keys in the Apply Layout list. For example, for this list, the hot key combination for the
Statistics layout is CTRL+ALT+1.
Figure 91. Manage Result File Layouts dialog box

Use these buttons to change the order

of the layouts.

Changing the order changes the

associated hot keys. The first 10 layouts
in the list have associated hot keys.

2. Do the following as applicable:

• To delete a layout, select it and click Delete.
• To rename a layout, select it and click Rename. Then, in the Rename Result Layout
dialog box, rename the layout and click OK.
• To make the layout the default layout, select it and click As Default.
• To change the list order, select a layout, and use the Up/Down buttons, , to move
the layout up or down in the list.

Edit compound annotations

Annotations include the compound name, formula, annotation source, FISh coverage score,
and structure.

Use the Compound Annotation Editor dialog box to edit the annotations for compounds of
interest in the compounds table (Compounds table or Expected Compounds table) and the
Structure Proposals table.

Saving a custom annotation overwrites the original processing results.

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Edit compound annotations

Y To edit a compound annotation

1. Double-click the row of interest in the compounds table or related Structure Proposals
table.
The Compound Annotation Editor dialog box opens.
The application automatically populates the Molecular Weight/Error in Da and
Molecular Weight to Fit boxes. If the formula, structure, and name are available, the
application also populates these fields.
Figure 92. Compound Annotation Editor dialog box

Open
(structure file)
Save
(structure file)
Drawing area

The application
populates these
boxes as you draw
the structure.

Opens the ChemSpider Search dialog box.

2. To add a structure to the drawing area, do any of the following:

• Use the structure drawing tools. See “Structure drawing tools and commands.”
• Open a structure file. See “Load a structure from a structure file.”
• Run a ChemSpider search and select one of the hits. See “Find a structure in the
ChemSpider database.”
3. Click Save to save your custom annotations in the result file.

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Edit compound annotations

Table 89 describes the parameters in the Compound Annotation Editor dialog box.
Table 89. Compound Annotation Editor parameters
Parameter Description
Description page
Formula Displays the elemental formula of the structure in the drawing
area or the assigned formula.
Formula to Fit Displays the elemental formula of the component found by the
Find Expected Compounds node in a targeted analysis for an LC
study.
Molecular Displays the molecular weight (MW) of the structure in the
Weight/Error in Da drawing area and the difference between the structure’s calculated
MW and the MW for the selected compound—that is, the MW
in the Molecular Weight to Fit box.
Molecular Weight to Displays the molecular weight (based on the formula) of the
Fit compound selected in the Compounds table or the Expected
Compounds table.
Name Displays the name of the compound from an online or local
database search.

To change the name, type alphanumeric text in this box.

Buttons and check box at the bottom of the dialog box
ChemSpider Opens the ChemSpider Search dialog box for searching the
ChemSpider database.
Apply FISh Scoring Select this check box and click Save to run the FISh Scoring
algorithm.
Save Saves the changes.
Cancel Cancels the changes and closes the dialog box.
FISh Scoring page

See “Apply FISh scoring.”

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Add or delete proposed structures for a compound

Add or delete proposed structures for a compound

In a result file, every compound in the compounds table (Compounds table or Expected
Compounds table for an LC study) has a related Structure Proposals table.

For details about adding or deleting proposed structures for a compound, see the following
topics:
• Add structure proposals
• Delete structure proposals

Add structure proposals

Y To add a structure proposal to a Structure Proposals table

1. Select a compound in the main compounds table (Compounds table or Expected

Compounds table).
2. Click Show Related Tables below the compounds table.
3. Do one of the following:
a. Click the Structure Proposals tab.
b. Right-click anywhere below the Structure Proposals tab and choose Structure
Proposals > Add Structure Proposal.
–or–
a. Open any of the search results tables for the selected compound.
b. Right-click the entry of interest in the search results table and choose Add to
Structure Proposals.
4. Edit the structure proposal by following the instructions in “Edit compound
annotations.”

Delete structure proposals

In a result file, the Structure Proposals table is a related table for the compound selected in the
main compounds table (Expected Compounds table or Compounds table).

Y To delete a structure proposal from a Structure Proposals table

1. Select the compound of interest in the main compounds table.

2. Click Show Related Tables at the bottom left of the result page.
3. Click the Structure Proposals tab.
4. Right-click the entry and choose Structure Proposals > Delete Structure Proposal.

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Replace an annotation with a structure proposal

Replace an annotation with a structure proposal

In a result file, annotations include the name, formula, annotation source, FISh coverage
score, and structure for a compound.

Y To replace the annotations for a compound in the main compounds table

1. Select the compound of interest in the main compounds table (Expected Compounds
table or Compounds table).
2. Click Show Related Tables at the bottom left of the result page.
3. Do one of the following:
• Click the Structure Proposals tab. Then, right-click a row in the Structured Proposals
table and choose Structure Proposals > Use As Compound Annotation.
• Open any of the related results tables, right-click the entry of interest and choose Use
as Compound Annotation.

Apply FISh scoring

You can apply FISh scoring to a selected entry in the compounds table (Expected Compounds
table or Compounds table) or the entries in the following compound-related search result
tables: Structure Proposals, mzCloud Results, mzVault Results, Mass List Search Results,
BioCyc Results, Metabolika Results, and ChemSpider Results. You can also apply FISh
scoring from the Compound Annotation Editor dialog box.

The FISh scoring algorithm uses the structure in the structure column of the result table or
the drawing area of the Compound Annotation Editor dialog box. The selected entry in the
compounds table must have MS2 data (check the indicator in the MS2 column).

For details about running the FISh scoring algorithm, see the following topics:
• Apply FISh scoring by using a shortcut menu command
• Apply FISh Scoring from the Compound Annotation Editor dialog box
• Specify the FISh scoring parameter settings

Apply FISh scoring by using a shortcut menu command

You can apply FISh scoring to a compound that has a structure and MS2 data from the
compounds table, the related Structure Proposals table for the compound, or a related results
table for the compound.

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Apply FISh scoring

Y To apply FISh Scoring from a result table

1. Make sure that the entries of interest include structures.

2. To open the Specify FISh Scoring Settings dialog box (Figure 93), do one of the
following:
• To submit a compound, right-click the selection and choose Apply FISh Scoring.
• To submit a single selection in a Structure Proposals table, right-click the selection
and choose Structure Proposals > Apply FISh Scoring to Selection.
• To submit all of the entries in a Structure Proposals table, right-click the table and
choose Structure Proposals > Apply FISh Scoring to All.
• To submit an entry in a related search result table, right-click the table and choose
Add to Structure Proposals and Apply FISh Scoring.
Figure 93. Specify FISh Scoring Settings dialog box

3. Set up the parameters. See “Specify the FISh scoring parameter settings.”
4. Click OK.
In the FISh Scoring Queue view to the left of the table, one job appears for each selected
entry. For each entry that includes a structure, the application runs the FISh scoring
algorithm. The run time increases as the complexity of the structure increases. When an
entry does not include a structure, the job ends in failure and is highlighted with a red
border.

Apply FISh Scoring from the Compound Annotation Editor dialog box
Y To apply FISh Scoring from the Compound Annotation Editor dialog box

1. To open the FISh Scoring page of the Compound Annotations dialog box, right-click an
entry in the compounds table and choose Edit Compound Annotation.
2. Make sure that the drawing area on the Description page includes a structure.
3. Click the FISh Scoring tab.
4. Select the Apply FISh Scoring check box.

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Apply FISh scoring

Figure 94. FISh Scoring page of the Compound Annotation Editor dialog box

5. Specify the parameter settings. See “Specify the FISh scoring parameter settings.”
6. Click Save.

Specify the FISh scoring parameter settings

Y To set up the FISh scoring parameters

1. In the Specify FISh Scoring Settings dialog box or on the FISh Scoring page of the
Compound Annotation Editor dialog box, make the following selections:
• To annotate the full spectrum tree, select the Annotate Full Spectrum Tree check
box.
• To use the general fragmentation rules, select the Use General Rules check box.
• To use the fragmentation libraries, select the Use Fragmentation Libraries check
box.

Tip If time allows, select the Use Fragmentation Libraries check box. Using the
fragmentation libraries provides significantly more structural information;
however, it can also add a significant amount of processing time.

• To allow aromatic cleavage as one of the fragmentation steps, select the Allow
Aromatic Cleavage check box.
• In the Max. Depth list, select the maximum number of steps allowed in the
fragmentation pathway.
2. Use the default values or type new values in the following boxes:
• For the FTMS scans, type a value in the High Accuracy Mass Tolerance box and
select the appropriate units.
• For the ITMS scans, type a value in the Low Accuracy Mass Tolerance box and select
the appropriate units.
• In the S/N Threshold box, type a value for the FTMS scans.

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Filter the data for data reduction

Table 90 describes the parameter settings for the FISh scoring algorithm.
Table 90. FISh scoring parameters
Parameter Description
Annotate Full Annotates the full spectrum tree (MS/MS, MS3, and so on) in the
Spectrum Tree Mass Spectrum view.
Use General Rules Uses the general fragmentation rules.
Use Fragmentation Uses the fragmentation libraries.
Libraries
Allow Aromatic Allows aromatic cleavage as one of the reaction steps.
Cleavage
Max. Depth Specifies the maximum number of fragmentation reactions to
consider in the fragmentation pathway.

Default: 5; range: 1–20

High Accuracy mass Specifies the mass tolerance for FTMS data.
tolerance and units
Default: 2.5 mmu
Low Accuracy Mass Specifies the mass tolerance for ITMS data.
Tolerance and units
Default: 0.5 Da
S/N Threshold Specifies the signal-to-noise threshold for FTMS data. The FT
mass analyzer calculates the S/N level for each centroid.

Filter the data for data reduction

To show only the most pertinent data, use the Result Filters view to apply filters to the
processed data. By default, the left pane of the Result Filters view lists the main tables in the
current result file. The right pane displays the filters for the table that you select in the left
pane.
Figure 95. Result Filters view with an empty filter for the Compounds table (LC study)

Adds the visible related tables to

the result filters list.

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Filter the data for data reduction

Note The filters for each table are independent of other table filters. For example, a
retention time filter for the Merged Features table does not affect the entries in the other
tables that include a retention time column. In addition, filtering only removes rows from
the display; it does not update or change any of the calculated values.

To set up and apply the data reduction filters, see these topics:
• Set up, apply, and save filter sets
• Create a result filter with an AND logical conjunction
• Create a result filter with an OR logical conjunction
• Create a result filter with both of the logical conjunctions
• Load a saved filter set
• Result Filters view parameters

Components of a result table filter

You can filter each result table in a result file by one or more filters. Each filter consists of the
property (table column in blue) and one or more operators or conditions (in pink). In
addition, some filters take one or more values (in green) and a final data entry value or input
file name.
Result table

Value
Table Operator
column

Property

Specifies a column in the selected result table. The dropdown list contains all the columns in
the selected result table.

The columns in a result table contain the following types of entries:

• Numeric (value)
• Alphanumeric (text)
• Status (for example, color indicators)
• Condition (for example, the check boxes in the Checked column and the tags in the Tags
column) entries

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One or more operators or conditions

After you select the result column to filter, you select the operator to filter by. Some filters are
single operators and some filters require multiple operators. The available operators depend
on the type of data that you are filtering: numeric values, alphanumeric text, indicators, or
conditions.

When you set up filters with multiple operators, not all combinations of the operators make
sense. For example, for the Gap Status column of a main compounds table, you can set up the
following filter: Gap status > Has No Value > In Every File Holding a Value. This filter hides
every compound in the table.

Value

Filters for numeric columns with numeric values— for example, the RT column—end with a
text box for entering the numeric value or a selection list of the input files.

Filters for columns with alphanumeric strings—for example, the Name column—end with a
text box for entering the string.

Set up, apply, and save filter sets

This topic describes how to set up, apply, and save a set of result filters (FILTERSET) for the
result tables in a result file.

Y To set up, apply, and save a filter set

1. Open a result file.

2. From the application menu bar, choose View > Result Filters.
The Result Filters view opens as a floating window or as a docked view and displays the
filter tree for the current table.
Each table has its own set of filter conditions.
3. (Optional) To display a filter tree that includes all the visible result tables in the result file,
select the Show All Tables check box.

Note To change which tables are visible, use the Select Visible Tables dialog box.

4. In the Result Filters view, select the table of interest in the left pane.
The table name appears in the right pane. The following selection tree appears below the
table name.
Table Name
AND Add group

Add property Click to open a dropdown list of table columns.

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Filter the data for data reduction

5. Click Add Property.

A list that begins with the AND and OR logic selections followed by the columns in the
selected table appears.
6. Select the table column (property) that you want to filter by.
7. Do any of the following:
• For the Checked property, select a condition.
This figure shows the condition list for the Checked property.

Condition list
Selected
property

• For a numeric-value property, such as retention time (RT), select an operator

(mathematical relationship) and type a value in the adjacent box, if applicable.

Tip When you select the Is Equal To operator, type a numeric value to a
minimum precision of two decimal places or a minimum precision that is equal
to the number of decimal places that are displayed in the column, whichever is
greater. For example, for any of the Area columns, type a numeric value with two
decimal places, even though the Area column displays a numeric value with no
decimal places.

This figure shows the operator list for numeric properties.

Operator list
Value box
Selected
property

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Filter the data for data reduction

This figure shows a set of filter conditions that limits the displayed results to
chromatographic peaks from 2 to 7 minutes.

• For a non-numeric property (alphanumeric string), such as Name, select a condition

and type a value in the value box if applicable.
This figure shows the condition list for non-numeric properties.

Condition list
Value box

• For a status property, such as Gap Status, select one or more conditions and values as
applicable. For a multiple condition filter, not all combinations make sense. Clicking
Remove at the end of a filter removes the individual filter.
This figure shows a filter for the Gap Status column.

8. Do any of the following:

• To apply the filters in the current filter set, click Apply Filters.
• To save a filter to a FILTERSET file, click Save or Save As. Then, browse to the
location where you want to store the file, name the file, and click Save.
• To turn off the filters for a specific table, click ON to the left of the table name in the
left pane of the Result Filters view.

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Filter the data for data reduction

The indicator icon to the left of the table name turns from green to yellow, and the
button displays OFF.

These two filters are off.

• To clear the filters for a specific table, select the table in the left pane of the Result
Filters view. Then, click Clear.
• To clear all the filters in a filter set, click Clear All.

Create a result filter with an AND logical conjunction

This topic describes how to use the AND logical conjunction in a result filter.

Y To create a filter set using the AND logical conjunction

Note When you use the AND logical conjunction, all of the connected property
conditions must be True.

1. In the Result Filter view, keep the AND logical conjunction as the first item in the filter
tree.
2. For each property that you want to conjoin with the AND conjunction, click Add
Property, select a property from the list, and set the property boundaries.
This figure shows a filter set that uses three properties conjoined with an AND
conjunction. When you apply this filter set to the data in a compounds table, only those
rows that meet all three conditions remain; that is, you see only those detected
chromatographic peaks with a retention time greater than 3.00 minutes, with an
integrated peak area greater than 1 000 000, and where the compound has
data-dependent scans for the preferred ion.

Three properties
connected to an
AND conjunction

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Filter the data for data reduction

Create a result filter with an OR logical conjunction

This topic describes how to use the OR logical conjunction in a result filter.

Y To create a filter set using the OR logical conjunction

Note When you use the OR logical conjunction, only one of the connected property
conditions must be True.

1. Select the OR logical conjunction as the first item in the filter tree.
2. For each property that you want to conjoin with the OR conjunction, click Add
Property, select a property from the list, and set up the property conditions.
This figure shows a filter set that uses two properties conjoined with an OR conjunction.
When you apply this filter set to the data in the result table, those rows that meet at least
one of the conditions remain—that is, you see the rows where the FISh coverage value is
greater than or equal to 30 or where the FISh coverage column has no reported value.

Two properties
connected to an
OR conjunction

Create a result filter with both of the logical conjunctions

This topic describes how to use both of the logical conjunctions in a result filter.

Y To create a filter set using both the AND and the OR logical conjunctions

1. Keep the AND logical conjunction as the first item in the filter tree.
2. To conjoin two properties with the OR conjunction, do the following:
a. Click Add Property and select OR from the dropdown list.

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Filter the data for data reduction

b. Set up the properties that you want to conjoin with the OR conjunction.
This example shows the condition where the FISh Coverage must be greater than or
equal to 30 or have no value. (For LC studies, the FISh scoring algorithm does not
calculate scores for DIA scans.)

Add Property list Add Property list

that connects to the that connects to the
AND conjunction OR conjunction

3. For each property that you want to conjoin with the AND conjunction, click the Add
Property list that connects to the AND conjunction, select a property from the list, and
set up the property boundaries.
Figure 96 shows a result filter that keeps chromatographic peaks that meet the following
conditions:
• A FISh Coverage score that meets one of these conditions:
– A FISh Coverage score that is greater than or equal to 30
–or–
– No FISh Coverage score
–and–
• A Retention Time from 4 to 7 minutes
Figure 96. Filter that uses both AND and OR conjunctions

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Filter the data for data reduction

Load a saved filter set

This topic describes how to load the filters from a FILTERSET file.

Y To load a saved filter set

1. In the Result Filters view, click Load.

The Load Filter Set dialog box opens.
2. Browse to the appropriate folder and select the filter set of interest.
3. Click Open.
If the filter set contains filter conditions for tables that are not in the current result file,
the application automatically hides the unused filters. You can modify the filter
conditions for the applicable tables only.

Result Filters view parameters

Use the Result Filters view to create data reduction filters for the tables in a result file. The
Result Filters view is a floating window that can remain open while you work in other areas of
the application.

Table 91 describes the panes, buttons, icons, and check box in the Result Filters view.
Table 91. Result Filters panes and buttons (Sheet 1 of 2)
Feature Description
Left pane Lists the main tables included in the current result file. An On/Off
button and an indicator icon appear to the left of the table name.
ON/OFF button Use to turn on or turn off the conditions for the associated main
table.
Indicator icons ( ) Gray—Indicates that the table is unfiltered.

( ) Green—Indicates that a filter has been applied to the table.

( ) Yellow—Indicates that the table filter is off.

Right pane

Displays the filter settings for the selected table. You can modify these settings as described
in “Set up, apply, and save filter sets.”
AND or OR Specifies the logical connection between properties or groups.
Add Group Adds a group.
Add Property Adds a property.

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View the result summaries

Table 91. Result Filters panes and buttons (Sheet 2 of 2)

Feature Description
Check box
Show All Tables Selecting this check box adds the related tables to the table list.
Buttons
Load Opens the Load Filter Set dialog box where you can select a saved
filter set and open it.
Save If a saved filter set is open, clicking Save overwrites the original
settings in the file with the current filters in the Result Filters window.
Save As Opens the Save Filter dialog box where you can name the file and
select a folder for a FILTERSET file.
Clear All Clears all the filters for the current filter set.
Clear Clears the current filter.
Apply Filters Applies all the filters for the current filter set.

View the result summaries

In the Summaries view on a result page, you can view the following summaries:
• Workflow summary
• Processing Messages summary
• Filter summary
• Study summary
• Grouping & Ratios summary

Y To open the Summaries view

1. Open the result file of interest. See “Open, close, and update result files.”
2. From the menu bar, choose View > Result Summary.
The Summaries view includes these five pages: Workflow, Processing Messages, Filter,
Study, and Grouping & Ratios.

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View the result summaries

Figure 97. Summaries view

Workflow summary
To view the processing workflow that the analysis used to create the active result file, open the
Workflow page. This page lists the name of the processing workflow, the creation date for the
result file (.cdResult), the raw data files (.raw) that were processed to create the result file, and
the parameter settings for the workflow nodes.

For information about creating a processing workflow, see Chapter 6, “Create and edit
processing workflows.”

Processing Messages summary

To view a summary of the processing steps that the analysis used to create the active result file,
open the Processing Messages page.

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View the result summaries

Filter summary
To view a summary of the filters used to reduce the data in the results window, open the Filter
page. This page lists the name of the latest filter set (FILTERSET file type) that you applied to
the result file and the filter conditions in the filter set. Use the Result Filters view to create
filter sets. See “Filter the data for data reduction.”

Study summary
To view a summary of the study settings for the input files that make up the result file, open
the Study page. This page lists the following:
• Name and creation date of the study
• Directory location of the study
• Study factors and their values
• Sample names (Xcalibur RAW files) and their directory location

Grouping & Ratios summary

To view a summary of the sample groups and ratios for the analysis, open the Grouping &
Ratios page.

Figure 98 shows an example summary of the sample groups and ratios for an analysis. The
summary lists the selected study variables, sample groups, and ratios in order from top to
bottom.

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Shortcut menu commands for the result tables

Figure 98. Grouping & Ratios Summary page

Shortcut menu commands for the result tables

To access the shortcut menu commands for a result table, right-click the result table.

Note Shortcut menus are also known as context menus or right-click menus.

For information about the shortcut menus for the result tables on a result page, see these
tables:
• Table 92 describes the commands in the shortcut menus for the result tables in either type
of study.
• Table 93 describes the shortcut menu commands that are specific to LC studies.

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Shortcut menu commands for the result tables

Table 92. Shortcut menu commands for the result tables (Sheet 1 of 4)
Command Description
All main and related result tables
Copy With Headers Copies the current table row and its associated column
headings to the Clipboard.
Copy Copies the current table row to the Clipboard. Does not
copy the column headings.

See “Copy table entries to the clipboard.”

Clear Selection Undoes any row selections. Clears the Chromatograms view,
the Mass Spectrum view, or both of these views if they are
populated with data.
Cell Selection Mode Turns on the cell selection mode. When the Cell Selection
Mode is on, you cannot sort the table columns.
Enable Column Fixing or Turns on the column pins. Pinning (or freezing) a column
Disable Column Fixing moves it to the left of the Checked column.

See “Freeze table columns.”

Export > As Plain Text Exports the data to a comma-separated values file.

See “Export the result table contents to a text file.”

Export > As Excel Exports the data to an Excel™ spreadsheet file.

See “Export the result table contents to a spreadsheet.”

All result tables with a Structure column

You can copy the structures in the following tables to the Clipboard:
• For LC studies only: Compounds and Expected Compounds
• For either study type: BioCyc Results, mzCloud Results, mzVault Results, ChemSpider
Results, Mass List Search Results, Metabolika Results, and Structure Proposals
Copy Structure > As MOL Copies the selected structure in MOL format to the
Clipboard.
Copy Structure > As InCHI Copies the selected structure in InCHI format to the
Clipboard.
Copy Structure > As InCHI Copies the selected structure in InCHI Key format to the
Key Clipboard.
All related tables with a Structure column
Use as Compound Uses the annotations in the selected entry for the related
Annotation compound in the main compounds table (Expected
Compounds table or Compounds table).

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Shortcut menu commands for the result tables

Table 92. Shortcut menu commands for the result tables (Sheet 2 of 4)
Command Description
Add to Structure Proposals Add the selected entry to the Structure Proposals table for the
related compound in the main compounds table (Expected
Compounds table or Compounds table).
Add to Structure Proposals Add the selected entry to the Structure Proposals table for the
and Apply FISh Scoring related compound in the main compounds table (Expected
Compounds table or Compounds table) and runs the FISh
scoring algorithm.
All result tables with a Tags column

See “Add or remove custom tags.”

Add Tag Adds the selected tag to the current row.
Remove Tag Removes the selected tag for the current row.
Set Tags Opens the Set Tags dialog box where you can add tags to
multiple entries, all the entries in the current table, or all the
entries in the current table and all its subtables.
Remove All Tags in All Clears all the tags in all the result tables in the current result
Tables file.
All result tables with a Checked column
Check Selected Places a check in the selected row’s check box.
Check All Selects the check boxes for all of the table rows.
Uncheck Selected Clears the check box for the selected row.
Uncheck All Clears the check boxes for all of the table rows.
Remove All Checkmarks in Clears the check boxes in all the result tables.
All Tables
All result tables with expanding table headings
Expand All Column Expands the collapsed column headings.
Headers
Collapse All Column Collapses the expanded column headings.
Headers
Compounds table and Expected Compounds table
Edit Compound Annotation Opens the Compound Annotation Editor where you can
name the compound, add a structure that matches the
formula and molecular weight, run a ChemSpider search,
and apply the FISh Scoring algorithm. If the table does not
already include the Name and FISh Coverage columns, adds
these columns.

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Shortcut menu commands for the result tables

Table 92. Shortcut menu commands for the result tables (Sheet 3 of 4)
Command Description
Clear Compound Removes the annotation, which includes the structure, name,
Annotation formula, annotation source, and FISh coverage score if
applied.
Apply FISh Scoring Applies the FISh scoring algorithm to the selected entries and
populates the FISh Coverage column with the calculated
score.
Compounds table only
Molecular Networks > Send Opens the molecular networking viewer in a web browser.
to Viewer See “Modify the simulation in the molecular networks
viewer.”

The Generate Molecular Networks node adds this command

to the shortcut menu for the result table.
Molecular Networks > Mark If the Clipboard contains information from nodes (RT and
Selected > tag selection MW for each node copied to the Clipboard) in the
Molecular Network viewer, this command marks the
matching compounds in the result table with the selected tag.
Structure Proposals table
Structure Proposals > Add Adds a new row to the Structure Proposals table that includes
Structure Proposal the formula and molecular weight from the selected row in
the main Compounds or Expected Compounds table. See
“Add structure proposals.”

You can type a name in the Name column and a description

in the Comments column. Double-click the new row to
open the Compounds Annotation Editor where you can
draw the compound’s structure, open a structure file, or run a
ChemSpider search.
Structure Proposals > Edit Opens the Compound Annotation Editor where you can
Structure Proposal name the compound, add a structure that matches the
formula and molecular weight, run a ChemSpider search,
and apply the FISh Scoring algorithm.
Structure Proposals > Delete Removes the selected row from the Structure Proposals table.
Structure Proposal See “Delete structure proposals.”
Structure Proposals > Use as Replaces the annotations in the selected row of the main
Compound Annotation compounds table with the annotations in the current row of
the Structure Proposals table.

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Shortcut menu commands for the result tables

Table 92. Shortcut menu commands for the result tables (Sheet 4 of 4)
Command Description
Structure Proposals > Apply Opens a dialog box where you can specify the settings for the
FISh Scoring to Selected FISh scoring algorithm and submit the information in the
selected row. See “Apply FISh scoring.”

To apply FISh scoring, the selected row in the Structure

Proposals table must include a formula or a structure.
Structure Proposals > Apply Opens a dialog box where you can specify the settings for the
FISh Scoring to All FISh scoring algorithm and submit all the rows in the
Structure Proposals table.
All related tables that have a corresponding main table
Go to Same Item in Main Opens the main table with the same name as the related table
Table and selects the corresponding table row in the main table.

Table 93. Shortcut menu commands found only in LC studies (Sheet 1 of 2)

Command Description
Compounds table and Expected Compounds table
Export > As Xcalibur Exports information about all of the compounds in the table
Inclusion/Exclusion List or only the selected compounds in the table to a text file in
the format required for the selected mass spectrometer. The
information includes the m/z value of the monoisotopic ion
and the start and stop times for the chromatographic peak.

See “Export an Xcalibur inclusion or exclusion list from a

compounds table.”
Export > Add Compound to Exports a selected compound to an existing mzVault library.
Existing mzVault Library See “Add a compound to an existing mzVault library.”
Export > As mzVault Library Exports the selected compounds to a new mzVault library.
See “Create a new mzVault library.”
Compounds table
Export > As TraceFinder List Exports information about all of the compounds, only the
named compounds, or only the checked compounds in the
table to a CSV file in a format appropriate for the
TraceFinder application. See “Export the contents of the
Compounds table to TraceFinder.”
Export > As Mass List Exports the selected items to a new mass list. See “Export
compounds from the Compounds table to a new mass list.”
Add Selected Compounds to Adds the selected compounds to the specified mass list. See
Existing Mass List “Export compounds from the Compounds table to an
existing mass list.”

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Export the tabular data in a result file to an external file

Table 93. Shortcut menu commands found only in LC studies (Sheet 2 of 2)

Command Description
Expected Compounds table
Reset Compound Resets the annotations of the selected entries to the original
Annotation data processing results.

Export the tabular data in a result file to an external file

These topics describe how to export the contents of a result table to an external file:
• Shortcut menu commands for the result tables
• Export the result table contents to a spreadsheet
• Export the result table contents to a text file
• Export an Xcalibur inclusion or exclusion list from a compounds table
• Export the contents of the Compounds table to TraceFinder
• Export spectral data to a new or existing mzVault library

Export the result table contents to a spreadsheet

Use the Export > As Excel command to export result table items to a spreadsheet application.

You can export the contents of any of the result tables to a spreadsheet file. When you open
the Export to Excel dialog box from any of the main tables, the Level 1 selection in the dialog
box defaults to the active result table. When you open the Export to Excel dialog box from
any of the related tables, the Level 1 selection defaults to the main compounds table, which
depends on the processing workflow.

For LC studies, the main compounds table is the Compounds table when the processing
workflow includes the Detect Compounds node or the Detect Compounds node and the
Expected Compounds node. When the processing workflow includes only the Expected
Compounds node, the compounds table is the Expected Compounds table.

Y To export the contents of a result table to a spreadsheet file

1. Right-click the result table that you want to export and choose Export > As Excel.
The Export to Excel dialog box opens.
The default storage path is C:\Users\Public\Documents\result file name.

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Export the tabular data in a result file to an external file

The default selection in the Level 1 box depends on where you opened the dialog box:
• If you opened the dialog box from a main table, the default selection in the Level 1
box is the name of the active result table.
• If you opened the dialog box from a related table, the selection in the Level 1 box is a
main compounds table.
Figure 99. Export to Excel dialog box with the Compounds table selected

2. Make the appropriate selections in the Export to Excel dialog box as follows:
If you open the Export to Excel dialog box from a main table, the Level 1 selection is the
table where you opened the dialog box. If you open the Export to Excel dialog box from a
related table, the Level 1 selection is a main compounds table.
You can modify the export options in any order.
Table 94. Export options (Sheet 1 of 2)
Export option Procedure
Change the directory folder, Click the browse icon, , next to the Path box. Then,
the file name, or both. select a directory folder and rename the file as
appropriate, select the spreadsheet type (XLS or
Microsoft Excel File), and click Save.
Select the result tables to If necessary, select a different result table from the Level
export. 1 list. Then, as appropriate, select an available table from
the Level 2 list, followed by an available table from the
Level 3 list.

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Export the tabular data in a result file to an external file

Table 94. Export options (Sheet 2 of 2)

Export option Procedure
In the Options area, select Select one of these options:
which items you want to
export. All Items—Exports all the visible table rows in all the
selected tables.

Selected in This Table and All Subtables—Exports all

the visible table rows in the main table where the check
box in the Checked column is selected.

Selected in This Table—Exports all the visible table rows

in the main table and all the visible table rows in the
selected related tables where the check box in the Check
column is selected.
In the Options area, select If you want the spreadsheet file to open in a spreadsheet
whether you want the application after you click Export, select the Open File
spreadsheet file to open after After Export check box.
you click Export.

3. Click Export to export the data to a spreadsheet.

When the export is complete, a confirmation prompt appears with the name and location
of the file.
4. At the prompt, click OK.

Export the result table contents to a text file

You can export the contents of any of the result tables to a text file.

Y To export the contents of a result table to a text file

1. Right-click the result table that you want to export and choose Export > As Plain Text.
The Export to CSV File dialog box opens. The File Name box displays the name of the
selected result table.
2. Select the folder where you want to store the file, name the file as necessary, and click
Save.
The text file (CSV) appears in the selected folder.

Export an Xcalibur inclusion or exclusion list from a compounds table

You can export the contents of the Compounds table or the Expected Compounds table to an
Xcalibur Inclusion/Exclusion list and then import this list into an instrument method that
controls your Thermo Scientific mass spectrometer.

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Export the tabular data in a result file to an external file

Y To export an Xcalibur inclusion or exclusion list

1. Right-click the Compounds table or the Expected Compounds table and choose Export
> As Xcalibur Inclusion/Exclusion List.
The Export Xcalibur Inclusion/Exclusion List dialog box opens.
Figure 100. Export Xcalibur Inclusion/Exclusion List dialog box

2. Make the appropriate selections and entries (Table 95).

3. Click Export.
The application attempts to save the text file to the specified location. If the file name
conflicts with an existing file, a confirmation message appears. In the absence of a
conflicting file, a completion message appears indicating that the exported file is in the
selected folder.
4. If a confirmation message appears, do one of the following:
• To overwrite the existing file, click Yes, and then click OK when the completion
message appears.
• To cancel the export, click No.

Table 95 describes the parameters in the Export to Xcalibur Exclusion List dialog box.
Table 95. Export to Xcalibur Inclusion/Exclusion List dialog box parameters (Sheet 1 of 3)
Parameter Description
Path Specifies the file name and directory path of the text file that
contains the inclusion/exclusion list for your Xcalibur instrument
method.

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Export the tabular data in a result file to an external file

Table 95. Export to Xcalibur Inclusion/Exclusion List dialog box parameters (Sheet 2 of 3)
Parameter Description
Options
IMPORTANT An Orbitrap Fusion mass spectrometer accepts a retention time range of
0.01 to 999 minutes.

Make sure that the retention time window for each compound falls within the retention
time range of the instrument method.
• Expected RT – Left RT Tolerance > Minimum retention time for the instrument
method
• Expected RT + Right RT Tolerance < Maximum retention time for the instrument
method
Left RT Tolerance Specifies the minimum start time for the chromatographic peak. If
[min] the Expected RT minus the Left RT Tolerance setting is less than
zero, the application exports a value of zero.

Default: 1
Range: 0.001 to 1000
Right RT Tolerance Specifies the maximum stop time the chromatographic peak.
[min]
There is no error checking for the calculated maximum retention
time.

Default: 1
Range: 0.001 to 1000
Checked Items Only Specifies that the application exports only the selected compounds
to the named text file.

Default: Clear
Include Isotopic Peaks Adds an entry for each isotopic spectral peak.
LTQ Orbitrap Options
Mass Precision Specifies the mass precision.
(Decimals)
For the LTQ Orbitrap, the mass precision of the exported data
must match the required mass precision for your Xcalibur
instrument methods. You specify the required mass precision for
Xcalibur instrument methods in the Instrument Configuration
dialog box of the Foundation platform.

Default: 5; range: 0 to 5

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Export the tabular data in a result file to an external file

Table 95. Export to Xcalibur Inclusion/Exclusion List dialog box parameters (Sheet 3 of 3)
Parameter Description
Max. Concurrent Specifies the maximum number of entries with overlapping time
Entries windows.

Default: 500; range: 1 to 2000

Remove Charge Specifies whether the application exports the m/z value of the best
ion for each detected compound or the neutral mass of each
detected compound.

Default: Clear
Instrument
LTQ Orbitrap Exports the list in the appropriate format for the LTQ Orbitrap
instrument control software.
Q Exactive Exports the list in the appropriate format for the Q Exactive
instrument control software.

The mass list includes the formula of each compound in the

Comment column when the formula is available.
Orbitrap Fusion Exports the list in the appropriate format for the Orbitrap Fusion
instrument control software.

If the table contains both positive and negative scans, the

application creates two mass lists.

The maximum number of target compounds for an Orbitrap

Fusion mass list is 50 000. If the table includes more than 50 000
compounds, filter the table or check the compounds of interest
before you export the mass list.
Buttons and check box
Open File(s) after Specifies that the file opens after the application completes the
Export export.
Export Exports the specified information to a text file.
Close Closes the dialog box.

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Export spectral data to a new or existing mzVault library

Export the contents of the Compounds table to TraceFinder

You can export the contents of the Compounds table to a CSV file that the TraceFinder
application can use for data processing.

Y To export a compounds list for the TraceFinder application

1. Right-click the Compounds table and choose Export > As TraceFinder List.
The Export to TraceFinder dialog box opens. The default folder is either
drive:\Users\Public\Documents or the last folder that you selected. The default file name
is the name of the active result file.
Figure 101. Export to TraceFinder dialog box

2. Select the folder where you want to store the file.

3. Do the following, as applicable:
• To exclude unnamed compounds, select the Exclude Items Without Name check
box.
• To include only the checked compounds, select the Checked Items Only check box.
• To automatically display the exported compounds list, select the Open File After
Export check box.
4. Click Export.
A status box appears when the export process finishes.
5. Click OK.

Export spectral data to a new or existing mzVault library

To export spectral data to a new or existing mzVault Library file, see the following topics:
• Add a compound to an existing mzVault library
• Create a new mzVault library

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Export spectral data to a new or existing mzVault library

Add a compound to an existing mzVault library

From a Compounds table or an Expected Compounds table, use the Export > Add
Compound to Existing mzVault Library shortcut menu command to export a selected
compound to an existing mzVault library.

Tip The application comes with an empty library named Custom mzVault Library.db. For
information about creating a new spectral library, see “Spectral Libraries view.”

Y To add a compound to an existing mzVault Library

1. Open a result file. See “Open, close, and update result files.”
2. Open one of these tables by clicking its tab—Compounds table or Expected Compounds
table.
3. Right-click a compound in the table and choose Export > Add Compound to Existing
mzVault Library.
The Export to mzVault Library dialog box opens. Its Spectra view displays the available
fragmentation spectra for the selected compound.
Figure 102. Export to mzVault Library dialog box populated with a Compounds table compound

4. Do the following:
• In the spectrum tree, select the check boxes for the spectra that you want to add to
the compound entry.
• In the mzVault Library area, select the existing mzVault library from the Selected
Library list.

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Export spectral data to a new or existing mzVault library

5. Do one of the following:

• To add the spectra to an existing compound entry in the library, select the entry in
the Similar Compounds Found in Library list. Then, click Add to Selected.
• To add the compound and the selected spectra as a new compound entry, click Add
as New.
6. Close the dialog box.

Create a new mzVault library

From a Compounds table or an Expected Compounds table, use the Export > Compounds to
a New mzVault Library shortcut menu command to export all or selected compounds to new
mzVault library.

Y To export compounds to a new mzVault library

1. Open a result file. See “Open, close, and update result files.”
2. Open one of these tables by clicking its tab—Compounds table or Expected Compounds
table.
3. (Optional) Filter the table to display only the compounds of interest or select the check
boxes for the compounds of interest.
4. Right-click the table and choose Export > As mzVault Library.
The New mzVault Library dialog box opens. By default, the application populates the
Library Name box with the name of the opened result file.

5. Do the following:
• Type a new library name or keep the default name.
• In the Options area, select whether to exclude compounds without a name, export
only the compounds with selected check boxes, or both.
6. Click Export.

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Export compounds to a new or existing mass list

7. At the prompt, click OK.

The new library appears in the Spectral Libraries list.
8. To modify a library with the mzVault 2.3 application, export it to another folder. Then,
use the Replace command to replace the existing library with the modified library.

Export compounds to a new or existing mass list

You can create new mass lists or add compounds to existing mass lists by exporting
compounds from the Compounds table of a result file. The application automatically adds
exported mass lists to the table of available mass lists in the Lists & Libraries > Mass Lists view.

For details about exporting compounds to a mass list, see the appropriate topic:
• Export compounds from the Compounds table to a new mass list
• Export compounds from the Compounds table to an existing mass list

Export compounds from the Compounds table to a new mass list

Y To create a new mass list by exporting a set of compounds from the Compounds table

1. Open the result file of interest.

2. Open the main Compounds table or a related Compounds table.
3. (Optional) To export only the checked compounds, select the check boxes for the
compounds of interest in the Checked column.
4. Right-click the Compounds table and choose Export > As Mass List.
5. In the Export to New Mass List dialog box, do the following:
a. In the Mass List Name box, type a name for the mass list.
b. In the Options area, do any of the following:
• To export only checked compounds, select the Checked Items Only check box.
• To export only named compounds, select the Exclude Items without Name
check box.
• To include the retention time information in the mass list, select the Export
Retention Time check box.
c. Click Export.
6. At the prompt, click OK.
The new mass list appears in your Mass Lists library.

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Export compounds to a new or existing mass list

Export compounds from the Compounds table to an existing mass list

Y To export compounds to an existing mass list

1. Open the result file of interest.

2. Open the main Compounds table or a related Compounds table.
3. Highlight the compounds of interest by using the SHIFT and CTRL keys.
4. Right-click your selection and choose Export > Add Selected Compounds to Existing
Mass List.
The Export to Existing Mass List dialog box opens.
Figure 103. Export to Existing Mass List dialog box

If you select the Do Not Add Duplicate Names

check box, the data entry boxes in the Entries
Matching area become unavailable.

5. Do the following:
• In the dropdown Mass List Name list, select the mass list where you want to add the
selected compounds.
• (Optional) To add the retention time information to the mass list, select the Export
Retention Time check box.
6. To avoid exporting named compounds that are already in the mass list, do one of the
following:
• To exclude a named compound only if its mass and retention time match the
duplicate compound in the mass list within specified tolerances, make sure that the
Do Not Add Duplicate Names check box is not selected. Then, in the Entries
Matching area, enter the tolerances that you want the application to use to exclude
duplicate named compounds from being exported to the mass list.

Note If you do not want to exclude a named compound unless both its mass and
retention time are an exact match to the named compound in the mass list, set
both tolerance values to 0.

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Copy or save graphical views for publication

• To exclude any named compound with a name that matches that of a named
compound in the existing mass list, select the Do Not Add Duplicate Names check
box.

Note This feature is case-sensitive.

Figure 104. Export to NIST Formatted File dialog box

Copy or save graphical views for publication

You can copy the contents of a graphical view to the Clipboard as editable text, as an image, or
to an external file.
• To save a graphical view as a raster image, save it as one of these file types: PNG, GIF,
JPG, TIF, or BMP.
• To save a graphical view as a vector image, save it as an EMF file.

For information about the graphical views that are available when a result page is active in the
application window, see “Graphical views for a result file.”

Table 96 lists the shortcut menu commands for copying data to the Clipboard or an external
file.
Table 96. Commands for copying an image of a graphical view (Sheet 1 of 2)
Copy the image Copy the data points to the Copy the data to an Copy the data to a
Graphical view
to the Clipboard Clipboard image file TEXT or CSV file
Chromatograms view Copy > Image Copy > Points Export > Image As Export > Points As
Mass Spectrum view Copy > Image Copy > Points—Copies the Export > Image As Export > Points As
scan label and the m/z and
intensity values for annotated
centroids to the Clipboard.
Copy > Raw Points—Copies
the m/z and intensity values
for all centroids to the
Clipboard. Does not copy the
scan label.
Scatter Chart Copy > Image Copy > Data Export > Image As Export > Data As
Histogram Chart Copy > Image Copy > Data Export > Image As Export > Data As
Bar Chart Copy > Image Copy > Data Export > Image As Export > Data As
Pie Chart Copy > Image Copy > Data Export > Image As Export > Data As

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Copy structures to the Clipboard for use in other applications

Table 96. Commands for copying an image of a graphical view (Sheet 2 of 2)

Copy the image Copy the data points to the Copy the data to an Copy the data to a
Graphical view
to the Clipboard Clipboard image file TEXT or CSV file
Trend Chart Copy > Image Copy Information to Export > Image As Export > Data As
Clipboard
Principal Component Copy > Image Copy > Points Export > Image As Export > Points As
Analysis view (CSV file)
PLS-DA view Copy > Image Copy > Points Export > Image As Export > Points As
(CSV file)
Copy > Point Details
Export > Point
Details As
Descriptive Statistics Copy > Image Copy Information to Export > Image As Save Information
view Clipboard As (CSV file)
Differential Analysis Copy > Image Copy > Points Export > Image As Export > Points As
view
Copy > Point Details (Use this Export > Point
command if the Details As
corresponding table includes
structures.)
KEGG Pathways Copy N/A Save Picture As (a N/A
PNG or BMP file)
Retention Time Copy > Image Copy > Points Export > Image As Export > Points As
Correction
Compound Area Copy > Image Copy > Points Export > Image As Export > Points As
Corrections

Copy structures to the Clipboard for use in other applications

You can copy structures from any result table that has a Structures column to the Clipboard
for use in other applications.

Y To copy structures from a result table for use in other applications

1. Open a result file from an analysis that included a structure search.

For an LC study, any of the search node or mapping nodes can return a structure. For a
GC study, a NIST library search or any of the search nodes or mapping nodes can return
a structure.
2. Open the result table of interest.

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Copy structures to the Clipboard for use in other applications

3. If the Structures column is hidden, do the following:

a. Click the Field Chooser icon, , for the table.
b. In the Field Chooser dialog box, select the check box for the Structure column.
c. Close the Field Chooser dialog box.

Tip You can copy structures without opening the Structure column. But opening
the Structures column lets you confirm that the entry you want to copy has a
structure annotation.

4. Right-click the entry of interest and choose Copy Structure > As Mol, As InChi, or As
InchIKey.
Figure 105. Shortcut menu for a result table with a Structure column

5. Open the application where you want to paste the structure and press CTRL+V.
Figure 106. ChemSpider search box with pasted InChi string

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Graphical views for a result file

The following topics describe how to use the graphical views that are available from the View
menu:
• Chromatograms view
• Mass Spectrum view
• Result Charts view
• Trend Chart view
• Isotopologues Distribution Chart view
• Mass Defect Plot view
• Principal Component Analysis view
• Descriptive Statistics view
• Differential Analysis view
• Partial Least Squares Discriminant Analysis view
• KEGG Pathways view
• BioCyc Pathways view
• Metabolika Pathways view
• Retention Time Corrections view
• Compound Area Corrections view
• Hierarchical Clustering Analysis view
• mzLogic Analysis view
• FISh Scoring Queue view

Note Use the Result Charts view to create histograms, bar charts, pie charts, and scatter
plots of the result data.

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Chromatograms view

For details about the Result Filters view, see “Filter the data for data reduction.” For details
about viewing a summary of the analysis parameters for a result file, see “View the result
summaries.”

Chromatograms view
For LC studies, when you initially open a result file, the Chromatograms view displays the
XIC traces for the compound in the first row of the Compounds table or the Expected
Compounds table. By default, the display zooms in on the detected peaks for the selected
rows.

The Chromatograms view consists of a collapsible pane on the left and the graphical view on
the right. Right-clicking the graphical view opens a shortcut menu (see Table 98).

The following topics describe how to review the chromatographic data:

• View a chromatogram
• Add a chromatogram plot
• Overlay multiple chromatogram plots
• Change the grouping in the collapsible pane of an opened result file
• Hide the traces for a study variable value
• Update all the chromatogram plots simultaneously
• Manually integrate chromatographic peaks
• Chromatograms view shortcut menu commands

View a chromatogram
In an opened result file, you can display chromatogram traces (a plot of intensity versus time)
by selecting a row in any of these result tables:
• Untargeted LC/MS workflow
– Compounds
– Compounds per File
– Features
• Targeted LC/MS workflow
– Expected Compounds
– Expected Features per File
– Expected Compounds per File

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Chromatograms view

– Merged Features
– Expected Formulas
• General LC/MS traces
– FISh Trace Fragments
– Specialized Traces: TIC, BPC, XIC, isotope pattern, and FISh
– Manual Peaks

Y To view a chromatogram

1. Open a result file that contains chromatographic data.

2. If the Chromatograms view is closed, open it by choosing View > Chromatogram from
the menu bar.

Note When you select a row for a filtered study file, the Chromatograms view does
not display a trace. For example, if the Blank check box is clear under Filter By
Sample Type and you select a row for a Blank sample, the Chromatograms view
remains empty. By default, the Blank Sample Type check box is clear until you select
it.

3. Do one of the following:

• Click the Compounds tab or the Expected Compounds tab and select a row.
The Chromatograms view displays overlaid traces of the chromatographic peaks that
were detected across the input files for the molecular weight and retention time
(MW × RT dimensions) listed in the selected table row. Each trace is a composite of
the adducts found. For the Expected Compounds table, the chromatographic peak
for each row is also derived from the same parent compound and reaction steps.
• Click the Expected Formulas tab and select a row.
The Chromatograms view displays overlaid traces for all of the chromatographic
peaks found for an expected elemental composition (same MW, parent compound,
and elemental composition).
• Click the Merged Features tab and select a row.
The Chromatograms view displays overlaid traces of the chromatographic peaks
detected by the Detect Compounds and Find Expected Compounds nodes for the
selected feature (same m/z × RT dimensions).
• Click the Features tab or the Expected Features tab and select a row.
The Chromatograms view displays the integrated chromatographic peak for the
selected table row (m/z × RT dimensions).

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Chromatograms view

• Click the Compounds per File tab or the Expected Compounds per File tab and
select a row.
The Chromatograms view displays the integrated chromatographic peak for the
selected table row (MW × RT dimensions). Each trace is a composite of its related
adducts, and the peak area for a compound is the sum of the areas for its related
adducts (parent area for the adducts listed in the Expected Features table or the
Features table).
• Click the FISh Trace Fragments tab and select a row.
The Chromatograms view displays a trace for the structure displayed in the selected
table row. The FISh Trace Fragments table appears in the main table set when you
select True for Individual Traces in the Create FISh Trace node of a processing
workflow.
• Click the Specialized Traces tab and select a row.

Note The Specialized Traces table contains traces generated by these nodes:
Create Mass Trace, Create Analog Trace, Create Pattern Trace, and Create FISh
Trace.

Table 97. Workflow nodes that generate specialized traces

Workflow node Generates any of these trace
Create Mass Trace An extracted ion (mass range) chromatogram (XIC), a
base peak chromatogram (BPC), or a total ion
chromatogram (TIC)
Create Analog Trace A UV-Vis trace from a UV-Vis or PDA detector, up to
three traces from a PDA detector, or an analog trace from
an LC detector that you connected to one of the analog
input channels of a Thermo Scientific mass spectrometer
Create Pattern Trace A TIC trace of the summed intensities of the mass
spectral peaks (across the entire scan) that match the
user-defined isotope pattern
Create FISh Trace • A summed FISh trace of all the matching fragment
ion scans (data-dependent acquisition [DDA] or data
independent acquisition [DIA]) when you select True
in the Summed Trace list.
• An individual FISh trace for each fragment ion when
you select True in the Individual Traces list. To view
the individual trace for each fragment ion, see the
FISh Trace Fragments table.

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• Open the related tables, click the Filled Gaps tab, and select a row.

Tip By default, the Filled Gaps table is hidden. To display this table, open the
Select Visible Tables dialog box, select the Filled Gaps check box, and click OK.
For more information, see “Filled Gaps table.”

4. To determine the origin of a trace in a result file that includes multiple input files,
right-click the Chromatograms view and choose Display Options > Show Legend.
5. To decrease or increase the number of legends displayed, right-click the Chromatograms
view and choose Display Options > Legend Size > #Rows, where # is an integer value
from 1 to 10.
In Figure 107, the vertical red line indicates the peak apex of an integrated
chromatographic peak. The triangle below the retention time label indicates the
corresponding data point in the XIC trace.
Figure 107. Chromatograms view showing the shortcut menu (LC/MS data)
Red line indicating the apex of the Triangle indicating the data
integrated chromatographic peak point that corresponds to the
(RT in compounds table) retention time label in the plot

When the number of legend lines becomes too large for the available display space, the
application displays an empty view with the following text:
Not enough space for drawing the chart properly.

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Add a chromatogram plot

Y To add a plot to the Chromatograms view

1. Open a result file that contains chromatographic data.

2. Right-click the Chromatograms view and choose Plots > Add Plot.
The new plot appears below the original plot.

Note The size of the Chromatograms view limits the number of plots the view can
display. When the application can no longer draw the plots properly, the following
message appears:
Not enough space for drawing plot properly

To display more plots, you can resize the view or drag the view to a second monitor
and expand the view to fill the monitor.

In a Chromatograms view with more than one plot, a light blue bar on the left border
highlights the active plot (see Figure 108). If you right-click the Chromatograms view and
choose Plots > Remove Plot, the application removes the active plot.
Figure 108. Chromatograms view with two plots

Light blue bar on the left border

of the active plot
Plots shortcut menu

Note Manual Peak Integration is available only for specialized traces in LC studies.

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Overlay multiple chromatogram plots

Y To overlay multiple chromatograms in one chromatogram plot

1. Open a result file that contains chromatographic data.

2. Do one of the following:
• Hold down the Shift key and select a range of contiguous rows.
• Hold down the CTRL key and select contiguous or noncontiguous rows one by one.
• Hold down the Shift key and press the down arrow on the keyboard.

Tip Take care to avoid clicking an editable column in the result table, as doing so
undoes the row selection and sets the focus to the table cell.

Change the grouping in the collapsible pane of an opened result file

Y To change the grouping of the chromatogram traces

1. Open the collapsible left pane by clicking the icon, .

2. Under Group By, select or clear one or more of the check boxes.
3. To display all of the study file traces in different colors, clear all of the check boxes under
Group By, or under Group By, select only the Samples check box.

Hide the traces for a study variable value

Y To hide the chromatogram trace or traces for a study variable value

Under Filter By, clear the check box for the study variable value.

Update all the chromatogram plots simultaneously

Y To simultaneously update all the plots in the Chromatograms view

1. Open a result file that contains chromatographic data.

2. Add two or more plots to the Chromatograms view.
3. Right-click the view and choose Plots > Distribute to All Selections.
As you select different table rows, all of the plots update. When Distribute to All
Selections is not enabled, only the active plot updates.

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Manually integrate chromatographic peaks

Y To manually integrate chromatographic peaks

1. Open a result file that contains specialized traces.

Note These workflow nodes generate specialized traces: Create Mass Trace, Create
Analog Trace, Create Pattern Trace, and Create FISh Trace.

2. In the Specialized Traces table, select the trace of interest.

3. Right-click the Chromatograms view and choose Manual Peak Integration.
Two red dashed lines appear and the integrated peak area appears in blue.
4. Drag one line to the beginning of the chromatographic peak and the other line to the end
of the chromatographic peak.
The integrated peak area changes as you move the start and end points of the
chromatographic peak.
5. Place the cross-hair cursor on the peak.
A pop-up box appears with the selected retention time range and the Apply and Cancel
buttons.
Figure 109. Manually integrated chromatographic peak

Pop-up box with

retention time
range

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6. To add the manual peak to the Manual Peaks table, do one of the following:
• Click Apply.
• On the keyboard, press A.
If the result file did not already contain a Manual Peaks table, the new table appears in the
main table tab set. The Manual Peaks table contains a row for the new manual peak.

Chromatograms view shortcut menu commands

Table 98 describes the shortcut menu commands for the Chromatograms view.
Table 98. Shortcut menu commands for the Chromatograms view (Sheet 1 of 5)
Command Description
Note The default zoom settings are as follows:
• X-axis Zoom > To Detected Peaks (Active Plot)
• Y-axis Zoom > Auto Scale Y-axis
Undo Last Zoom/Pan Undoes the last zoom or pan movement.
Undo All Zoom/Pan Zooms out to the full data acquisition time for the chromatogram on the x axis and the
height of the largest chromatographic peak on the y axis.
X-axis Zoom > Keep Maintains the same x-axis zoom range as you select different table rows. Overrides the
Zoom Zoom to Detected Peaks command.
X-axis Zoom > Full Displays the full data acquisition time for the chromatogram.
Range
X-axis Zoom > To Zooms the x axis to the detected peaks for the selected table rows.
Detected Peaks (Active
Plot)
X-axis Zoom > To Zooms the x axis to display the detected peaks in all of the plots.
Detected Peaks (All
Plots)
Y-axis Zoom > Auto Default selection—Scales the y axis to the maximum intensity within the current x-axis
Scale Y-Axis (retention time) zoom range.

Manual zooming of the y axis is unavailable in this mode.

Y-axis Zoom > Manual Scales the y axes of all the plots to the same scale. Manual zooming on both axes is available.
(Synchronize All Plots)
To reset the y-axis scaling, choose Y-axis Zoom > Auto Scale Y-Axis, and then choose Undo
All Pan/Zoom.
Y-axis Zoom > Manual Only changes the y-axis scaling of the current plot. Manual zooming on both axes is
(Each Plot Individual) available.

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Table 98. Shortcut menu commands for the Chromatograms view (Sheet 2 of 5)
Command Description
Copy > Image Copies an image of the Chromatograms view (including the legend) to the Clipboard.

You can paste the image into a Microsoft Office document as a raster image or into a
vector-drawing program as a vector image.
Copy > Points Copies the data as a two-column list of data points and copies the scan header. The first
column lists the retention time and the second column lists either the relative intensity or
the counts.
Export > Image As Opens the Save As dialog box where you can specify a file name and save the contents of the
Chromatograms view as one of these selectable image formats: EMF, PNG, GIF, JPG, TIFF,
or BMP. The EMF format is a vector image.
Exports > Points As Opens the Save As dialog box where you can specify a file name and save the contents of the
Chromatograms view as a text file. The default file name is Chart.txt.

When the chromatogram is a plot of relative intensity versus retention time, the application
saves the data points as a two-column list. The first column lists the retention time and the
second column lists the relative intensity (%). When the chromatogram is a plot of area (in
counts) versus retention time, the second column lists the area for the peaks.
Plots > Add Plot Adds an empty, active plot to the Chromatograms view. Only the screen size limits the
maximum number of displayed plots. When you reach the screen’s limit, the
Chromatograms view appears to be empty and the following message appears:
Not enough space for drawing chart properly.
Plots > Remove Plot Removes the active plot, which has a gray border.

Adding more than one plot makes this command available.

Plots > Remove Other Removes all of the plots in the Chromatograms view.
Plots
Adding more than one plot to the Chromatograms view makes this command available.

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Table 98. Shortcut menu commands for the Chromatograms view (Sheet 3 of 5)
Command Description
Plots > Freeze Content Keeps the chromatogram of the currently selected row in the view when you select another
row (in the current table or another result table). The application uses dashes to distinguish
the frozen chromatogram trace.
Frozen peak with dashes

Plots > Clear Frozen Clears the frozen chromatogram from the view.
Content
Plots > Distribute Updates all of the plots simultaneously as you select different table rows. When Plots >
Selection to All Distribute Selection to All is not enabled, only the active plot updates.
Display Options > Displays a pop-up box with the following information, from top to bottom, when you place
Show Tooltips the cursor, +, over a chromatographic peak:
• Parent compound and any applicable transformations for an expected compound
• Chemical formula for an expected compound
• Adduct ion (feature)
• m/z value (feature)
• Molecular weight (compound or expected compound)
• Selected retention time, in minutes
• Intensity (height), in counts, of the selected point on the chromatogram trace
• File name of the input file

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Table 98. Shortcut menu commands for the Chromatograms view (Sheet 4 of 5)
Command Description
Chromatogram with a tooltip for an entry in the Compounds per File table.

Chromatogram with a tooltip for an entry in the GC EI Compounds per File table

Display Options > Adds grid lines to the Chromatograms view.

Show Gridlines
Display Options > Uses a fill color for the integrated area under the detected chromatographic peaks.
Show Detected Peaks
Turning off this command removes the fill color.
Tip To see the peaks underneath the larger peaks in a set of overlaid traces, turn off the
Show Detected Peaks command.
Display Options > Displays a legend for the sample groups at the top of the view.
Show Legend
Display Options > Specifies the number of legend lines that you want the application to display.
Legend Size
Selections: 0 to 10

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Table 98. Shortcut menu commands for the Chromatograms view (Sheet 5 of 5)
Command Description
Display Options > Displays the y-axis scale as relative intensity (0 to 100%). The legend changes to Intensity
Relative Intensity [%].

The default y-axis scale is an absolute scale; the y-axis legend is intensity [counts].
Display Options > Redraws only the chromatographic peaks of the displayed traces. Does not redraw the
Crop to Detected Peaks baseline portions of the traces as you select different table rows.
Manual Peak Use to add a manual peak to a specialized trace. Adding a manual peak adds the Manual
Integration Peaks table to a result file. See “Manually integrate chromatographic peaks.”

Selecting a trace in the Specialized Traces table makes this command available.

Table 99 describes the traces that you can display in the Chromatograms view.
Table 99. Chromatograms view traces (Sheet 1 of 2)
Trace type Description
UV Displays a chromatogram created from the UV signal from a
UV-Vis detector or the analog channel of a PDA detector.
Analog Displays a trace of response versus time.

Raw data files can contain analog data from a device that is
hard-wired to the analog channels of a Thermo Scientific mass
spectrometer.
PDA total scan Displays a chromatogram of the total absorbance for the entire
scan wavelength range for each time point.
PDA spectrum Displays a chromatogram of the highest absorbance reading in the
maximum wavelength range for each time point.
PDA wavelength range Displays a chromatogram of the total absorbance for the specified
wavelength range for each time point.
Base peak Displays a chromatogram of the most intense mass spectral peak
chromatogram (BPC) in the specified mass range for each time point.
Total ion Displays a chromatogram of the total intensity from all the mass
chromatogram (TIC) spectral peaks in the specified mass range for each time point.

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Table 99. Chromatograms view traces (Sheet 2 of 2)

Trace type Description
Extracted ion Displays an XIC trace, which is a mass range trace, when you
chromatogram (XIC) select a row in any of these tables: Merged Features, Expected
Compounds, Expected Compounds per File, Expected
Compound Features, Compounds, Compounds per File,
Unknown Compound Features, FISh Trace Fragments, or
Specialized Traces.

The XIC trace is made up of the mass spectral peaks that match
the specified mass value within the specified mass tolerance.
Pattern trace Displays a TIC trace of the summed intensities of the mass
spectral peaks that match a specified pattern for each time point.
FISh trace Displays a TIC trace of the summed intensities of the mass
spectral peaks in a fragmentation scan (MS/MS or MS3) that
match the predicted fragments of the selected library compound
and its transformation products for each time point.

Mass Spectrum view

The Mass Spectrum view displays the spectral tree of a selected component in the result table
and the mass spectrum of the selected scan in the spectral tree.

For details, see these topics:

• Display a mass spectrum
• Change the zoom level of the Mass Spectrum view
• View annotated fragment structures for targeted compounds
• View annotated fragment structures for untargeted compounds
• Create a mirror plot
• Search the mzCloud database for a matching fragmentation spectrum
• Spectral tree pane of the Mass Spectrum view
• Isotope pattern matching for compounds with formulas
• Mass Spectrum view shortcut menu commands

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Display a mass spectrum

Y To display a specific mass spectrum

1. Open a result file.

2. If the Mass Spectrum view is closed, choose View > Mass Spectrum from the menu bar.
3. Do the following:
a. Select an entry in any of these result tables.

LC studies
• Compounds table • Features table
• Compounds per File table • Expected Features table
• Expected Compounds table • mzCloud Results table
• Expected Compounds per File table • Structure Proposals table

The Mass Spectrum view displays the matching spectral tree and a zoomed-in view of
the full MS scan.
b. Select the scan of interest from the spectral tree.

Change the zoom level of the Mass Spectrum view

In the Mass Spectrum view for a result file, you can independently zoom in or out on the x or
y axis by dragging the cursor horizontally or vertically, respectively, or you can zoom in or out
of a rectangular section of the plot.
Table 100. Working with the zoom level in the Mass Spectrum view
Task Procedure
Zoom in on the x axis. Drag the cursor to the right over the
m/z range of interest.
Zoom out on the x axis. Drag the cursor horizontally to the left over
the m/z range of interest.
Zoom in on the y axis. Drag the cursor vertically down the y axis.
Zoom out on the y axis. Drag the cursor vertically up the y axis.
Zoom in on a section of the plot. Drag the cursor diagonally across the section.
Undo the last zoom-in action. Right-click the plot and choose Zoom Out.
Change the zoom level to the full m/z range Right-click the plot and choose Undo All
on the x axis and the full response range on Zoom/Pan.
the y axis.

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View annotated fragment structures for targeted compounds

For studies where you are targeting specific compounds, you can add the FISh Scoring node
to the processing workflow or apply the FISh scoring algorithm to expected compounds in the
result file.

Y To review the matching fragment structures predicted by the FISh scoring algorithm

1. Open a result file generated by a processing workflow that included the Expected
Compounds node and the FISh Scoring node. Then, select a compound in the Expected
Compounds table.
2. (Optional) Enlarge the Mass Spectrum view.
3. In the spectral tree, select an MS2 or higher scan.
4. Review the color-coded mass spectral peaks, the theoretical fragment structures, and the
transformations for the shifted mass spectral peaks.
The FISh Scoring node annotates centroids that match the m/z value of a theoretical
fragment ion with its theoretical structure and color-codes the centroids in a
fragmentation scan as follows.

Color Meaning
( ) Green Direct match—Matches the m/z value of a theoretical fragment ion.
( ) Blue Shifted match—Matches the m/z value of a theoretical fragment ion
with at least one transformation applied.

Figure 110 shows an annotated fragmentation spectrum.

Figure 110. Fragmentation spectrum with FISh annotations (targeted analysis)

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View annotated fragment structures for untargeted compounds

For LC studies, you can apply the FISh scoring algorithm to compounds in the Compounds
table and the related Structure Proposals table that have MS2 spectra and assigned structures.

Y To run the FISh scoring algorithm on an untargeted compound and view the structure
annotations in the Mass Spectrum view
1. Open a result file from an untargeted analysis that returns structures.
For LC studies, the processing workflow must include the Detect Compounds node,
Group Compounds node, Predict Compositions node, Assign Compound Annotations
node, and any of the identification or pathway mapping nodes that return structures. In
addition, the input files must include fragmentation scans.
2. Display the FISh Coverage and Structure columns as follows:
a. Open the Field Chooser dialog box by clicking the icon, , in the upper-left corner
of the Compounds table.
b. Select the FISh Coverage and Structure check boxes, and then close the Field Chooser
dialog box.
3. Right-click a compound of interest that has a structure and fragmentation spectra and
choose Apply FISh Scoring.
The Specify FISh Scoring Settings dialog box opens.
4. Specify the fragmentation settings and click OK.
The FISh Scoring Queue opens, and the application starts processing the MS2 scans
against the structure. When processing is completed, the calculated FISh coverage score
appears in the FISh Coverage column.
5. If the Mass Spectrum view is closed, open it by choosing View > Mass Spectrum from
the menu bar.
6. In the spectral tree at the left of the Mass Spectrum view, select an MS2 scan.
The annotated spectrum appears in the Mass Spectrum view. The spectrum header
displays the number of centroids that the FISh scoring algorithm matched to theoretical
fragments, the number of theoretical fragments that had no matching centroid, and the
number of fragments that it did not attempt to match (skipped) because their expected
intensity was below the signal-to-noise setting.

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The FISh scoring algorithm annotates each centroid that matches the m/z value of a
theoretical fragment ion with its theoretical structure, m/z value, and formula. In
addition, the application displays matching centroids in green with a green circle at the
top.

Create a mirror plot

In a result file that includes MS2 scans, you can create a mirror plot to compare an
experimental spectrum to a reference spectrum.

Y To create a mirror plot of two fragmentation scans

1. Open a result file with fragmentation scans.

2. If the Mass Spectrum view is closed, choose View > Mass Spectrum from the menu bar.
3. In the spectral tree pane, select a reference scan.
4. Right-click the Mass Spectrum view and turn off the Show Library Spectra as Reference
command if it is available.

Note The Use As Reference command is unavailable when the Show Library Spectra
As Reference command is available.

5. Right-click the Mass Spectrum view and choose Use As Reference.

6. Select the fragmentation scan that you want to compare.
The reference scan appears on the bottom and the comparison scan appears on the top.
7. To remove the reference scan from the plot, right-click the Mass Spectrum view and
choose Clear Reference.

Search the mzCloud database for a matching fragmentation spectrum

From the Mass Spectrum view, you can submit a query fragmentation spectrum to the online
mzCloud mass spectral database.

Y To manually search the mzCloud database for a matching fragmentation spectrum

Note The mzCloud database is compatible only with the Internet Explorer™ web
browser. To access the mzCloud spectral database from the Compound Discoverer
application, set Internet Explorer as your default Internet browser.

1. Open a result file with data-dependent fragmentation data.

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Mass Spectrum view

2. In the spectral tree pane of the Mass Spectrum view, select a fragmentation scan.
3. Right-click the spectrum plot and choose Submit To mzCloud.
The online mzCloud application opens to the Select Spectrum dialog box and displays
the selected query spectrum.
4. Optimize the settings and click OK.
Figure 111. mzCloud search for a query spectrum of Chlorpyrifos

Spectral tree pane of the Mass Spectrum view

For an LC study, the collapsible pane on the left of the Mass Spectrum view contains a
spectral tree with the high-resolution scans for preferred ions that elute within the following
retention time window:
• Peak apex (RT) ± the peak’s full width at half maximum (FWHM)

–or–

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• From the start time to the end time for the chromatographic peak as defined by the peak
detection algorithm

For MS1 scans, the tree lists the scan number, the retention time at the apex of the
chromatographic peak, the mass analyzer, and the scan polarity.

For MSn scans, the tree lists the scan number, the retention time at the apex of the
chromatographic peak, the mass analyzer, the scan polarity, and the fragmentation
information, including the scan power, collision cell type, and the fragmentation type
(data-dependent acquisition [DDA] or data-independent acquisition [DIA]).

Isotope pattern matching for compounds with formulas

For LC studies, selecting an entry in the following result tables populates the Mass Spectrum
view with a spectral tree for the entry in the left pane and the first MS1 scan for the selected
compound or feature in the right pane.
• Expected Compounds
• Expected Compounds per File
• Expected Features
• Compounds

If the analysis predicts a formula for the compound or feature, the MS1 scan shows the
isotope pattern fit for the detected compound. Colored rectangles highlight the mass spectral
peaks (centroids) that match the theoretical isotope pattern. These rectangles have a
minimum display width to ensure that they are still visible when you zoom out or use the
Undo All Zoom/Pan shortcut menu command.

Note The isotope pattern fit algorithm is “resolution aware”; that is, in addition to the list
of elemental compositions provided by the Generate Expected Compounds node or the
Predict Compositions node, it uses the resolution information provided with the scan data
to perform an isotope pattern fit and calculate a spectral distance score.

If the resolution information is unavailable, it uses the setting for the Unrecognized MS
Resolution parameter in the Select Spectra node.

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Figure 112. MS1 scan with color-coded mass peaks and the shortcut menu (LC study)

Table 101 describes the color coding for the centroids in an MS1 spectrum.
Table 101. Color coding for the centroids in an MS1 spectrum for a compound with a formula
annotation
Color Meaning
( ) Lavender Indicates the most intense centroid in the spectrum.
Note The A0 isotope (monoisotopic ion) is always the isotope with the
lowest m/z value, but it is not necessarily the isotope with the highest
intensity. For example, for compounds with more than one bromine
atom, a bromine atom and a chlorine atom, or more than four chlorine
atoms, the M + 2 (A2) isotope is the most intense isotope.
( ) Green The labeled centroid matches the delta mass and the relative intensity of
the theoretical isotope pattern for the formula annotation within the
specified tolerances.
( ) Red The expected centroid for this m/z value is missing or its intensity does not
fall within the tolerance range for the theoretical isotope pattern for the
formula annotation.
( ) Light blue The expected centroid for this m/z value (for the formula annotation)
might be missing because its theoretical intensity is at the level of the
baseline noise.

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Mass Spectrum view shortcut menu commands

Table 102 describes the shortcut (right-click) menu commands for the Mass Spectrum view.
Table 102. Mass Spectrum view shortcut menu commands (Sheet 1 of 2)
Command Description
Show Position Tooltips Displays the m/z value and intensity of the mass spectrum peaks
as you point to them.
Zoom Out Undoes the last zoom-in action.
Undo All Zoom/Pan Changes the zoom level to the full m/z range on the x axis and the
full response range on the y axis.
Copy > Image Copies the mass spectrum as a bitmap (raster) image to the
Clipboard.
Copy > Points Copies the data points and the scan header for the selected scan
to the Clipboard. Also copies all text annotations, such as the
FISh fragment annotations and the adduct information.

Use this command to copy the FISh annotations to the

Clipboard.
Copy > Raw Points Copies the data points for the selected scan to the Clipboard.

Use this command to copy points to a library search application.

Export > Image As Opens the Save As dialog box, where you can type a name and
select a file type for the current scan. The available file types are
BMP, EMT, GIF, JPG, PNG, and TIF.
Export > Points As Opens the Save As dialog box, where you can type a name and
select a file type for the current scan. The available file type is
TXT.

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Table 102. Mass Spectrum view shortcut menu commands (Sheet 2 of 2)

Command Description
Submit to mzCloud Opens the Spectrum Search dialog box for the mzCloud database
where you can submit a search for the selected fragmentation
scan.

Available for an MS/MS data-dependent scan.

IMPORTANT The mzCloud web application is compatible
only with the Internet Explorer™ web browser.
Tip To test your computer’s ability to connect to the mzCloud
database, choose Help > Communication Tests from the
application toolbar. Click the mzCloud tab, and then click
Run Tests.

To set up the mass tolerances for manual searches, choose Help

> Configuration from the application toolbar. In the left pane,
select Submit Single Spectrum to mzCloud Options. Edit the
settings as applicable.
Use As Reference Creates a mirror plot that initially consists of the currently
selected scan. When you select another scan, the reference scan
remains in the –y-axis portion of the graph and the new scan
appears in the +y-axis portion of the graph.

Unavailable when the Show Library Spectra Reference command

is enabled.
Clear Reference Removes the reference plot from the Mass Spectrum view.
Show Library Spectra as Displays the recalibrated library spectrum from the mzCloud
Reference database in the bottom portion of the mirror plot.

Available when you select a row in the mzCloud Results table.

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Result Charts view

Result Charts view

Use the Result Charts view to plot the data in a result table as a scatter plot, histogram, bar
chart, or pie chart.

For details about the Result Charts view, see the following topics:
• Open the Result Charts view
• Use the copy, export, and zoom commands for the Result Charts view
• Display and pin the Options Pane for the Result Charts view
• Histogram charts
• Bar charts
• Pie charts
• Scatter plots

Open the Result Charts view

Y To open the Result Charts view

1. Open a result file. See “Open, close, and update result files.”
2. In the menu bar, choose View > Result Charts.
By default, the Result Charts view opens as a floating window. You can resize the window,
drag the window to another screen, or dock the window. See “Rearrange the tabbed pages
and graphical views.”
The Options pane for modifying the appearance of a chart view is a collapsible pane to
the left of each chart.
Figure 113. Floating Result Charts view with the collapsed (unpinned) Options pane at the left

Collapsed Options pane

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Use the copy, export, and zoom commands for the Result Charts view
Y To access and use the shortcut menu commands for a Result Charts page

1. On the selected page of the Result Charts view, select the variables that you want to plot.
2. Click Refresh to plot the data.
3. Right-click the chart and choose one of the commands listed in Table 103.
Table 103. Common shortcut menu commands for the Result Chart viewsa
Command Availability Function
Undo All Pan/Zoom Scatter Chart, Histogram Undoes all panning and zooming.
Chart, and Bar Chart Returns the view to the default
magnification.
Zoom Out Scatter Chart, Histogram Undoes the last zoom-in action.
Chart, and Bar Chart
Copy > Image All Copies a raster image of the plot to
the Clipboard.
Copy > Data All Copies a list of the data points to the
Clipboard.
Export > Image As All Saves the plot in the selected file
format.

File types: EMF, PNG, GIF, JPG,

TIF, and BMP
Export > Data As All Exports a list of data points to a text
file.
a
The shortcut menu for the Scatter Chart view has additional commands.

Display and pin the Options Pane for the Result Charts view
The Options pane of the Result Charts view contains the formatting options for the grid
lines, fonts, and so on.

Y To display and pin the Options pane

1. Point to the vertical Options tab on the left.

2. To keep the pane open, click the pin icon, , in the upper-right corner of the Options
pane.

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Histogram charts
Use the Histogram Chart page of the Result Charts view to plot the frequency distribution of
a variable (result table column). You can display the data as a column chart, a bar chart, a line,
or a stepped line chart.

Y To display the data as a histogram

1. Open a result file.

2. Choose View > Result Charts.
3. Click the Histograms Chart tab.
4. From the Data Source list, select the variable (result table column) that you want to plot.
5. Click Refresh.
6. (Optional) To change the appearance of the histogram, do the following:
a. Open the Options pane.
b. Modify the settings for the colors, labels, and legends of the display, as necessary.
–or–
Click Load to load the settings that you most recently saved.
c. To save the settings, click Save in the Options pane.
The new settings overwrite any previously saved settings. The application loads these
new settings when you click Load.
d. To return the settings to the original default settings, click Factory Defaults in the
Options pane.

Table 104 describes the parameters for the Histogram Chart page.
Table 104. Histogram Chart parameters (Sheet 1 of 6)
Parameters Description
Data Source Specifies the source of the data that you want to plot. The
available data sources are the result table columns in the result file.
Refresh Refreshes the display with data points from the selected data
source.
Options pane commands
Load Loads the Option pane settings that you saved with the Save
command.
Save Saves the settings that you selected in the Options pane.
Factory Defaults Resets the settings of the options in the Options pane to the
defaults in effect when you installed the application.

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Table 104. Histogram Chart parameters (Sheet 2 of 6)

Parameters Description
1. Chart Options
Chart Type Determines how the application plots the data.
• (Default) Column: Displays the data as columns extending
from bottom to top.
• Bar: Displays the data as bars extending from left to right.
• Line: Displays the data as a line. Reported and excluded items
are not stacked as they are in column and bar types.
• StepLine: Displays the data as a line drawn in a series of
90-degree angles.
Show Cumulative Determines whether the application displays a cumulative
histogram, which can be useful if you want to compare
distribution curves. For these charts, the application calculates the
column height as the height of the current column plus the sum
of all previous columns. The rightmost column height is therefore
the total count or 100%, depending on the y-axis settings.
• (Default) True: displays a cumulative histogram.
• False: Displays a non-cumulative histogram.
Horizontal Grid Lines Determines whether the histogram displays horizontal grid lines
and specifies the style of these lines.
• (Default) None: Displays no horizontal grid lines on the
histogram.
• Solid: Displays solid horizontal grid lines on the histogram.
• Dotted: Displays dotted horizontal grid lines on the
histogram.
Vertical Grid Lines Determines whether the histogram displays vertical grid lines and
specifies the style of these lines.
• (Default) None: Displays no vertical grid lines on the
histogram.
• Solid: Displays solid vertical grid lines on the histogram.
• Dotted: Displays dotted vertical grid lines on the histogram.

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Table 104. Histogram Chart parameters (Sheet 3 of 6)

Parameters Description
2. Column Options
Show Column Amount Determines whether the chart displays the amount or count of
items.
• True: Displays the amount or count of items in the chart.
• (Default) False: Does not the display the amount or count of
items in the chart.
Show Percentages Determines whether percentage values appear above the columns
or to the right of the bars.
• True: Displays percentage values above the columns or to the
right of the bars.
• (Default) False: Does not display percentage values above the
columns or to the right of the bars.
Column Display Specifies the appearance of the columns or bars.
• (Default) Flat: Displays the columns or bars as flat rectangles.
• Cylinder: Displays the columns or bars as cylinders.
• Emboss*: Displays the columns or bars as three-dimensional
rectangles.
• LightToDark: Displays the columns or bars as shaded
rectangles.

*Emboss is misspelled as Embross in the dropdown list.

Column Width Specifies the relative width of the columns as a decimal between 0
and 1.

Default: 0.8
Column Label Font Specifies the font of the column labels that appear on top of the
bars in the histogram. These labels are visible if you set Show
Column Amount to True.

Default: 8-point Arial

3. Axis Options
X-Axis Number Format Specifies the notation of the numbers used for the x axis.
• (Default) Decimal: Uses decimal notation.
• Scientific: Uses scientific notation.

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Table 104. Histogram Chart parameters (Sheet 4 of 6)

Parameters Description
X-Axis Title Specifies the label for the x axis.

The default x-axis title is the category selected from the Data
Source list.
Y-Axis Type Specifies the axis type (scale) of the y axis.
• (Default) Linear: Plots the data on a linear scale.
• Log: Plots the data on a logarithmic scale.
• Percent: Plots the data as a percentage of the number of items.
Y-Axis Title Specifies the label for the y axis. The default y-axis title is Count.
Reduce Number of Determines whether the application increases readability by
Axis Labels reducing the maximum number of axis labels to 30. If the chart
includes more than 30 values, it displays only every second or
every third label.
• (Default) True: Reduces the maximum number of axis labels
to 30.
• False: Does not reduce the maximum number of axis labels to
30.
Axis Title Font Specifies the font used to denote the labels of the x and y axes.

Default: 12-point Arial

Axis Scale Font Specifies the font used to denote the scale of the x and y axes.

Default: 10-point Arial

4. Binning Options
Binning Method Specifies the number of data groups to display or the width of a
single data group.
• (Default) Auto: Groups the data by estimating the number of
columns to display the number of data items.
• FixedWidth: Groups the data according to the Width value.
• FixedNumber: Groups the data according to the Number of
Categories value.
Number of Bins Specifies the number of categories used to group the data.

Default: 20
Note For discrete numbers, the actual group number might be
different.

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Table 104. Histogram Chart parameters (Sheet 5 of 6)

Parameters Description
Bin Width Specifies the width of a single category used to group the data.

Default: 1
Note For discrete numbers, the actual group number might be
different.
Use Full Series Value Determines the range of data values that the application uses to
Range compile the histogram.
• (Default) True: Uses all data for the histogram.
• False: Uses only the data between the values specified by the
Minimum Value option and the Maximum Value option.
Minimum Value Specifies the minimum value of the displayed data range. When
you use this parameter and the Maximum Value parameter, set
Use Full Data Range to False. Use these two parameters when you
want to show only a subrange of the data in a histogram.
Maximum Value Specifies the maximum value of the displayed data range. When
you use this option and the Minimum Value option, set the Use
Full Data Range parameter to False.
5. Legend Options
Show Legend Determines whether a legend appears and where it appears.
• (Default) None: Does not display a legend.
• Top: Displays a legend at the top of the histogram.
• Left: Displays a legend to the left of the histogram.
• Bottom: Displays a legend at the bottom of the histogram.
• Right: Displays a legend to the right of the histogram.
Legend Font Specifies the font for the legend.

Default: 8-point Arial

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Table 104. Histogram Chart parameters (Sheet 6 of 6)

Parameters Description
6. Series Options
Show Only Checked Determines whether the chart is compiled from data in all result
Items rows or only data in result rows marked by check marks.
• True: Compiles the chart only from data in result rows
marked by check marks.
• (Default) False: Compiles the chart from data in all result
rows.
Target Series Color Specifies the color of the target series.

Default: Firebrick

Bar charts
Bar charts plot categorical and ordinal data types in columns with the count of the data types
as the column height.

The Data Source list contains the numerical data categories that are available for the bar chart.
The Options pane contains the different options that you can use to customize the bar chart.
Moving the cursor over the columns in the chart activates a tooltip with information about
the data category.

Y To display the data as a bar chart

1. In an open result file, choose View > Result Charts.

2. Click the Bar Charts tab in the Result Charts view.
3. From the Data Source list, select the type of data to display as a bar chart.
4. Click Refresh to draw the chart.
5. (Optional) To change the chart’s appearance, do the following:
a. Open the Options pane and adjust the colors, labels, and legends of the display. Or,
click Load to load the option settings that you most recently saved.
b. To save all the settings, click Save in the Options pane.
The new settings overwrite any previously saved settings. The application loads these
new settings when you click Load.
c. To return the Options pane settings to the original default settings, click Factory
Defaults in the Options pane.

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Table 105 describes the parameters on the Bar Chart page of the Result Charts view.
Table 105. Bar Chart parameters (Sheet 1 of 3)
Command or option Description
Options pane
Load Loads the Option pane settings that you saved with the Save
command.
Save Saves the settings that you selected in the Options pane.
Factory Defaults Resets the options in the Options pane to the default settings in
effect when you installed the application.
Chart Options
Chart Type Determines how the application plots the data.
• (Default) Column: Displays the data as columns extending
from bottom to top.
• Bar: Displays the data as bars extending from left to right.
Horizontal Grid Lines Determines whether the bar chart displays horizontal grid lines
and specifies the style of these lines.
• (Default) None: Displays no horizontal grid lines in the bar
chart.
• Solid: Displays solid horizontal grid lines in the bar chart.
• Dotted: Displays dotted horizontal grid lines in the bar chart.
Axis Options
X-Axis Title Specifies the label for the x axis. The default x-axis title is the
category selected from the Data Source list.
Y-Axis Title Specifies the label for the y axis. The default y-axis title is Count.
Y-Axis Type Specifies the axis type (scale) of the y axis.
• (Default) Linear: Plots the data on a linear scale.
• Log: Plots the data on a logarithmic scale.
• Percent: Plots the data as a percentage of the number of items.
Axis Title Font Specifies the font used to denote the labels of the x and y axes.

Default: 12-point Arial

Axis Scale Font Specifies the font used to denote the scale of the x and y axes.

Default: 10-point Arial

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Table 105. Bar Chart parameters (Sheet 2 of 3)

Command or option Description
Bar Options
Show Rotated Scale Determines whether the scale labels along the x axis are slightly
rotated to the right.
• (Default) True: Rotates the scale labels.
• False: Does not rotate the scale labels.
X-Axis Scale Angle Specifies the angle between the label and the x axis for the labels
when the Show Rotated Labels parameter is set to True.

Range: –90 to 90 degrees

Default: 30
Bar Display Specifies the appearance of the columns or bars.
• (Default) Flat: Displays the columns or bars as flat rectangles.
• Cylinder: Displays the columns or bars as cylinders.
• Emboss*: Displays the columns or bars as three-dimensional
rectangles.
• LightToDark: Displays the columns or bars as shaded
rectangles.

*Emboss is misspelled as Embross in the dropdown list.

Bar Width Specifies the relative width of the columns.

Range: 0.1–1.0

Default: 0.8
Show Amount Determines whether the amount, or count of items, is displayed in
the chart.
• True: Displays the amount or count of items in the chart.
• (Default) False: Does not the display the amount or count of
items in the chart.
Show Percentage Determines whether percentage values are displayed above the
columns or to the right of the bars.
• True: Displays percentage values above the columns or to the
right of the bars.
• (Default) False: Does not display percentage values above the
columns or to the right of the bars.

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Table 105. Bar Chart parameters (Sheet 3 of 3)

Command or option Description
Column Label Specifies the font of the column labels that appear on top of the
bars in the bar chart.

Default: 8-point Arial

Legend Options
Show Legend Determines whether a legend appears and where it appears.
• (Default) None: Does not display a legend.
• Top: Displays a legend at the top of the bar chart.
• Left: Displays a legend to the left of the bar chart.
• Bottom: Displays a legend at the bottom of the bar chart.
• Right: Displays a legend to the right of the bar chart.
Legend Font Specifies the legend font.

Default: 8-point Arial

Series Options
Show Only Checked Determines whether the chart is compiled from data in all result
Items rows or only data in result rows marked by check marks.
• True: Compiles the chart only from data in result rows
marked by check marks.
• (Default) False: Compiles the chart from data in all result
rows.
Series Color Specifies the color of the bars.

Default: CornflowerBlue
Data Source Displays the result category used to plot the data.

Pie charts
The Pie Chart page shows several categories of data as a solid circle composed of slices (a pie)
or as a ring (a doughnut). You can use a pie chart or a doughnut chart to indicate the relative
size of quantities of data.

Y To display the data as a pie chart

1. With an active result file, choose View > Result Charts from the menu bar.
2. Click the Pie Chart tab in the Result Charts view.

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3. From the Data Source list, select the type of data to display.
4. Click Refresh to draw the chart.
5. (Optional) To change the chart’s appearance, do the following:
a. Open the Options pane and adjust the colors, labels, and legends of the display and
specify how the chart displays small slices. Or, click Load to load the option settings
that you most recently saved.

Tip By default, the application consolidates small slices of 5% or less. To change

this setting, do one of the following:
• Select False for Collect Small Segments.

–or–
• Change the Small Slice Threshold (%) setting.

b. To save all the settings, click Save in the Options pane.

The new settings overwrite any previously saved settings. The application loads these
new settings when you click Load.
When you close the Result Charts view, the application stores the chart settings that
you selected. When you reopen the chart, it displays these stored settings if they are
available.
c. To return the Options pane settings to the original default settings, click Factory
Defaults in the Options pane.

Table 106 describes the parameters on the Pie Chart page of the Result Charts view.
Table 106. Pie Chart page parameters (Sheet 1 of 3)
Command or Option Description
Options pane
Load Loads the Option pane settings that you saved with the Save
command.
Save Saves the settings that you selected in the Options pane.
Factory Defaults Resets the options in the Options pane to the default settings in
effect when you installed the application.
Chart Options
Chart Type Specifies the type of chart to display:
• (Default) Pie: Displays the chart as a solid circle composed of
slices.
• Doughnut: Displays the chart as a ring.

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Table 106. Pie Chart page parameters (Sheet 2 of 3)

Command or Option Description
Vertical Rotation Specifies the angle of rotation around the vertical axis.

Default: 0
Angle of First Slice Specifies the location of the first chart slice.

Default: 0
Pie Slice Options
Show Type Name with Determines whether the application displays the name of the data
Value group next to the value.
• True: Displays the name of the data group next to the value.
• (Default) False: Does not display the name of the data group
next to the value.
Show Slice Amount Determines whether the application displays the amount of each
slice.
• (Default) True: Displays the amount of each slice.
• False: Does not display the amount of each slice.
Show Slice Percentage Determines whether the application displays the percentage of
each slice.
• (Default) True: Displays the percentage of each slice.
• False: Does not display the percentage of each slice.
Label Style Specifies the label style of the chart segments.
• Disabled: Does not display a label.
• (Default) Inside: Displays the label on top of the chart
segment.
• Outside: Displays the label outside the chart segment.
Labels Font Specifies the font of the data set labels.

Default: 9-point Microsoft Trebuchet bold

Small Slices Options
Collect Small Segments Determines whether the application consolidates small segments
together into a single slice.
• (Default) True: Consolidates small segments into a single
slice.
• False: Leaves small segments as is.

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Table 106. Pie Chart page parameters (Sheet 3 of 3)

Command or Option Description
Small Slice Threshold Specifies a percentage threshold for the slices to be consolidated
(%) into a single slice.

Default: 5%
Small Slice Collection Specifies the label for the pie segment composed of consolidated
Label segments.

Default: Other
Small Slice Collection Specifies the color of the pie segment composed of consolidated
Color segments.

Default: Gray
Show as Supplemental Determines whether to display small segments as a supplemental
Pie pie chart.
• True: Displays small segments as a supplemental pie chart.
• (Default) False: Leaves small segments as is.
Supplemental Pie Size Specifies the size of the supplemental pie chart relative to the
original pie chart.
• Largest: Displays the supplemental pie chart as much larger
than the original pie chart.
• Larger: Displays the supplemental pie chart as larger than the
original pie chart.
• Comparable: Displays the supplemental pie chart as about the
same size as the original pie chart.
• (Default) Smaller: Displays the supplemental pie chart as
smaller than the original pie chart.
• Smallest: Displays the supplemental pie chart as much smaller
than the original pie chart.
Data Source Displays the result category used to plot the data.

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Scatter plots
Use the Scatter Chart page to set up a scatter plot for visualizing whether there is a linear or
logarithmic relationship between two or three variables (columns) in a result table.

For details about working with scatter plots, see these topics:
• Set up a scatter plot
• Use a filter set to filter the scatter plot
• Customize the appearance of a scatter plot
• Customization options for a scatter chart plot
• Scatter Chart page parameters
• Scatter Chart page shortcut menu commands

Set up a scatter plot

Y To set up a scatter plot

1. Open a result file.

2. In the menu bar, choose View > Result Charts.
By default, the Result Charts view opens as a floating window.
3. Click the Scatter Chart tab.
4. In the Data Source list, select one of the available result tables.
The available selections depend on the workflow nodes in the processing workflow.
5. Select the variables as follows:
a. In the X Data list, select the variable that you want to plot against the x axis.
b. In the Y Data list, select the variable that you want to plot against the y axis.
c. To create a three-dimensional scatter plot, select the variable in the Z Data list that
you want to plot against the z axis.
Selecting a data value for the z axis adds a color gradient to the plotted data points
ranging from the lowest to the highest Z data value.
6. Click Refresh.

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Depending on your selections, a two- or three-dimensional linear plot of the data points
appears. With the default appearance settings, the data points appear as blue circles in a
2D plot and as circles of varying colors in a 3D plot. For a 3D plot, a color legend for the
lowest to the highest Z data value appears to the right of the scatter chart.
Figure 114. Three-dimensional scatter chart

Color legend for

the z-axis data

Use a filter set to filter the scatter plot

Y To interactively filter the scatter plot by using the Result Filters view

1. Set up and apply a set of result filters in the Result Filters view.
On the Scatter Chart page of the Result Charts view, the Refresh button turns orange.
2. Click Refresh to refresh the scatter chart plot.

Customize the appearance of a scatter plot

Y To customize the appearance of a scatter plot

1. Open the Options pane on the Scatter Plot page of the Result Charts view and pin it. See
“Display and pin the Options Pane for the Result Charts view.”
2. In the Options pane, do any of the following:
• To change the scaling, colors, labels, and legends in the display, under Axis Options,
make the appropriate changes.
• The application applies the changes as you make them.

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• To change the font size or font type of the axis labels, click the expand icon to the left
of Axis Scale Font or Axis Title Font. Then, make the appropriate selections or click
the browse icon to open the Font dialog box where you can make your selections.
• A browse icon and a set of font parameters appear.
• To return the option settings to the original default settings, click Factory Defaults.

Customization options for a scatter chart plot

Table 107 describes the formatting options for the Scatter Chart page.
Table 107. Options pane for a Scatter Chart (Sheet 1 of 2)
Parameter Description
Buttons
Load Loads the saved Options pane settings. Only click Load to apply a
set of saved settings; otherwise, the view reverts to the last saved
set.
Save Saves the new settings.
Tip The Scatter Chart view automatically updates as you change the settings in the
Options pane. However, the application does not save the settings until you click Save. If
you click Load before saving the new settings, the view reverts to the previously saved
settings.
Factory Defaults Resets the options in the Options pane to the default settings in
effect when you installed the Compound Discoverer application.
Axis Options
X Axis Type Specifies the axis type (scale) of the x axis: Linear or Logarithmic.
Y Axis Type Specifies the axis type (scale) of the y axis: Linear or Logarithmic.
Z Axis Type Specifies the axis type (scale) of the z axis: Linear or Logarithmic.
Axis Scale Font Specifies the font used to denote the scale of the x and y axes.
Axis Label Font Specifies the font used for the titles of the x and y axes.
X-Axis Title Specifies the title of the x axis.
Y-Axis Title Specifies the title of the y axis.
Series Options
Points Specifies the appearance of the points in the scatter chart. Also
specifies whether to show the points in the scatter chart.
Selected Points Specifies both the appearance of the selected points in the scatter
chart and whether to show the points in the scatter chart.

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Table 107. Options pane for a Scatter Chart (Sheet 2 of 2)

Parameter Description
Filtered-out Points Specifies the appearance of the filtered-out points in the scatter
chart and whether to show the points in the scatter chart.
Excluded Points The Compound Discoverer workflow nodes do not generate
excluded data points.

Scatter Chart page parameters

Table 108 describes parameters that are visible on the Scatter Chart page. Use these
parameters to set up the scatter plot.
Table 108. Scatter Chart parameters
Parameter Description
Data Source Specifies the data source for the plot. The data source is one of the
available result tables produced by the processing workflow.
Note The X, Y, and Z Data boxes list the available variables for the selected data source.
The variables are the available columns in the selected data source (result table).
X Data Specifies the variable to plot against the x axis.
Y Data Specifies the variable to plot against the y axis.
Z Data Specifies the variable to plot against the z axis.
Plot grid Two-dimensional grid where the application plots the data points.
By default, the plot area has no grid lines.

To add horizontal and vertical lines to the plot, make the

appropriate selection under Options in the Options pane.
Axis labels The default axis labels are the selected variable names.
Color legend When you create a 3D plot, the scatter chart includes a color
legend for the z-axis color gradient. The numeric value of the
highest z-axis data point appears above the color legend.
Options pane Use the parameters in this pane to customize the Scatter Chart
page. For more information, see Table 107.
Buttons
Refresh Refreshes the content of the chart area.

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Scatter Chart page shortcut menu commands

Table 109. Scatter Chart shortcut menu commands (Sheet 1 of 2)
Command Description
Show Position Tooltips Displays a tooltip when you place the cursor over a data point.
Zoom Out Decreases the zoom of both axes.
Undo All Zoom/Pan Displays the full x-axis range of the plot.
Copy > Image Copies the scatter chart plot as a bitmap (raster) image to the
Clipboard.
Copy > Data Copies the data points for the selected variables to the Clipboard.
Export > Image As Saves the plot to any of these file types: EMF, PNG, GIF JPG,
TIF, and BMP
Export > Data As Opens the Save As dialog box where you can save the data as a
plain text file.

By default, the application saves the file to the last open folder
and uses the following convention to name the file:
ResultTable_x_XDataSelection_Range_YDataSelection_Range
_z_ZDataSelection_Range_DataPointType.txt

Use the Browse icon to select a different folder.

Exporting data from a scatter plot creates three text files: File
name Filtered-out Points.txt, File name Points.txt, and File name
Selected Points.txt.
Select Item for Point Highlights the appropriate row in the result table (selected Data
Source).
Check Point By default, changes the selected point to a red diamond and
selects the check box in the Checked column for the selected
point (row in the selected Data Source result table). You can
change the appearance of selected points by making the
appropriate selections in the Series Options > Checked Points
area of the Options pane. When you save the data to a text file,
the Selected Points.txt file lists the selected points.

To select a point, right-click the point of interest on the plot and

choose Check Point.
Uncheck Point Undoes the selection of a selected point. You can change the
appearance of points by making the appropriate selections in the
Selected Options > Points area of the Options pane.

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Table 109. Scatter Chart shortcut menu commands (Sheet 2 of 2)

Command Description
Check All Visible Points Selects all of the visible points in the scatter plot.
Uncheck All Visible Undoes the selection of the visible points in the scatter plot.
Points

Trend Chart view

Use the Trend Chart view to compare the chromatographic peak areas for compounds by
sample group.

You define the sample groups by selecting one or more check boxes under Group By in the
collapsible pane to the left of the chart. In addition, you can change the sort order of each
sample group and the hierarchy of the sample groups.

You can use the Trend Chart view to plot the data for a compound (or feature) in these result
tables: Compounds, Expected Compounds, and Merged Features. For a single compound, the
chart can plot the data as a trendline plot or a box-and-whisker plot. For two or more
compounds, the chart displays the data only as a trendline plot, with one trendline for each
compound.

Note The trendline plot can plot sample groups that include only one data point;
however, to plot the error bars for a group, it requires a minimum of two data points.
With two data points, the circle represents the calculated median and the error bars
represent the minimum and maximum areas.

The box-and-whisker plot requires a minimum of two data points to plot the box for a
sample group. It does not plot sample groups that include only one data point. If none of
the sample groups includes the minimum number of data points, the following text
appears in the chart area: No results available to plot.

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Trend Chart view

By default, the trendline plot type plots the median peak area for the selected component on
the y axis against equally spaced sample groups on the x axis and connects the data points with
straight lines. Each data point appears as a solid circle with two error bars. The circle
represents the median. If the group includes a least three data points, the application uses the
following equation to calculate the standard error of the median and draw the error bars:
standard error of the median = π ⁄ 2 × std. dev (x) ⁄ ( N )
Figure 115. Trendline display of the data distribution

Error bars = standard error Median

of the median

The box-and-whisker chart plots the peak area for a selected component on the y axis as a
rectangle against equally spaced sample groups on the x axis. The height of the rectangle
represents the peak areas in the interquartile range (see Figure 116). The application uses the
following equations to calculate the upper and lower whiskers:
Interquartile range (IQR) = Quartile 3 (Q3) – Quartile 1 (Q1)
Upper whisker = Q3 + IQR × 1.5
Lower whisker = Q1 – IQR × 1.5

When the data set contains a small number of data points, the whiskers typically end at the
highest and lowest data points. If the data set does not include a data point between the top of
the interquartile range and the calculated value for the upper whisker, the application does not
draw an upper whisker. If the data set does not include a data point between the bottom of the
interquartile range and the calculated value for the lower whisker, the application does not
draw a lower whisker.
Figure 116. Box-and-whisker display of the data distribution
Upper whisker

Third quartile

Interquartile
range Median
First quartile

Lower whisker

Note To calculate the quartiles, the application uses a method that is similar to the type 6
method in the R statistical computing software.

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Trend Chart view

For details about working with the Trend Chart view, see the following topics:
• Open the Trend Chart view
• Define the sample groups to compare
• Compare the peak areas for a single compound by sample group
• Change the sort order of the defined groups
• Compare the peak areas for multiple compounds by group
• Change the hierarchy of the variables used for grouping
• Show the error bars in a trendline chart
• Trend Chart view parameters

Open the Trend Chart view

Y To open the Trend Chart view

1. Open the result file of interest.

2. From the menu bar, choose View > Trend Chart.
The Trend Chart view opens as a docked window to the right of the result tables.
• If the active result table does not contain a consolidated compounds list, the
following text appears in the graph area: No Results Available to Plot. The
Compounds, Expected Compounds, and Merged Features tables contain a
consolidated compounds list.
• If the active result table contains a consolidated compounds list and you select a row,
a box-and-whisker plot appears in the graph area with data from the first table row.

Define the sample groups to compare

Y To define the sample groups for a trend chart plot

1. Open the result file of interest, and then open the Trend Chart view.
2. In the left pane, under Group By, select the appropriate check boxes to define the sample
groups.

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Trend Chart view

Compare the peak areas for a single compound by sample group

Y To compare the peak areas for a single compound by sample group

1. Open a result file, open the Trend Chart view, and define the sample groups that you
want to compare.
2. In the Compounds, Expected Compounds, or Merged Features table, select the
compound (or feature) of interest.
3. Right-click the graph area and choose Show Legend.
The legend displays the sample group colors.
4. In the Plot Type list, select Trendline Chart or Box Whisker Chart.
Depending on the selection, either a trendline plot or a box-and-whisker plot appears in
the graph area. A tooltip opens when you place the cross-hair cursor anywhere on a box or
whisker in the box-and-whisker plot or on data point in a trendline plot.
Figure 117 shows a box-and-whisker plot. Placing the cross-hair cursor on a box or
whisker opens a tooltip with descriptive statistics.
Figure 117. Box-and-whisker plot for one compound

Change the sort order of the defined groups

In the Trend Chart view, you can display the defined groups from left to right in ascending or
descending order by chromatographic peak area.

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Trend Chart view

Y To change the sort order of the defined groups in the Trend Chart view

In the left pane, under Group By, click the sorting icon, , next to the study variable to
sort and choose Sort Ascending or Sort Descending.
Changing the sort order changes the order of the groups on the x axis (Figure 118).
Figure 118. Trend chart with compounds grouped by solvent and sorted in ascending or
descending order by chromatographic peak area

Sorted in
ascending
order

Sorted in
descending
order

Compare the peak areas for multiple compounds by group

Y To compare the peak areas for multiple compounds by group

1. Open the result file of interest, open the Trend Chart view, and define the sample groups.
2. To select the compounds to plot, press the CTRL key and select rows in the result table
(Compounds, Expected Compounds, or Merged Features), taking care to avoid clicking
an editable table cell.
The plot changes to a scaled trendline. The data points represent the group median. The
legend displays the name (if available), molecular weight, and retention time of each
selected compound.
Figure 119 shows a scaled trendline chart. To view descriptive statistics for the data
points, click anywhere in the plot to activate the cross-hair cursor, and then place the
cross-hair cursor on each data point of interest.

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Trend Chart view

Figure 119. Trendline chart with three compounds

Change the hierarchy of the variables used for grouping

Changing the hierarchy of the variables used for grouping in the Trend Chart view modifies
the sample grouping.

Y To change the hierarchy of the variables used for grouping

Use the handle ( ) next to the variable to drag the variable up or down in the list.

Show the error bars in a trendline chart

Y To view error bars for each data point in a trendline chart

1. In the Scaling list above a trendline plot in the Trend Chart view, select Unscaled.
2. Right-click the plot and choose Show Standard Errors.
The application plots the group median with error bars for the standard error of the
median (Figure 120).

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Trend Chart view

Figure 120. Trendline chart with error bars

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Isotopologues Distribution Chart view

Trend Chart view parameters

Table 110 describes the parameters in the Trend Chart view.
Table 110. Trend Chart view parameters
Parameter Description
Plot Type Controls the plot type in the graph area.

Selections: Trendline Chart or Box Whisker Chart

The Box Whisker Chart selection is only available for displaying

a single compound.
Scaling (for the Select the chart scaling:
trendline chart) • Unscaled—Enables the Show Standard Errors command in
the shortcut menu.
• Scaled
• Scaled to Study Factor Value
Use Normalized Areas Displays the normalized areas for the data.

Available when the processing workflow included the Normalize

Areas node.

Isotopologues Distribution Chart view

For LC studies, if the analysis included the Analyze Labeled Compounds node, labeled
samples, and at least one unlabeled reference sample, you can view a distribution chart of the
detected isotopologues.

Y To open the Isotopologues Distribution Chart and review the isotopologues

1. Open a result file for a stable isotope labeling analysis.

2. From the application menu bar, do one of the following:
• Choose Window > Apply Layout > Stable Isotope Labeling.
The Isotopologues Distribution Chart, Trend Chart, and Metabolika Pathways view
open as a tabbed group to the right of the result tables. Under Group By, the File
check box is selected.
–or–
• Choose View > Isotopologues Distribution Chart.
The Isotopologues Distribution Chart opens to the right of the result tables. Under
Group By, all the check boxes are clear.

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Isotopologues Distribution Chart view

The compound’s name, elemental composition, MW, and RT appear above the graph
(Figure 121). The bars are colorized by input file.
Figure 121. Isotopologues Distribution Chart with no grouping selected

3. Do any of the following:

• To display a tooltip for a bar, point to the bar.

Tip By default, the Show Position Tooltips feature is turned on. If a tooltip does
not appear, click the chart. If a tooltip still does not appear, right-click the chart
and choose Show Position Tooltips.

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Isotopologues Distribution Chart view

Figure 122. Isotopologues Distribution Chart with a tooltip

• To group the isotopologues by input file, under Group By, select the File check box.
• To group the isotopologues by sample type, under Group By, select the Sample Type
check box.
Figure 123. Isotopologues grouped by sample type

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Mass Defect Plot view

Mass Defect Plot view

Use the Mass Defect Plot view to find similar compounds by visualizing the calculated mass
defects for a set of compounds against their molecular weights. Your choices for calculating
the mass defect in this view are the same as those for the Calculate Mass Defect and Filter By
Mass Defect nodes.

Y To set up the mass defect plot and examine it for similar compounds

1. Open a result file from a processing workflow that included the Detect Compounds
node.
2. From the application menu bar, choose View > Mass Defect Plot.
The compounds listed in the Compounds table appear as blue circles in the Mass Defect
plot. The y-axis label displays the mass defect type, and the red dashed lines indicate the
valid range of the mass defect values.
3. To specify how to calculate the mass defect, do the following:
• From the Type list, select the mass defect calculation. Then, if you selected Kendrick
Mass Defect, enter the Kendrick formula.
• From the Rounding list, select Ceiling, Floor, or Round.
4. To highlight the compounds that have an assigned name in orange, select the Highlight
Named Compounds check box.
5. To work interactively with the plot, do the following:
• Use the shortcut menu commands for the view to do any of the following:
– Zoom in or out of the plot.
– Copy the image or the data points to the Clipboard.
– Export the image or the data points to an external file.
– Check or clear the visible data points. Checking a data point highlights the data
point in red and places a check mark in the Checked column for the compound
in the Compounds table.
• Double-click a data point to navigate to the compound in the Compounds table.
• Point to a compound to display a tooltip with information about the compound’s
mass defect, name, elemental composition, molecular weight, and retention time.

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Principal Component Analysis view

Figure 124. Mass Defect Plot view with its shortcut menu displayed

For more information, see “Mass defect types and visualization techniques.”

Principal Component Analysis view

Use the Principal Component Analysis view to visualize the correlation between multivariate
data in a set of observations. A principal component analysis transforms a set of observations
for possibly correlated variables into an artificial set of independent linear combinations of the
original variables known as principal components (PC1, PC2, PC3 and so on). PC1 has the
most variation and the highest principal component has the least variation.

The Principal Component Analysis view contains three pages: Scores Plot, Loadings Plot, and
Variances Plot. The scores plot shows the correlation among the observations. The loadings
plot shows the relationship among the variables for a given pair of principal components. The
variance plot shows the percentage and cumulated percentage of the variance that a principal
component accounts for. In general, as the proportion of variance increases for the first two or
three principal components, the dissimilarity between the sample groups increases.

For details about working with the Principal Component Analysis view, see the following
topics:
• Set up a principal component analysis
• Interpret the scores plot
• Interpret the loadings plot
• Work interactively with the loadings plot

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Principal Component Analysis view

• Interpret the variance plot

• Principal Component Analysis view parameters

Set up a principal component analysis

Y To set up a principal component analysis

1. Open a result file that contains any of these result tables:

• Compounds
• Expected Compounds
• Merged Features
2. From the menu bar, choose View > Principal Component Analysis.
If the result file contains a Compounds table, the Principal Component Analysis view
opens with the Compounds table selected as the data source.
3. Do the following:
• In the Data Source list, select the appropriate result table as appropriate for the data
set.
• In the X Data list, select PC1, PC2, PC3, PC4, or PC5.
In most cases, select PC1 or PC2, as these principal components have the most
variation.
• If the data points differ by several orders of magnitude, select the Center and Scale
check box.
• If the processing workflow included the Normalize Areas node, select the Use
Normalized Areas check box as appropriate.
• To remove points from the plot, clear the check boxes under Filter By as appropriate.
Using the new population, the application recalculates the principal components,
including their contribution to the variance, and shifts the coordinates of the remaining
data points.
4. To view additional information, do any of the following:
• To display a legend at the bottom of the plot, right-click the plot and choose Show
Legend.
• To show a tooltip when you place the cross-hair cursor on a data point in the plots,
right-click the plot and choose Show Position Tooltips.

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Principal Component Analysis view

Interpret the scores plot

Use the scores plot of the Principal Component Analysis view to interpret the relationship
among the sample groups. Sample groups that are near each other are similar.

The Principal Component Analysis view is available for result files that include any of these
tables: Compounds, Expected Compounds, or Merged Features.

Y To review and interpret the scores plot

• Check the percentage values for the principal components. The labels on the x and y axes
include the proportion of variance that the principal components add to the total variance
as a percentage.
• Place the cross-hair cursor on a data point to view its coordinates.
Figure 125 shows the scores plot for the compounds that leach out of four o-ring types
soaked in ethanol. The black, brown, and white O-rings show a similar variance for PC1,
while the red O-rings show a significant variance in the other direction for PC1. The
brown and white O-rings show a similar variance for PC2.
Figure 125. Scores plot for four O-ring types (white, brown, red, and black)

Figure 126 shows the scores plot for the compounds found in two sources of oregano.
The principal components for the two groups are in opposite quadrants, which means the
two groups are significantly different.

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Principal Component Analysis view

Figure 126. Scored plot for two sources of oregano

Interpret the loadings plot

Use the loadings plot to interpret the relationship among the variables.

Y To interpret the loadings plot

1. To determine the relative correlation between various data points, review their relative
location in the plot.
• Data points that are near each other are similar.
• Data points that are on opposite sides of the origin have a negative correlation.
• Data points in the corners of the plot have a strong contribution to both principal
components—that is, these data points differentiate between groups.
2. Place the cross-hair cursor on a data point to display a tooltip information about the
compound.
For LC studies the tooltip displays the principal component coordinates, molecular
weight, retention time, maximum peak area, and number of adduct ions. See Figure 127.

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Principal Component Analysis view

Figure 127. Loadings plot with its shortcut menu displayed (LC study)

Shortcut menu

Tooltip for the data point under the cross-hair pointer

Work interactively with the loadings plot

The Loadings Plot is interactive with the selected data source table—that is, double-clicking a
data point in the loadings plot selects its row in the data source table and updates the other
opened graphical views. In addition, checking data points (compounds, expected compounds,
or features) in the Loadings Plot checks the corresponding data points in these interactive
views—Differential Analysis, Partial Least Squares Discriminant Analysis, and Descriptive
Statistics.

Y To select a data point or check one or more data points in the Loadings Plot

• To select a data point, double-click it.

The application highlights the corresponding row in the data source table and updates the
other opened and interactive views.
• To check a single data point, right-click the point and choose Check Point.

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Principal Component Analysis view

• To check multiple points, drag the mouse pointer across a rectangular area of the plot to
zoom in on that area, then right-click the plot and choose Check All Visible Points.
The application selects the check boxes for the checked data points in the data source
table and changes the color of the selected points to blue in the loadings plot. The color
of the checked data points also changes to blue in the interactive views.
Figure 128. Loadings plot with checked points shown in blue

Selected data points in the loadings plot

• To clear all the selected check boxes in the result table, right-click the result table and
choose Uncheck All > In This Table.

Interpret the variance plot

Use the variance plot to determine the relative differentiation between sample groups.

Y To interpret the variance plot

Compare the contribution of the first two or three principal components to the
cumulative variance.
For example, Figure 129 shows the variance plot for the compounds leached from red
O-rings soaked either in water or an aqueous solution of sodium chloride.
Figure 130 shows the variance plot for the same type of O-rings soaked either in water or
ethanol.

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Principal Component Analysis view

The PC1–PC3 components make up more of the cumulative variance when comparing
the extraction strength of water to ethanol than when comparing water to a salt solution.
From these results, you can infer that the extraction strengths of water and ethanol differ
more than the extraction strengths of water and a salt solution.
Figure 129. Water versus an aqueous solution of sodium chloride (extraction strength)

Figure 130. Water versus ethanol (extraction strength)

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Descriptive Statistics view

Principal Component Analysis view parameters

Table 111 describes the parameters in the Principal Component Analysis view.
Table 111. Principal Component Analysis parameters
Parameter Description
Data Source Specifies the source of the data. The selection list depends on the
processing workflow.

Selections: Compounds, Expected Compounds, and Merged

Features
X Data Specifies the principal component to plot on the x axis.

Selections: PC1, PC2, PC3, PC4, or PC5

Y Data Specifies the principal component to plot on the y axis.

Selections: PC1, PC2, PC3, PC4, or PC5

Center and Scale Centers and scales the data.
Use Normalized Areas Uses the normalized data.

Available if the processing workflow includes the Normalize

Areas node.
Scores Plot page Displays a plot of one principal component versus a second
principal component.
Loadings Plot page Displays the compounds in the selected table plotted against the
selected principal components.

This plot is interactive with the selected results table.

Variances Plot page Displays the proportion and the cumulative proportion of the
variance contributed by each principal component.

Descriptive Statistics view

Use the Descriptive Statistics view to visually compare the statistics of the peak areas for all
compounds currently displayed in one of the following result tables as a box-and-whisker plot:
• Compounds
• Expected Compounds

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Descriptive Statistics view

A box-and-whisker plot displays the data for a variable as a rectangular box with a set of
whiskers at each end. The line through the rectangle represents the median value in the data
set. The lower portion of the rectangle represents the data points that fall within the second
quartile and the upper portion represents the data points that fall within the third quartile.
The circles that fall outside the fence whiskers are outliers.

The application uses the following equations to calculate the upper and lower fences:
Interquartile range (IQR) = Quartile 3 (Q3) – Quartile 1 (Q1)
Upper fence = Q3 + IQR × 1.5
Lower fence = Q1 – IQR × 1.5

Note To calculate the quartiles, the application uses a method that is similar to the type 6
method in the R statistical computing software.

Figure 131. Box-and-whisker display of the data distribution

Outlier data points

Upper fence

Third quartile

Interquartile
range Median

First quartile

Lower fence

Outlier data point

By default, the graph displays the data for all the samples and duplicates the grouping on the
Grouping and Ratios page of the analysis. Each group appears in a different color. The legend
shows the colors of the sample groups.

Use the Group By check boxes in the collapsible pane to change the grouping. Use the Filter
By check boxes to remove samples from the plot.

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Descriptive Statistics view

For more information about the shortcut menu commands, see “Copy or save graphical views
for publication.”
Table 112. Common tasks for the Descriptive Statistics view
Task Procedure
Copy or save the data as an image. 1. Right-click the plot and choose Show Legend.
2. Right-click the plot and choose Copy > Image to copy an image to the
Clipboard.
–or–
Right-click the plot, choose Export > Image As, and select an image type
to save the data to an image file.
Copy or save the data as editable Right-click the plot and choose Copy > Data to copy the text to the
text. Clipboard.

You can paste this text to Notepad, an Excel spreadsheet, and so on. The data
appears in a columnar format.

–or–

Right-click the plot and choose Export > Data As to save the data to a text file.

The file contains two data sets. The first set consists of these columns from left
to right: Groups, Name, Minimum Value, Maximum Value, Std. Deviation,
Mean, Median, Q1 Value, Q2 Value, and Q3 Value. The second set lists the
outlier data points and consists of these columns from left to right: Groups,
Name, and Outlier.
View the entry in the result table for In the plot, double-click the data point.
an outlier data point.
Select the check box for an outlier In the plot, right-click the data point and choose Check Point.
data point.
In the result table, the check box is selected for the corresponding compound
or expected compound.
Export the outlier data points to a 1. In the view, zoom in on the outlier points so that they are the only visible
spreadsheet. points on the screen.
2. Right-click the plot and choose Check All Visible Points to select the
rows for these outliers in the compounds table.
3. In the compounds table, sort the checked rows by the variable of interest.
For example, sort the rows by molecular weight, retention time, or both.
4. Right-click the compounds table and choose Export > Export to Excel.
5. In the Export to Excel dialog box, select a folder and name the file, select
the Checked Items Only check box, and click Export.

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Descriptive Statistics view

Table 113 describes the components of the Descriptive Statistics view.

Table 113. Descriptive Statistics view parameters
Parameter Description
Data Source Specifies the result table for the source data.

Selections: Compounds or Expected Compounds

Log-transform Data Determines whether the data appears in a linear scale or the log10
scale.

Selecting this check box transforms the area counts to the log10
scale.
Use Normalized Areas Select to display normalized chromatographic peak areas.

Available when the processing workflow includes the Normalize

Areas node.
Graph
x axis Displays the name of the sample group.
y axis Displays the area in a linear scale or in a log10 scale.
Outlier data points The circles represent outlier points. When the Show Position
Tooltips command is enabled, placing the cursor over a data point
displays the following information: MW, RT, Max. Area, and
#Adducts.
Rectangle The rectangles represent the second and third quartiles for the
data set.

When the Show Position Tooltips command is enabled, placing

the cursor over the rectangle displays the following information:
filename, group, maximum value (including the outliers), 3rd
quartile, median, 1st quartile, minimum value (including the
outliers).
Legend By default, the legend is hidden.

Choosing Show Legend from the shortcut menu displays the

legend. The legend shows the group colors.

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Differential Analysis view

Differential Analysis view

Use the Differential Analysis view to display a volcano plot of the differential analysis
performed during data processing or to run a new differential analysis.

For details about working with the Differential Analysis view, see the following topics:
• Review the initial differential analysis
• Change the analysis settings for a differential analysis
• Run a new differential analysis
• Differential Analysis view parameters and shortcut menu commands

Review the initial differential analysis

Y To open the Differential Analysis view and review the initial analysis

1. Open the result file for an analysis that included at least two raw data files.
2. In the menu bar, choose View > Differential Analysis.
If the processing workflow included the Differential Analysis node, the Differential
Analysis view opens with the differential analysis from data processing. The ratios in the
Comparison list match the ratios on the Grouping and Ratios Summary page of the
Summaries view. The initial p-value setting is 0.05 (–log10 0.05 = 1.3) and the initial
Log2 Fold change setting is 1 (a ratio of 2 to 1). Depending on the setting for the Log10
Transform parameter in the Differential Analysis node, the y-axis scale spans the p-value
range (0–1) or the –log10 p-value range (–log10 0 = Infinity, –log10 1 = 0).
3. To show the legend, right-click the plot and choose Show Legend.
The data points are color-coded, as defined by the legend.
Figure 132 shows a comparison between two extraction solvents—water and an aqueous
solution of 50% ethanol.

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Differential Analysis view

Figure 132. Differential Analysis view with the analysis run during data processing (LC study)

Analysis summary for the negative fold Analysis summary for the positive fold
changes (down-regulated compounds) changes (up-regulated compounds)

Change the analysis settings for a differential analysis

Y To change the analysis displayed in the volcano plot

• Select a different ratio from the Comparison list. This changes the data points in the plot.
• Change the p-value setting by dragging the slider. This changes the y-axis range of the
shaded areas.

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Differential Analysis view

Figure 133 shows the effect of changing the p-value setting.

Figure 133. P-value decreased from 0.05 to 1E–12

• Change the fold change setting by dragging the slider. This changes the x-axis range of the
shaded areas.
Figure 134 shows the effect of changing the Log2 Fold Change setting.
Figure 134. Fold change increased from 1 to 8

Run a new differential analysis

Use the Perform New ANOVA Calculation dialog box to set up and compare different ratios
than those on the Grouping and Ratios page of the analysis.

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Differential Analysis view

Y To run a new differential analysis

1. In the Differential Analysis view, click the Perform New ANOVA Calculation icon, ,
to the right of the Data Source box.
The Perform New ANOVA Calculation dialog box opens.
Figure 135. Perform New ANOVA Calculation dialog box in front of the Differential Analysis
view

2. In the Data Source list, select a different result table if applicable.

3. In the Fixed Effect area, select one or more variables to create new sample groups.
4. In the Reference list, select one of the new sample groups as the denominator for the
group ratios.
5. (Optional) To transform the data to the log10 scale, select the Transform Data check box.
6. (Optional) To normalize the chromatographic peak areas, select the Use Normalized
Areas check box. This check box is available if the processing workflow included the
Normalize Areas node.
7. (Optional) To calculate p-values for a nested design, select the Use Nested Design check
box. This check box is available if the original analysis included a biological study factor
and nested sample groups.
8. Click Calculate.

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The Perform New ANOVA Calculation dialog box closes, and the Pending Results area
appears at the bottom of the view. The Pending Results area displays the data source
(result table), the reference group, and the progress of the new calculation.

When the calculation is complete, the new ratio (sample group vs. reference group) appears
in the Comparison list.
9. To view the analysis, select the data source in the Data Source list and the new ratio in the
Comparison list.
The volcano plot updates with the selected analysis.

Differential Analysis view parameters and shortcut menu commands

Table 114 describes the parameters in the Differential Analysis view.
Table 114. Differential Analysis view parameters (Sheet 1 of 2)
Parameter Description
Data Source Specifies the result table for the source data.

Selections: Compounds or Expected Compounds table

Perform New Opens the Perform New ANOVA Calculation dialog box for
ANOVA setting up a new differential analysis.
Calculation
Comparison Specifies the ratio for comparison.

Selections: Generated ratios on the Grouping and Ratios page of

the analysis and any new analyses that you have run and saved

To save the differential analyses run in the Differential Analysis

view, save the result file.
P-value Specifies the p-value for the null hypothesis.

Use the slider to change the value in the corresponding box.

Default: 0.05 (–log10 0.05 = 1.3)

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Differential Analysis view

Table 114. Differential Analysis view parameters (Sheet 2 of 2)

Parameter Description
Log2 Fold Change Specifies the fold change (ratio in the log base 2 scale) between the
sample group and the reference group. This value creates an upper
and lower threshold for each group ratio.

Use the slider to change the value in the corresponding box. Data
points that fall outside the upper and lower thresholds are in the
shaded regions.

Default: 1 (two-fold change)

Graph
x axis Displays the log2 fold change.
y axis Displays the p-value in a linear scale or in a –log10 scale.
Analysis summaries The summaries display the number of data points with a p-value
above the statistical significance level and a fold change outside the
empirical threshold.
Shaded regions The region shaded in red identifies the data points that are
significantly different (populations differ based on the p-value
setting) and that fall outside the lower fold change threshold.

The region shaded in green identifies the data points that are
significantly different (populations differ based on the p-value
setting) and that fall outside the upper fold change threshold.
Legend By default, the legend is hidden.

Choosing Show Legend from the shortcut menu displays the

legend. The legend contains color-coded circles for these
conditions:
• Nonsignificant and does not meet FC (fold change) threshold
• Nonsignificant and greater than upper FC threshold
• Nonsignificant and less than lower FC threshold
• Significant and does not meet FC threshold
• Significant and greater than upper FC threshold
• Significant and less than lower FC threshold

Table 115 describes the shortcut menu commands for the Differential Analysis view.
Table 115. Shortcut menu commands for the Differential Analysis view (Sheet 1 of 2)
Command Description
Show Position Tooltips Displays information about the compound.
Zoom Out Undoes the last zoom.
Undo All Zoom/Pan Zooms out to the full plot range.

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Partial Least Squares Discriminant Analysis view

Table 115. Shortcut menu commands for the Differential Analysis view (Sheet 2 of 2)
Command Description
Copy and Export See “Export spectral data to a new or existing mzVault
commands library.”
Show Legend Displays the legend for the color-coded data points.
Note The color-coded data points (circles) represent compounds in the selected data
source. Selecting a data point turns it blue and selects the check box for the corresponding
compound in the data source table.
Check Point To activate this command, point to a data point.

Selects the data point in the view and the check box for the
corresponding compound in the data source table.
Uncheck Point To activate this command, point to a selected compound.

Returns the data point to its original color clears the

corresponding check box in the data source table.
Check All Visible Points Selects all the visible data points.
Uncheck All Visible Points Clears the check boxes for all the visible data points.
Check All Up-Regulated Selects all the data points in the pink-shaded region of the
Points plot.
Check All Down-Regulated Selects all the data points in the green-shaded region of the
Points plot.

Partial Least Squares Discriminant Analysis view

Use the Partial Least Squares Discriminant Analysis view to determine whether two groups are
different and to identify the variables that contribute to that difference.

See these topics:

• Identify a set of compounds to discriminate groups
• Partial Least Squares-Discriminant Analysis view parameters

Identify a set of compounds to discriminate groups

Y To determine a set of compounds that you can use to tell two groups apart

1. Open a result file from an analysis with study factors.

2. From the menu bar, choose View > Partial Least Squares - Discriminant Analysis.

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Partial Least Squares Discriminant Analysis view

The Partial Least Squares Discriminant Analysis view opens to the right of the tabbed
result tables.
3. In the collapsible pane on the left, under Discriminate By, select the study factors that you
want to discriminate by.
4. On the right above the plot, select the data source from the Data Source list.
5. In the #sPLS-DA Compounds box, type the number of compounds that you want to use
to differentiate the selected study factors.
6. To update the plot, click anywhere in the plot.
The orange circles represent the discriminating compounds.
7. Right-click the plot and choose Check All sPLS-DA Points.
The application selects the check boxes of the corresponding compounds in the selected
data source. The blue circles represent the checked discriminating compounds.
Figure 136. PLS-DA view with five checked discriminating compounds (LC study)

8. To view the list of compounds that you can use to differentiate the selected experimental
variables, set up a result filter to display only the checked compounds in the selected result
table.

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KEGG Pathways view

Partial Least Squares-Discriminant Analysis view parameters

Table 116 describes the parameters in the Partial Least Squares - Discriminant Analysis view.
Table 116. Partial Least Squares - Discriminant Analysis view parameters
Parameter Description
Data Source Specifies the result table for the source data.

Selections: Compounds table or Expected Compounds table

sPLS-DA Component Specifies the analysis component.

Selection: 1 to 6
#sPLS-DA Specifies the number of compounds that when used together can
Compounds discriminate between the values for the study variables selected
under Discriminate By.
Use Normalized Areas Uses the normalized areas in the result file.

Available when the processing workflow includes the Normalize

Areas node.

KEGG Pathways view

Use the KEGG Pathways view to display the reaction pathways for a mapped compound. You
can map compounds in the following compounds tables: Compounds table and Expected
Compounds table.

Y To view the KEGG pathways for a compound

1. Open a result file that contains mapped KEGG pathways—that is, a result file from an
analysis that included the Map to KEGG Pathways node.
2. In the main compounds table, select a compound.
3. Below the main compounds table, click Show Related Tables to show the related tables.
4. In the related tables pane, click the KEGG Pathways tab to make it the active result table.
5. In the KEGG Pathways table, select the pathway that you want to view.
6. In the menu bar, choose View > KEGG Pathways.
The selected KEGG pathway opens. The blue circle indicates the selected compound in
the KEGG pathway. The red circles indicate related compounds that were not found in
the mzCloud database. The green circles indicate related compounds that were found in
the mzCloud database.

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KEGG Pathways view

Figure 137 shows the selections of caffeine in the Compounds table and caffeine
metabolism in the KEGG Pathways table. The related Compounds tables shows the
compounds related to caffeine, which appear as red circles in the pathway diagram.
Figure 137. Caffeine metabolism pathway where caffeine appears as a blue circle (LC study)

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BioCyc Pathways view

BioCyc Pathways view

When the processing workflow for a result file includes the Map to BioCyc Pathways node,
use the BioCyc Pathways view to display the mapped pathways for a selected compound.

Y To view the BioCyc Pathways for a compound

1. Open a result file for an analysis that maps the detected compounds to their BioCyc
pathways.
2. In the main table pane, click the BioCyc Pathways tab.
3. Select a pathway of interest.
4. Below the BioCyc Pathways table, click Show Related Tables.
5. Click the BioCyc Results tab.
6. In the BioCyc Results table, select a compound of interest.

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BioCyc Pathways view

Figure 138. BioCyc Results table for the selected pathway

7. From the application menu bar, choose View > BioCyc Pathways.
The BioCyc Pathways view opens to the right of the result tables.
8. In the Omics-Overlay list, select Area.
Figure 139 shows a BioCyc pathway with an Area overlay.

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BioCyc Pathways view

Figure 139. BioCyc Pathways view with an area overlay

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Metabolika Pathways view

Metabolika Pathways view

Use the Metabolika Pathways view to display the mapped pathways for a selected compound.

Y To view a mapped pathway for a compound

1. Open a result file from an analysis that included the Map to Metabolika Pathways node.
2. In the Compounds table, select the compound.
3. Click Show Related Tables.
4. In the Related Tables pane, click the Metabolika Pathways tab.
5. Select the pathway that you want to view.
6. From the application menu bar, choose View > Metabolika Pathways.
The view opens to the right of the Compounds table and displays the selected pathway.
The structure for the selected compound is blue, the structures for other detected
compounds are red, and the structures for undetected compounds in the pathway are
black.
7. To overlay a data source, select the source from the Overlay Data Source list and type or
select a cell size from 6 to 30 pixels in width in the Overlay Cell Size box.
The data source selections depend on the processing workflow, but always include the
annotation source, chromatographic peak area, or Metabolika pathways graphic.

Retention Time Corrections view

When the processing workflow for a result file includes the Align Retention Times node and
the analysis includes more than one input file, use the Retention Time Correction view to
inspect the regression curves for the alignment features (the m/z × RT).

Y To open the Retention Time Corrections view

1. Open a result file for an analysis with multiple input files.

2. In the menu bar, choose View > Retention Time Corrections.
In the default layout, the Retention Time Correction view opens to the right of the
tabbed result tables. Because you need to select a row in the Input Files table, the view is
empty.
3. In the main result tables, click the Input Files tab.
4. Do the following, as applicable:
• To view the regression curve for one input file as well as the prediction interval for the
landmark features in the file, select one input file.

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Retention Time Corrections view

Figure 140. Retention Time Correction view with the regression curve for one input file

• To view overlaid regression curves for multiple input files, select multiple input files.
Figure 141. Retention Time Correction view with regression curves for multiple input files

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Compound Area Corrections view

Compound Area Corrections view

When the processing workflow for a result file includes a QC corrections node and the
analysis includes samples with the sample type assignment of Quality Control, use the
Compound Area Corrections view to inspect the corrected peak areas for each compound in
the compounds table.

For information about acquiring a set of raw data files with interspersed quality control
samples, see “Using quality control samples to compensate for batch effects.”

Y To open the Compound Area Correction view

1. Open a result file for an analysis with batch normalization—that is, an analysis that
includes QC samples and a processing workflow with a QC correction node.
2. In the compounds table, select one or more compounds.
3. From the menu bar, choose View > Compound Area Corrections.
In the default layout, the Compound Area Correction view opens to the right of the
tabbed result tables. The Compound Area Correction view displays a scatter plot of the
areas for the selected compound on the y axis against the acquisition time for each input
file on the x axis.
The legend below the plot describes the data point symbols and the regression curve or
curves.
The Apply QC Correction node generates two regression lines: a blue curve for the
original areas and an orange curve for the corrected areas.

Table 117 describes the data point symbols. The legend is not static. If a compound does not
include any gap-filled QC samples, the legend does not include the diamond symbols for that
compound.
Table 117. Compound Area Corrections view legend (Sheet 1 of 2)
Data point symbol Description
QC samples
( ) Blue triangle Original area for the QC sample
( ) Orange triangle Corrected area for the QC sample
( ) Blue diamond Original area for a gap-filled QC sample
( ) Orange diamond Corrected area for a gap-filled QC sample
Non-QC samples
( ) Blue circle Original area for a non-QC sample
( ) Orange circle Corrected area for a non-QC sample

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Compound Area Corrections view

Table 117. Compound Area Corrections view legend (Sheet 2 of 2)

Data point symbol Description
Regression lines from a processing workflow with the Apply QC Correction node
Blue line across the Regression curve for the corrected original compound areas in the
time axis QC samples
Orange line across the Regression curve for the corrected compound areas in the QC
time axis samples
Regression line from a processing workflow with the Apply SERRF QC node (LC studies only)
Orange line across the Regression curve for the corrected compound areas in the QC
time axis samples

The Apply QC SERRF Correction node generates only one

regression line.

Pointing to a data point (circle, triangle, or diamond) displays a tooltip with the input file
name, the compound area, and the status—original or corrected.

Figure 142 shows the Compound Area Corrections view for a compound with 12 QC
samples. The chromatographic peak area for three of the QC samples is gap-filled.

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Compound Area Corrections view

Figure 142. Compound Area Corrections view for an analysis with the Apply QC Correction node, 12
QC samples, and a compound with three gap-filled QC samples

Data points for

gap-filled Gap-filled
QC samples QC samples

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Compound Area Corrections view

For an LC study, if you use the Apply SERRF QC Correction node and the analysis includes
input files from more than one batch, a blue vertical line separates the batches in the plot.
Figure 143 shows an analysis with the Apply AC Correction node for a set of input files from
two batches.
Figure 143. Compound Area Corrections view (Apply SERRF QC node for LC studies))

Data points for Demarcation line Gap-filled

gap-filled for the two batches QC sample
QC samples

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Hierarchical Clustering Analysis view

Figure 144. Compound Area Corrections view for a selected compound (daidzein)

Hierarchical Clustering Analysis view

Use the Hierarchical Cluster Analysis view to visualize the correlation between detected
compounds and selected samples in a two-dimensional array of color-coded rectangles (heat
map) where each rectangle represents the relative amount (by area) of a specific compound in
a specific sample.

The application uses an agglomerative (bottom-up) approach to find the similarities between
samples and compounds. Initially, the hierarchical cluster analysis assigns each compound to
its own singleton cluster. The analysis then proceeds iteratively, at each stage joining the two
most similar clusters into a new cluster, continuing until there is one overall cluster
represented by a dendrogram.

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Hierarchical Clustering Analysis view

The dendrogram to the left of the heat map represents the distance (or dissimilarity) between
the compound clusters. The width of each node is proportional to the distance (or
dissimilarity) between two compounds at the lowest level or two compound clusters at the
higher levels. The dendrogram above the heat map represents the distance (or similarity)
between samples. The height of each node is proportional to the distances (or similarity)
between two samples at the lowest level or two sample clusters at the higher levels.

Pointing to a dendrogram node displays the distance between clusters, and pointing to a heat
map cell displays the compound and sample information.

By default, under Filter By, all the input files are selected, and under Other Settings, the Show
Labels check box for the compound labels is clear.
Figure 145. Hierarchical cluster analysis for the compounds detected in six samples from lean and
fat ZDF rats (LC studies)
Zoom Out (Rows) Zoom Out (Columns)
Display and Dendrogram that represents the distance
analysis (or similarity) between samples
Heat map legend (scaled areas)
options

Color bar (for

selected variable)

Red bar indicates

checked
compounds in the
data source table.

Column
labels

Dendrogram that represents the distance

(or dissimilarity) between compound

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Hierarchical Clustering Analysis view

To determine how to cluster the data, the application provides a choice of commonly used
distance functions and linkage methods (see Table 120 and Table 121).

Note The Heat Map supports clustering for 2 to 2000 compounds.

To set up a hierarchical clustering analysis and work interactively with the heat map’s cells, see
these topics:
• Set up a hierarchical clustering analysis
• Work interactively with the heat map grid
• Hierarchical Cluster Analysis view parameters

Set up a hierarchical clustering analysis

Y To set up the hierarchical clustering analysis

1. Filter the result table that you want to use as the data source. The analysis uses the only
visible compounds in the table.

Note When you apply a filter that displays only the checked compounds in the
selected result table, a red bar appears to the right of the heat map. If only a subset of
the compounds is checked, the bar is discontinuous, with red indicating a checked
compound and gray indicating an unchecked compound.

2. In the Data Source list, select the data source.

The Compounds table is the data source for untargeted analyses, and the Expected
Compounds table is the data source for targeted analysis. For a combination analysis that
generates a Compounds table and an Expected Compounds table, you can select either
table as the data source.
3. In the Scale Values list, select whether to scale the heat map data before or after clustering
or not at all.
4. To normalize the areas for the compounds, select the Use Normalized Areas check box.
5. In the left pane, under Filter By, select the check boxes for the samples to include in the
analysis.
By default, all the sample files are selected.

Note By default, under Other Settings, the following check boxes are selected:

Column Settings: Show Clusters and Show Labels—Displays a dendrogram above the
heat map and sample labels below the heat map.

Row Settings: Show Clusters—Displays a dendrogram to the left of the heat map.

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Hierarchical Clustering Analysis view

6. In the left pane, under Other Settings, select these analysis options:
• Under Distance Function, select how the analysis determines the distance between
the data points, where the data points are files (columns) or compounds (rows)
(Table 120).
• Under Linkage Method, select how the analysis performs the clustering analysis
(Table 121).
7. In the left pane, select these labeling options:
• Under Color By, select whether to display color bars above the heat map to visually
differentiate the samples by their study factor variables.
• Under Other Settings > Row Settings, select whether to display the compound labels.
Selecting the Show Labels check box under Row Settings displays the compound
labels to the right of the heat map.
• Under Other Settings > X-Axis Label, select the label for the sample columns.
8. To run the analysis, click Refresh.

Work interactively with the heat map grid

After you run a hierarchical heat map analysis, you can enlarge the heat map, zoom in and out
on the heat map, and point to specific cells in the heat map for more information.
Table 118. Common tasks for the heat map grid (Sheet 1 of 2)
Task Procedure
Enlarge the heat map. To increase the heat map width, drag its left or right edge.

To increase its height, drag its top or bottom edge.

Zoom in on an area of the heat Drag the pointer across the rectangular area of the heat
map. map.
Zoom out of an enlarged area of Right-click the heat map and choose one of the following:
the heat map by using the Zoom Out Column, Zoom Out Row, Undo All
shortcut menu commands. Column Zoom, or Undo All Row Zoom.
Zoom out of an enlarged area of To zoom out of a row selection, click the Zoom Out Row
the heat map by using the zoom icon, , or the Undo All Row Zoom icon, , below
icons. the heat map legend.

To zoom out of a column selection, click the Zoom Out

Column icon, , or the Undo All Column Zoom
icon, , to the right of the heat map legend.

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Hierarchical Clustering Analysis view

Table 118. Common tasks for the heat map grid (Sheet 2 of 2)
Task Procedure
View information about a heat Point to the cell.
map cell.
The tooltip displays the compound’s name (if available),
its MW, RT, file ID, and the study factor value (if
available).
View the distance value for a Point to the node.
dendrogram node.
The tooltip displays the distance value.

For an analysis where the

chromatographic peak areas are scaled
before clustering, the distance values are
scaled.

For an analysis where the

chromatographic peaks areas are
not scaled or are scaled after
clustering, the distance values are
not scaled.

Hierarchical Cluster Analysis view parameters

Table 119 describes the parameters in the Hierarchical Clustering Analysis view.
Table 119. Hierarchical Clustering Analysis view parameters (Sheet 1 of 3)
Parameter Description
Button
Refresh Runs the hierarchical clustering analysis on the compounds
displayed in the selected data source (result table) and the samples
selected in the left pane under Filter By.
Parameters in the right pane
Data Source Specifies the result table for the source data.

Selections: Compounds table or Expected Compounds table

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Hierarchical Clustering Analysis view

Table 119. Hierarchical Clustering Analysis view parameters (Sheet 2 of 3)

Parameter Description
Scale Values Specifies if and when to perform a z-score transformation on the
data points:
• None—The application does not scale the data. The heat map
legend displays a scale in area counts, and the dendrogram
nodes display the distance in area counts.
• Scale After Clustering— Applies a z-score transformation
after performing the hierarchical clustering. The heat map
legend displays the range of the scaled values, and the
dendrogram nodes display the distance in area counts.
• Scale Before Clustering—Applies a z-score transformation
before performing the hierarchical clustering. The heat map
legend displays the range of the scaled values, and the
dendrogram nodes display the scaled distance values.
Use Normalized Areas When selected, normalizes the chromatographic peak areas for the
selected compounds before running the analysis.
Parameters in the left pane
Color By
Displays the selected color bars for the selected variables above the heat map.
Filter By
By default, all the check boxes—except for the Blank sample type—are selected. Clearing a
check box removes the corresponding item from the analysis.
Other Settings
Column Settings
Show Clusters When selected, displays the dendrogram for the samples above the
heat map; that is, this selection displays the dendrogram for the
items selected under Filter By.
Show Labels When selected, displays the labels across the bottom of the heat
map for the items selected under Filter By. The X-Axis Label
parameter at the bottom of the left pane provides labeling options.
Row Settings
Show Clusters When selected, displays the dendrogram for the compounds to the
left of the heat map.
Show Labels When selected, displays the labels across the bottom of the heat
map for the items selected under Filter By. The X-Axis Label
parameter at the bottom of the left pane provides labeling options.

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Hierarchical Clustering Analysis view

Table 119. Hierarchical Clustering Analysis view parameters (Sheet 3 of 3)

Parameter Description
Color Schemes Specifies the color scheme for the heat map.

Default:
• Available values
• Missing values white

Selection:
Available values Missing values

Distance Function Specifies the distance function to use for calculating the distance
between data points (see Table 120).

Default: Euclidean
Linkage Method Specifies the method to use for hierarchical clustering (see
Table 121).

Default: Complete
X-Axis Label Specifies the labels for the sample columns.

Selections: All Factors, Selected Factors, File ID, Full File Name,
and Sample Name

Table 120. Distance functions (Sheet 1 of 2)

Distance function Description
Euclidean Computes the Euclidean distance between two data vectors,
which is the geometric distance in the multidimensional space.
Manhattan Computes the city-block (Manhattan) distance between two
vectors. The Manhattan distance between two data items is the
sum of the differences of their corresponding components. In
most cases, the Manhattan distance measure yields results similar
to the simple Euclidean distance. However, the effect of outliers is
dampened because the distances are not squared.
Maximum Computes the maximum distance on any one of the dimensions
between two vectors. Use this function to define two objects as
different if they differ in any one of the dimensions.

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Table 120. Distance functions (Sheet 2 of 2)

Distance function Description
Pearson Computes the Pearson product-moment correlation, which is a
measure for the shape similarity between two clusters.
Squared Euclidean Computes the squared Euclidean distance between two data
vectors. The Euclidean Squared distance metric uses the same
equation as the Euclidean distance metric, but it does not take the
square root.

Table 121. Linkage methods

Linkage method Description
Average Computes the distance between two clusters as the average
distance between all pairs of objects in the two different clusters.
Centroid Computes the distance between two clusters as the difference
between centroids. The centroid of a cluster is the average point in
the multidimensional space.
Complete Computes the distance between two clusters as the greatest
distance between any two objects in the different clusters (furthest
neighbors).
Median Computes the distance between two clusters as the difference
between centroids, using the size of each cluster as a weighting
factor.
Single Computes the distance between two clusters as the distance of the
two closest objects (nearest neighbors) in the clusters.
WARD Computes the distance between two clusters using Ward’s
method, which uses an analysis of variance approach to evaluate
the distances between clusters. The smaller the increase in the total
within-group sum of squares as a result of joining two clusters, the
closer they are. The within-group sum of squares of a cluster is
defined as the sum of the squares of the distance between all
objects in the cluster and the centroid of the cluster. Ward’s
method tends to produce compact groups of well-distributed size.
Weighted Average Computes the distance between two clusters as the average
distance between all pairs of objects in the two different clusters,
using the size of each cluster as a weighting factor.

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mzLogic Analysis view

mzLogic Analysis view

You can use the mzLogic Analysis view in two ways:
• To run an mzLogic analysis for a data set that was processed with a workflow that did not
include the Apply mzLogic node
• To update an older analysis with new similarity results from the mzCloud spectral
database

Note The application does not save the results from this mzLogic analysis to the result
file; however, you can add suitable candidates to the Structure Proposals table for a
compound and apply FISh scoring.

The ranking score provided by an mzLogic analysis is not a probability score. It is only a
measure of how similar a putative structure is to closely matching structures in the
mzCloud spectral database.

To run and review an mzLogic Analysis, see these topics:

• Perform an mzLogic analysis
• Review the results of an mzLogic analysis
• mzLogic Analysis view parameters

Perform an mzLogic analysis

Y To perform an mzLogic analysis

1. Open a result file from an untargeted analysis.

2. Select a compound in the Compounds table.
3. From the application menu bar, choose View > mzLogic Analysis.
The mzLogic Analysis view opens to the right of the Compounds table. If the selected
result file does not include results from an identity search, the Candidates area is empty.
Otherwise, the Candidates area contains candidates from the identity search nodes.
4. To add candidates from the ChemSpider database, click ChemSpider and run a search.
5. To run forward and reverse similarity searches on the candidates, click mzCloud
Similarity.
If the application finds similar structures in the mzCloud database, it populates the
Similar Structures from mzCloud area and the Calculate Score button becomes available.
The structure tiles in this area include an mzCloud Match score and a Coverage value at
the top and a formula and delta mass value at the bottom.
6. To display an mzLogic score for each candidate, click Calculate Score.

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Review the results of an mzLogic analysis

Y To review the results of an mzLogic analysis

1. In the mzLogic Analysis view, open the Similar Structures from mzCloud area.
2. In the Candidates area, click a candidate to select it.
In the Similar Structures from mzCloud area, the matching portions of the similar
structures are highlighted in blue.

mzLogic Analysis view parameters

Table 122. mzLogic Analysis view parameters (Sheet 1 of 2)
Parameter Description
ChemSpider Opens the ChemSpider Search dialog box. See “Find a structure in
the ChemSpider database.”
mzCloud Similarity Runs a forward and reverse mzCloud similarity search.
Calculate Score Calculates the mzLogic scores for the available candidates.

Available when the Candidates and Similar Structures from

mzCloud areas are populated.
Back Returns the focus to the previously selected compound in the
Compounds table.

Available when the Auto Refresh check box is clear and you select
a different compound in the Compounds table.
Refresh Refreshes the Candidates area when you select another
compound.

Available when the Auto refresh check box is clear.

Auto refresh Select so that when you select another compound, the application
automatically refreshes the Candidates area.
Size Controls the size of the structure tiles in the Candidates area.

Default: Medium

Selection: Small, Medium, or Large

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FISh Scoring Queue view

Table 122. mzLogic Analysis view parameters (Sheet 2 of 2)

Parameter Description
Candidates area Displays structure candidates as tiles. The structure candidates are
provided by identity searches during data processing or a separate
ChemSpider search from the result file. If the identity searches
find duplicate structures, the application consolidates them.

Right-clicking a tile displays a shortcut menu with the following

commands:
• Add to Structure Proposals—Adds the selected structure to
the Structure Proposals table for the selected compound.
• Add to Structure Proposals and Apply FISh Scoring—Opens
the Settings dialog box for applying the FISh scoring
algorithm. Then, runs the FISh scoring algorithm and adds
the structure and FISh Coverage score to the Structure
Proposals table for the selected compound.
Similar Structures from Displays the results of the mzCloud similarity search for the
mzCloud area selected compound.

Selecting a candidate highlights the maximum common

substructure in blue for the similar structures.
Sort By Sorts the similar structures by the selected parameter.

Default: mzCloud Match

Selection: mzCloud Match, Forward Coverage, or Reverse

Coverage

FISh Scoring Queue view

Use the FISh Scoring Queue view to display the progress of FISh scoring.

Y To submit compounds to the FISh Scoring Queue view

1. Open a result file.

2. From the menu bar, choose View > FISh Scoring Queue.
The FISh Scoring Queue opens to the right of the result tables.
3. Start the FISh scoring process as follows:
• For compounds with assigned structures, go to step 4.
• For compounds without assigned structures, go to step 5.

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FISh Scoring Queue view

4. For compounds with assigned structures, do the following:

a. To open the Settings dialog box, do one of the following:
• In the compounds table (Compounds table or Expected Compounds table),
right-click a compound and choose Apply FISh Scoring.
• In any of the related search results tables, right-click a compound and choose
Add to Structure Proposals and Apply FISh Scoring.
• In a Structure Proposals table, right-click a compound and choose either Apply
FISh Scoring to Selected or Apply FISh Scoring to All.
b. In the Settings dialog box, make the appropriate selections and click OK.
FISh scoring begins.
5. For compounds without assigned structures, do the following:
a. To open the Compound Annotation Editor dialog box, do one of the following:
• In the compounds table (Compounds table or Expected Compounds table),
right-click a compound and choose Edit Compound Annotations.
• In a Structure Proposals table, double-click a compound.
b. Enter the structure by opening a structure file, drawing the structure, or running a
ChemSpider search.
c. Click the FISh Scoring tab.
d. Make the appropriate selections for the FISh scoring algorithm.
e. At the bottom of the dialog box, select the Apply FISh Scoring check box and click
Save.
FISh scoring begins.

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 10

Descriptive information for the result tables

For general information about opening result files and working with the result tables, see
Chapter 8, “Review the analysis results.”

Note The Statistical Methods table is new in the Compound Discoverer 3.3 application.

For information about specific result tables, see the following topics:
• Common result tables
• Expected Compounds result tables
• Compound detection result tables
• Compound Identification result tables
• Pathway Mapping result tables
• Compound Scoring tables
• Statistical Methods table
• Differential analysis columns
• Descriptive statistics columns
• QC Correction columns
• Annotations Source column in a compounds table
• Peak Rating columns
• Peak quality factor (PQF) columns in the result tables

Common result tables

For information about the result tables that are independent of the analysis type, see these
topics:
• Adducts table
• Chromatogram Peaks table

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• File Alignments table

• FISh Trace Fragments table
• Input Files table
• Manual Peaks table
• Merged Features table
• Specialized Traces table
• Study Information table
• Structure Proposals table

Adducts table
Use the Adducts table to view the list of adducts in the Adducts library. By default, the
Adducts table is hidden. See “Show or hide result tables.”

Chromatogram Peaks table

Use the Chromatogram Peaks table to view information about the quality of the
chromatographic peak for a specific feature or a specific expected feature. The Chromatogram
Peaks table displays information about the chromatographic peak for the feature or expected
feature that you selected in the related table.

Table 123 describes the columns in the Chromatogram Peaks table.

Table 123. Chromatogram Peaks table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to label the entries with custom tags that you
created by using the Custom Tags Filter view. You can filter the
result table on these tags.
Area Displays the integrated peak area.
Apex m/z Displays the m/z value of the mass spectral peak at the
chromatogram peak apex.
Apex RT [min] Displays the retention time of the chromatogram peak apex.
Apex Intensity Displays the intensity at the chromatogram peak apex.
Left RT [min] Displays the start point for the chromatographic peak.
Right RT [min] Displays the end point for the chromatographic peak.

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Table 123. Chromatogram Peaks table (Sheet 2 of 2)

Column Description
Isotope Number (For chromatographic peaks detected by the Detect Compounds
(hidden) node in an LC study) Displays the index number for the isotopic
mass spectrum peak that the application used to create the XIC.
The Detect Compounds node creates an XIC trace for each
isotope.

(For chromatographic peaks found by the Find Expected

Compounds node in an LC study) Always displays a value of 0, as
the Find Expected Compounds node creates only one filtered XIC
trace for each ion. The Find Expected Compounds node creates
the filtered XIC trace by summing the intensity of all the mass
spectrum peaks that match the theoretical isotope pattern. When
even only one required isotope is missing, the intensity of the XIC
drops down to 0.

Peak Model Displays the peak model for the chromatographic peak and
includes information about the width and symmetry of the peak.

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File Alignments table

For LC studies, use the File Alignments table to check the alignment process for each input
file.

The retention time alignment node creates the File Alignments table. See “Align Retention
Times node.”

Table 124 describes the columns in the File Alignments table.

Table 124. File Alignments table
Column Description
Study File ID Displays the study file ID (F#) of the sample where the algorithm
has corrected the measured retention time of the detected features
against a set of features from the reference file.
Ref. File ID Displays the study file ID (F#) of the input file that the analysis
used as the reference file.
Kind Displays the parameter that the algorithm used in the regression
model. Retention time (RT) is the current regression model.
Description Displays a description of the alignment process.
• For the original Align Retention Times node, this column
displays the alignment model.
• For the Align Retention Times (ChromAlign) node, this
column displays the following statement—Mapped to
Reference File.

If you did not select a reference input file for the node’s Reference
File parameter, the node automatically selects the first sample file
(assigned the Sample Type of Sample) in the Files for Analysis
area.
#Landmarks For the original Align Retention Times node, this column displays
the number of features that the analysis used to align the specified
file to the reference file.

For the Align Retentions Times (ChromAlign) node, this column

displays the value 0 (zero), as this node does not use landmarks to
align the features across the input files.
RMSE Displays the estimated error for the corrected retention times of
the features in the selected input file as the root-mean-square
error.

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FISh Trace Fragments table

Use the FISh Trace Fragments table to view the structures and the summed intensities of the
expected fragment ions.

The Create FISh Trace node creates the FISh Trace Fragments table when the Individual
Traces parameter for this node is set to True. See “Create FISh Trace node.”

Table 125 describes the columns in the FISh Trace Fragments table.
Table 125. FISh Trace Fragments table
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to label the entries with custom tags that you
created by using the Custom Tags Filter view. You can filter the
result table on these tags.
Parent Compound Displays the selected compound in the Create FISh Traces node.
Formula Displays the elemental composition of the fragment ion.
Ion Displays the ion description.
m/z Displays the mass-to-charge ratio of the ion.
TIC Displays the total ion current for the fragment ion.
Mode Displays the fragmentation mode.
File ID Displays the integer that the application assigned to the input file.
Study File ID Displays the study file ID (F#) of the input file.
Structure Displays the ion’s molecular structure.

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Input Files table

Use the Input Files table, which is common to all processing workflows, to view information
about the input file set (Xcalibur RAW files) that the application processed to produce the
result file.

For a result file from an analysis of multiple input files from an LC/MS acquisition sequence,
use the related File Alignments table to check the chromatographic alignment of the features
in the input files.

Table 126 describes the information displayed in the Input Files table.
Table 126. Input Files table
Column Description
Alignment Score For the Align Retention Times (ChromAlign) node, displays the
alignment score (0.000 to 1.000).
Creation Date Displays the acquisition time stamp from the data system.
File Name Displays the file name of the input file.
Instrument Hardware Displays the hardware version of the Thermo Scientific mass
(hidden) spectrometer or analog detector used to acquire the raw data file.
Instrument Name Displays the mass spectrometer type used to acquire the raw data
file.
Max. Mass [Da] Displays the maximum mass that the analysis processed.
Min. Mass [Da] Displays the minimum mass that the analysis processed.
RT Range [min] Displays the data acquisition time for the raw data file.
Software Revision Displays the software version of the instrument control software
used to acquire the raw data file.
Ref. File ID For LC studies, this column displays the reference file that the
retention time alignment algorithm used.
Sample Type Displays the sample type.
Study File ID Displays the file identification number (F#) assigned by the
Compound Discoverer application.
Study factor columns Each study factor column displays the study factor value (item).

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Manual Peaks table

Use the Manual Peaks table to view information about the manual peaks that you add to the
result file.

The Manual Peaks table is a main table. It is also related to the main Specialized Traces table.
To create this table, you must add a manual peak to a specialized trace. See “Manually
integrate chromatographic peaks.”

Table 127 describes the columns in the Manual Peaks table.

Table 127. Manual Peaks table
Column Description
Trace Type Displays the trace type. The trace type can be any of the
specialized traces, including Analog, UV, PDA, TIC, BPC, XIC,
Pattern Trace, or FISh Trace.
Area Displays the chromatographic peak area.
Left RT [min] Displays the start point of the chromatographic peak.
Right RT [min] Displays the end point of the chromatographic peak.
Study File ID Displays the study file ID (F#) of the input file.

Merged Features table

Use the Merged Features table to view ion conflicts between the Features and Expected
Features tables. Also use the Merged Features table to correlate the chromatographic peaks
detected by an analog detector to the chromatographic peaks detected by the mass
spectrometer.

The Merge Features Node adds the Merged Features table to the result file. The Merged
Features table has the following primary related tables: Expected Compounds, Expected
Compounds per File, Compounds, Compounds per File, and Manual Peaks.

Tip When you add the Merge Features node to the processing workflow, the Find
Expected Compounds node and the Detect Compounds node automatically connect to it.
The Merge Features node consolidates the chromatographic peaks from these two input
nodes.

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Table 128 describes the columns in the Merged Features table.

Table 128. Merged Features table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to label the entries with custom tags that you
created by using the Custom Tags Filter view. You can filter the
result table on these tags.
Name Use this column to describe or name the found chromatographic
peak. To name the chromatographic peak, type alphanumeric text
in the Name table cell.
Apex m/z Displays the area weighted average mass of all related features.

 m/z × Area
-------------------------------
 m/z
RT [min] Displays the area weighted average retention time of all related
features (same m/z × RT dimensions within the specified
tolerances).

 RT × Area
-------------------------------
 RT
Max. Area Displays the area of the largest chromatographic peak found in the
data set for the current m/z × RT dimensions.
Ion Conflict Status Indicates whether there is a conflict between the Detect
Compounds and Find Expected Compounds nodes.
( ) Green No conflict—Both nodes assigned the same ion to this
chromatographic peak.
( ) Orange Not found by the Detect Compounds node.

Indicates that the expected compound might be in doubt because

the Detect Compounds node did not detect it.
( ) Gray Found only by ‘Detect Compounds’ node or ‘Find Expected
Compounds’ node—Only the stated node found this ion.
( ) Red Conflicting ions or Multiple ions per node—Either the two nodes
assigned different ions or one of the nodes assigned more than one
ion to this m/z value and retention time.

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Table 128. Merged Features table (Sheet 2 of 2)

Column Description
Detect Compounds Indicates whether the Detect Compounds node found the current
feature in each input file.
( ) Gray No matches found
( ) Green Single match found
( ) Orange Multiple matches found
Find Expected Indicates whether the Find Expected Compounds node found the
Compounds current feature in each input file.
( ) Gray No matches found
( ) Green Single match found
( ) Orange Multiple matches found
Max. Area Displays the maximum area of all the features from both the
Features per File table and the Expected Features table for this
compound across the set of input files.
Max. Areas (for each For each input file, displays the maximum chromatographic peak
input file) area for the features with the same m/z × RT dimensions (within
the specified tolerances) found by the Find Expected Compounds
node, the Detect Compounds node, or both nodes.
Note The Differential Analysis node generates these columns: Group Areas, Ratio, and
Log2 Fold Change. For information about these columns, see “Differential analysis
columns.”
Comments Use this column to store comments about the current feature
(unique m/z × RT dimensions). This column accepts
alphanumeric text and special characters.

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Specialized Traces table

Use the Specialized Traces table to view traces created by the tracer nodes.

The Specialized Traces table lists the specialized traces that you requested in the processing
workflow. For information about manually integrating chromatographic peaks in a specialized
trace, see “Manually integrate chromatographic peaks.”

For information about the Chromatograms view, see “Chromatograms view.”

Tip To view a trace in the Chromatograms view, select the trace of interest in the
Specialized Traces table.

Table 129 describes the columns in the Specialized Traces table.

Table 129. Specialized Traces table
Column Description
Checked Use this column to select the rows that you want to display in the
results table and in reports after you apply result filters.
Tags Use this column to label the entries with custom tags that you
created by using the Custom Tags Filter view. You can filter the
result table on these tags.
Study File ID Displays the study file ID (F#) of the input file.
Trace/Detector Type Displays the trace type generated during data processing.
• Create Mass Trace node—TIC, BPC, or XIC
• Create Analog Trace node—UV Trace, Total Scan, Spectrum
Maximum, Wavelength–Wavelength, or Analog trace
• Create FISh Trace node—FISh Trace
• Create Pattern Trace node—Pattern Trace
Custom Label Displays the text that you entered in the Custom Label box for the
processing workflow node that generated the trace.

You can edit the text in this column.

Description Displays a description of the trace.
Spectrum File Displays the file name of the raw data file that includes the trace.

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Study Information table

Use the Study Information table to review the sample, groups, and ratios information for the
set of processed input files.

Table 130 describes the columns in the Study Information table.

Table 130. Study Information table
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Sample Displays sample identifier.
Study File ID Displays the study file ID (F#) of the input file. See “Remove
input files or update their location.”
Sample Identifier Displays the file name of the raw data file.
File Name Displays the file name and file extension of the raw data file.
Sample Type Displays the sample type that you selected for the raw data file.
CF: study factor columns Displays the values of the named study variables.
Sample Group Displays the sample group.
Replicate Group Displays the replicate groups for biological samples.
(hidden)
Ratios Displays the ratios that include the raw data file.
Ratios (by Bio. Rep.) Displays the biological replicate ratios that include the raw data
(hidden) file.

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Structure Proposals table

Use the Structure Proposals table to store custom structure proposals for the selected
compound in the main compounds table (Expected Compounds table or Compounds table)
on the result page.

For information about adding structure proposals to the table, see “Add or delete proposed
structures for a compound.”

Table 131 describes the columns in the Structure Proposals table.

Table 131. Structure Proposals table
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to label the entries with custom tags that you
created by using the Custom Tags Filter view. You can filter the
result table on these tags.
Structure Displays the structure of the compound. See “Modify the result
page layout for ease of use.”
Name Displays an application-generated name or a user-specified name
for the compound.

To edit this entry, click the table cell and type text in the box.
Formula Displays the elemental composition formula of the compound.
Molecular Weight Displays the molecular weight of the compound.
FISh Coverage Displays the FISh coverage score that is based on the proposed
structure. See “FISh scoring for proposed structures.”
Comments Displays an application-generated comment or a user-specified
comment for the compound.

To edit this entry, click the table cell and type text in the box.

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Expected Compounds result tables

Expected Compounds result tables

For information about the result tables for a targeted workflow with the Find Expected
Compounds node, see these topics:
• Expected Compounds table
• Expected Compounds per File table
• Expected Features per File table
• Expected Formulas table
• Related Structures table
• Transformations table

Expected Compounds table

Use the Expected Compounds table to view information about the targeted compounds that
the analysis finds. This result table contains all of the expected compounds that the analysis
found in the input file set and groups these compound by formula, molecular weight, and
retention time (unique formula × MW × RT).

The Group Expected Compounds node adds the Expected Compounds table to the result
file.

Table 132 describes most of the columns in the main Compounds table and the first-level
related Compounds tables. For information about the differential analysis, descriptive
statistics, and quality control columns, see the applicable topic:
• Differential analysis columns

Note The Differential Analysis node generates the following columns: Group Areas,
Group CV[%], Ratio, Log2 Fold Change, P-value, and Adj. P-value.

• Descriptive statistics columns

Note The Descriptive Statistics node generates the following columns: Min. Area, Q1
Area, Median Area, Q3 Area, Mean Area, Area SD, and Area CV [%].

• QC Correction columns

Note The QC correction node generates the following columns: #Usable QC, RSD
QC Areas [%], RSD Corr. QC Areas [%], and Norm. Area.

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Expected Compounds result tables

Table 132. Expected Compounds table columns in alphabetical order (Sheet 1 of 5)

Column Node Description
#Adducts (hidden) Group Expected Displays the number of adduct ions that the analysis found for
Compounds the expected compound.
#BioCyc Pathways Map to BioCyc Displays the number of BioCyc pathways that include the
(hidden) Pathways expected compound.
#ChemSpider Results Search ChemSpider Displays the number of matching compounds found by the
ChemSpider search for the current composition or molecular
weight.

Use the related ChemSpider Results table to investigate the

matching compounds.
#KEGG Pathways Map to KEGG Displays the number of KEGG pathways that include the
(hidden) Pathways expected compound.
#Metabolika Pathways Map to Metabolika Displays the number of Metabolika pathways that include the
(hidden) Pathways expected compound.
#mzCloud Results Search mzCloud Node Displays the number of matching compounds found by the
mzCloud search for this molecular weight.

Use the related mzCloud Results table to investigate the

matching compounds.
#mzVault Results Search mzVault Displays the number of matching compounds found by the
mzVault search for this molecular weight.

Use the related mzCloud Results table to investigate the

matching compounds.
#Spectra with MSn Search mzCloud Displays the number of spectra with MS level > 2 that match the
(n>2) Hit mzCloud result for this compound.

Available when the Search MSn Tree parameter in the Search

mzCloud node is set to True. (The default setting in the
templates provided with the application is True. The default
setting in the Search mzCloud on the Workflow Nodes page is
False.)
Annot. Δ Mass [Da] Group Expected Displays the difference between the measured (observed in the
(hidden) Compounds spectrum) and theoretical molecular weight (calculated from the
formula) of the compound in daltons.
Annot. Δ Mass [ppm] Group Expected Displays the difference between the measured (observed in the
Compounds spectrum) and theoretical molecular weight (calculated from the
formula) of the compound in ppm. An orange background
indicates that the difference is greater than 5 ppm.

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Expected Compounds result tables

Table 132. Expected Compounds table columns in alphabetical order (Sheet 2 of 5)

Column Node Description
Annotation MW Group Expected Displays the molecular weight of the assigned formula.
(hidden) Compounds
Area (hidden when the Group Expected Displays the area for the compound (Formula × MW × RT) in
analysis includes study Compounds each sample (input file).
groups)
Area (Max.) Group Expected Displays the area of the largest chromatographic peak for the
Compounds compound (Formula × MW× RT) found in the sample set.
Background (hidden) Mark Background Displays a selected or clear check box that indicates whether the
Compounds compound was also found in the Blank sample above the
user-specified Sample/Blank or Blank/Sample level.
• Selected—Indicates that the compound is a background
compound.
• Clear—Indicates that the compound is not a background
compound.
BioCyc Pathways Map to BioCyc Indicates the BioCyc pathways where the analysis found the
(hidden) Pathways expected compound.
Calc. MW Group Expected Displays the neutral mass, in daltons, retrieved from the leftmost
Compounds isotopes (typically the monoisotopic isotope) of the related
compounds per file table.
Checked – Use this column to select the rows that you want to display in
the results table and in reports after you apply result filters.
Composition Change Group Expected Displays the composition change caused by any dealkylation or
Compounds dearylation reaction, any of the user-specified transformation
reactions, or both.
Dealkylated Group Expected When this column contains an X, the expected compound is the
Compounds product of a dealkylation reaction.
FISh Coverage FISh Scoring Displays the FISh coverage score from the FISh Scoring node.
See “FISh scoring for proposed structures.”
Formula Group Expected Displays the elemental formula of the parent compound and the
Compounds theoretical formulas for the dealkylation and transformation
products.
Gap Status (hidden) Group Expected Indicates the gap status for the compound:
Compounds
( ) Gray—Full Gap

( ) Green—No Gap

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Expected Compounds result tables

Table 132. Expected Compounds table columns in alphabetical order (Sheet 3 of 5)

Column Node Description
Group Areas Group Expected Displays the median chromatographic peak area for the
Compound compound in each study group.

Available if the analysis included study groups.

KEGG Pathways Map to KEGG Indicates the KEGG pathways where the analysis found the
(hidden) Pathways expected compound.
Mass List Matches Search Mass Lists Indicates the mass lists where the analysis found the expected
compound.
• ( ) Gray—No matches found
• ( ) Green—Single match found
• ( ) Orange—Multiple matches found
Metabolika Pathways Map to Metabolika Indicates the Metabolika Pathways where the analysis found the
(hidden) Pathways expected compound.
MS Depth (hidden) Group Expected Displays the depth of the available MSn data for the compound.
Compounds When the MS2 scans are not from an Identification Only
sample, you can view them by selecting the rows for the
compound in its related Expected Features table.
MS2 Group Expected Indicates whether the analysis found data-dependent
Compounds fragmentation scans for the compound.
• ( ) Red—No MSn—There are no available MSn scans.
• ( ) Green—ddMS2 for preferred ion—There is at least one
data-dependent MS2 scan for the preferred adduct ion.
• ( ) Blue—ddMS2 for other ion—There is at least one
data-dependent MS2 scan, but the scans are not for the
preferred adduct ion.
• ( )Orange—DIA only—Only data-independent [all ions
fragmentation (AIF)] scans are available.
mzCloud Best Match Search mzCloud Displays the score for the best hit from the mzCloud mass
spectrum database.
mzCloud Best Match Search mzCloud Displays the confidence value for the best hit from the mzCloud
Confidence mass spectrum database.

The confidence values addresses whether comparison spectra

have enough spectral peaks to make a confident match.

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Expected Compounds result tables

Table 132. Expected Compounds table columns in alphabetical order (Sheet 4 of 5)

Column Node Description
mzCloud Best Sim. Search mzCloud Displays the best similarity match of the mzCloud results found
Match for this compound.

Available when you select a Similarity Search in the Search

mzCloud node. By default, the Similarity Search parameter is set
None in the node. The setting for this parameter varies in the
various templates provided with the application. In the
metabolomics templates, the Similarity Search is set to
Confidence forward.
mzCloud Best Tree Search mzCloud Displays the best tree match in the mzCloud results found for
Match this compound considering all the submitted spectra with MS
level ≥ 2.

Available when Search MSn Tree you set Search MSn Tree to
True. 'mzCloud Best Tree Match' and '# Spectra with MSn
(n>2) Hit' columns will be available when Search MSn Tree is
set to 'True' in the Search mzCloud node
mzCloud Library Search mzCloud Indicates whether the search found matches in the selected
Matches (hidden) libraries.
• ( ) Gray—No matches found
• ( ) Green—Single match found
• ( )Orange—Multiple matches found
mzVault Best Match Search mzVault Displays the score for the best hit from the mzVault mass
spectrum library.
Name Group Expected Displays the user-specified compound name.
Compounds
To populate this cell, you can type a name or use the Edit
Compound Annotation command.
Parent Compound Group Expected Displays the targeted compound.
Compounds
For more information about the peak quality factors and the color-coded table cells, see “Chromatographic peak
rating filter.”
Peak Rating Group Expected Displays the calculated peak rating for the compound.
Compounds
PQF: FWHM2Base Group Expected Displays the calculated peak quality factor for the compound’s
Compounds chromatographic peak.
PQF: Jaggedness Group Expected Displays the calculated value for the jaggedness of the
Compounds compound’s chromatographic peak.

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Table 132. Expected Compounds table columns in alphabetical order (Sheet 5 of 5)

Column Node Description
PQF: Modality Group Expected Displays the calculated value for the modality of the compound’s
Compounds chromatographic peak.
PQF: Zig-Zag Index Group Expected Displays the calculated value for the zig-zag index of the
Compounds compound’s chromatographic peak.
Reference Ion Group Expected Displays the most common ion for the expected compound
Compounds across the input files.
RT [min] Group Expected Displays the weighted average of the retention times for the
Compounds chromatographic peak in the input files.
RT Tolerance [min] Group Expected Displays the retention time tolerance setting in the Group
(hidden) Compounds Expected Compounds node.
Structure (hidden) – Displays the structure of the compound from a custom
annotation.
Tags – Use this column to add custom tags to the result table items. You
can filter the result table by these tags. See “Custom color-coded
tags for result table entries.”
Transformations Group Expected Displays the chemical transformation for the expected
Compounds compounds that have undergone any of the user-specified
transformations.

Expected Compounds per File table

Use the Expected Compounds per File table to review the expected compounds found in each
input file. The uniqueness for each row is defined by the following expression:
Parent Compound × Formula × MW × Dealkylations and Transformations × RT

Clicking a row in the Expected Compounds per File table displays an XIC trace for the
selected compound. The XIC trace is a summation of the related ion traces. The integrated
peak area is shaded, the vertical red line indicates the chromatographic peak apex, and the
triangle indicates the data point that corresponds to the retention time (RT) label. When the
data has been chromatographically aligned (by using the Align Retention Times node), the
RT values for the labeled data points might differ slightly from those for the closest MS1 scan
in the spectral tree.

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Figure 146. Expected compound trace for a single input file

Triangle indicating the data point that
corresponds to the retention time label

Red line that indicates the

apex of the integrated
chromatographic peak

The Find Expected Compounds node creates the Expected Compounds per File table. The
primary tables related to this table are as follows: Expected Compounds, Input Files, Expected
Formulas, Merged Features, Expected Features, and Related Structures.

Table 133 describes the columns in the Expected Compound per File table. By default, some
of these columns are hidden.
Table 133. Expected Compounds per File table (Sheet 1 of 3)
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to add custom tags to the result table items. You
can filter the result table by these tags. See “Custom color-coded
tags for result table entries.”
Parent Compound Displays the user-specified parent compound or compounds.

You specify the parent compound or compounds in the Generate

Expected Compounds node or nodes.
Formula Displays the elemental formula of the expected compound.
Calc. MW Displays the calculated molecular weight (MW) of the expected
compound.
Dealkylated Displays an X when the parent compound has undergone a
dealkylation reaction.
Transformations Displays the chemical transformations for the expected
compound.

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Table 133. Expected Compounds per File table (Sheet 2 of 3)

Column Description
Composition Change Displays the composition change caused by a dealkylation
reaction, any of the user-specified transformation reactions, or
both.
RT [min] Displays the apex retention time (in minutes) of the largest
chromatographic peak that the node found for the expected
compound.

The chromatographic peak is a composite peak of all of the ionic

species (adduct ions) that the analysis found for the expected
compound. The chromatographic peak area is the summed area of
the adduct peaks.
FWHM [min] Displays the width of the chromatographic peak at its half-height.
Use this value to determine the best RT tolerance for peak
grouping.
Best SFit [%] Displays the best spectral fit value for the set of expected
compound ions for the expected compound. The spectral fit value
increases as the number of matching isotopes increases.
Best SD (hidden) Displays the best spectral distance value between the theoretical
and measured isotope pattern.
Max. #MI Displays the maximum number of matching isotopes for any of
the expected compound ions.
#Adducts Displays the number of detected adducts. The analysis detects
only the adduct ions that you specified for the Ions parameter in
the Generate Expected Compounds node. With the default
setting of [M+H]+1 only, the application finds only this one
adduct ion species for each compound.
Area Displays the summed chromatographic peak area for all of the
expected compound ions (adducts) that make up the
chromatographic peak.

To display the table of expected compound ions for the expected

compound, show the related tables and click the Expected
Features tab.
Parent Area [%] Displays the area of the selected component (Parent Compound ×
Formula × MW × Dealkylations and Transformations × RT) as a
percentage of the total chromatographic peak area for the related
components (Parent Compound × Formula × MW ×
Dealkylations and Transformations).

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Table 133. Expected Compounds per File table (Sheet 3 of 3)

Column Description
File ID Displays the integer that the application assigned to the input file.
Study File ID Displays the study file ID (F#) of the input file.

You can filter the data by using this integer; for example, the
following filter reduces the table to the expected compounds
found in one input file: Study File ID is equal to F1, F2, F3...F11,
and so on.

Expected Features per File table

Use the Expected Features per File table to review the expected features (chromatographic
peaks with the same m/z × RT dimensions) that the analysis found for a compound in a
specific input file.

The Find Expected Compounds node creates the Expected Features per File table.

Table 134 describes the columns in the Expected Features per File table.
Table 134. Expected Features per File table (Sheet 1 of 3)
Column Description
#MI Displays the number of matched isotopes for the ion.
Area Displays the summed area of all the related peaks (same expected
compound) in the current input file.
Charge Displays the charge of the ion.
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
File ID (hidden) Displays the integer that the application assigned to the input file.
FWHM [min] Displays the width of the chromatographic peak at its half-height
in minutes.
Intensity (hidden) Displays the maximum intensity of all the related peaks per input
file.
Ion Displays the ionized form of the compound.
m/z Displays the mass-to-charge ratio of the ion.
Molecular Weight Displays the molecular weight of the monoisotopic neutral
compound.

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Table 134. Expected Features per File table (Sheet 2 of 3)

Column Description
Parent Area [%] Displays the chromatographic peak area of the current ion as a
percentage of the total chromatographic peak area at the current
retention time (within the specified tolerance) for the expected
compound selected in the Expected Compounds per File table
For information about the peak quality factors, see “Peak quality factors.”
PQF: FWHM2B Displays the calculated peak quality factor for the ratio of the peak
width a half the maximum peak height versus the peak width at
the base of the expected compound’s chromatographic peak.
PQF: J Displays the calculated peak quality factor for the jaggedness of
the expected compound’s chromatographic peak.
PQF: M Displays the calculated peak quality factor for modality of the
expected compound’s chromatographic peak.
PQF: ZZI Displays the calculated peak quality factor for the zigzag index of
the expected compound’s chromatographic peak.
PQFs Pass Thresholds The settings for the PQF thresholds depend on the processing
workflow. When the processing workflow includes only a targeted
analysis, the PQF thresholds are hard-coded.

The hard-coded values are as follows:

• PQF:J (Jaggedness) ≤ 0.4
• PQF: ZZI (Zig-Zag Index) ≤ 0.25
• PQF: M (Modality) ≤ 0.9

When the processing workflow includes an untargeted analysis,

the targeted analysis uses the user-specified thresholds in the
Detect Compounds node.
RT [min] Displays the chromatographic retention time of the ion.
SD (hidden) Displays the spectral distance score.
SFit [%] Displays the similarity score between the theoretical and measured
isotope patterns as a percentage.
Study File ID Displays the study file ID (F#) of the input file.
Tags Use this column to label the entries with custom tags that you
created by using the Custom Tags Filter view. You can filter the
result table on these tags.

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Table 134. Expected Features per File table (Sheet 3 of 3)

Column Description
ΔMass [Da] Displays the mass difference, in daltons, between the theoretical
mass of the ion and the measured mass.
ΔMass [ppm] Displays the mass difference, in ppm, between the theoretical mass
of the ion and the measured mass.

Expected Formulas table

Use the Expected Formulas table to review the chemical formulas that the analysis found
across the input file set. This table lists the theoretical compounds that the Generate Expected
Compounds nodes predict by evaluating the effect of the user-specified dealkylation,
dearylation, and transformation reactions on the user-specified parent compounds.

Clicking a row in the Expected Formulas table displays overlaid XIC traces for the selected
expected compound, with one XIC trace for each input file where the compound is detected.
Each XIC trace is a summation of the ion traces for the same neutral elemental composition
(same molecular weight). By default, the Chromatograms view zooms in on the x-axis range of
the detected peaks for the same expected compound.

The Find Expected Compounds Node creates the Expected Formulas table, which has the
following primary related tables: Expected Compounds, Input Files, Expected Compounds
per File, Related Structures, and Transformations.

For information about targeted processing workflows, see “Targeted processing workflows for
expected compounds.”

Table 135 describes the columns in the Expected Formulas table.

Table 135. Expected Formulas table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in the
results table and in reports after you apply result filters.
Tags Use this column to label the entries with custom tags that you
created by using the Custom Tags Filter view. You can filter the
result table on these tags.
Order (related table) When you select the Expected Formulas table that is related to the
Transformations table, this column displays the order of the
selected transformation.

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Table 135. Expected Formulas table (Sheet 2 of 2)

Column Description
Parent Compound Displays the targeted compound.
Formula Displays the elemental formula of the parent compounds and the
theoretical formulas for the dealkylation and transformation
products.
Molecular Weight Displays the molecular weight (MW) of the expected compound.
Expected compounds include the parent compounds and their
theoretical dealkylation and transformation products.
Dealkylated When this column contains an X, the expected compound is the
product of a dealkylation reaction.
Transformations Displays the chemical transformation for the expected compounds
that have undergone any of the user-specified transformations.
Composition Change Displays the composition change caused by any dealkylation or
dearylation reaction, any of the user-specified transformation
reactions, or both.
Area (Max.) Displays the maximum summed chromatographic peak area for
the expected formula in one of the input files.
• When the result file contains data from only one input file,
this area matches the summed chromatographic peak area for
the expected formula.
• When the result file contains data from more than one input
file, this area comes from the input file with the largest
summed chromatographic peak area for the expected formula.

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Related Structures table

There is a Related Structures table for each feature in the Expected Features table and each
compound in the Expected Compounds per File table. The Related Structures table shows the
structure of the product compound generated by the dealkylation reaction.

Y To open the Related Structures table

1. Open a result file from a targeted analysis (Find Expected Compounds node).
2. Select a row in one of these tables—Expected Features or Expected Compounds per File.
3. Click Show Related Tables.
4. Click the Related Structures tab.

Table 136 describes the columns in the Related Structures table.

Table 136. Related Structures table
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Parent Compound Displays the user-specified parent compound or compounds.
Formula Displays the chemical formula of the parent compound or the
theoretical transformed compounds.
Molecular Weight Displays the molecular weight (MW) of the parent compound or
theoretical reaction product.
Dealkylated Displays an X when the parent compound has undergone a
dealkylation reaction.
Composition Change Displays the composition change caused by any dealkylation
reaction.
Structure When a compound is the result of transformations that include a
dealkylation step, this column displays the product of the
dealkylation step. Otherwise, this column displays the structure of
the parent compound.

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Transformations table
Use the Transformations table to review the transformations for each formula in the Expected
Formulas table.

Table 137 describes the columns in the Transformations table.

Table 137. Transformations table
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to label the entries with custom tags that you
created by using the Custom Tags Filter view. You can filter the
result table on these tags.
Name Displays the name of the transformation.
Phase Displays the Phase assignment for the transformation.
Leaving Group Displays the leaving group for the transformation.
Arriving Group Displays the arriving group for the transformation.
ΔMass [Da] Displays the neutral mass shift for the transformation in daltons.
Order Displays when the transformation was applied in the reaction
pathway.

Range: An integer from 1 to the user-specified maximum number

of steps.

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Compound detection result tables

For information about the result tables for the untargeted compound detection nodes (for
LC/MS/MS data), see these topics, listed in alphabetical order:
• Compounds table (LC studies)
• Compounds per File table
• Features per File table
• Filled Gaps table
• Labeled Features table
• Labeled Compounds per File table
• Similar Compounds Related table

Compounds table (LC studies)

Use the Compounds table to review the unknown compounds found across the input file set.

The Group Compounds node creates the Compounds table.

Tip For information using the shortcut menu commands for the Compounds table, see
“Shortcut menu commands for the result tables.”

Tip Clicking a row in the Compounds table displays XIC traces for the selected unknown
compound, with one XIC trace for each input file. Each XIC trace is the summation of all
the related ion traces. The summed XIC trace is made up of the data points with the
highest intensity at each time point.

To view the adduct ion traces for a compound detected in a specific input file, do the
following:
1. Select the compound in the Compounds table.
2. In the first set of related tables for the selected compound, select the input file in the
Compounds per File table.
3. In the second set of related tables (for the compound detected in the selected input
file), open the Features table and select the adduct ion of interest.

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Table 138 describes most of the columns in the main Compounds table and the first level
related Compounds tables. For information about the differential analysis, descriptive
statistics, and quality control columns, see the applicable topic:
• Differential analysis columns

Note The Differential Analysis node generates the following columns: Group Areas,
Group CV[%], Ratio, Log2 Fold Change, P-value, and Adj. P-value.

• Descriptive statistics columns

Note The Descriptive Statistics node generates the following columns: Min. Area, Q1
Area, Median Area, Q3 Area, Mean Area, Area SD, and Area CV [%].

• QC Correction columns

Note The QC correction node generates the following columns: #Usable QC, RSD
QC Areas [%], RSD Corr. QC Areas [%], and Norm. Area.

Table 138. Compounds table columns listed in alphabetical order (Sheet 1 of 10)
Column Node Description
Symbol = first character
#Adducts (hidden) Group Compounds Displays the number of adduct ions that the analysis found for the
compound.
#BioCyc Pathways Map to BioCyc Displays the number of BioCyc pathways that include the current
(hidden) Pathways compound.
#ChemSpider Results Search ChemSpider Displays the number of matching compounds found by the
ChemSpider search for the current composition or molecular
weight.

Use the related ChemSpider Results table to investigate the

matching compounds.
#KEGG Pathways Map to KEGG Displays the number of KEGG pathways that include the current
(hidden) Pathways compound.
#Metabolika Pathways Map to Metabolika Displays the number of Metabolika pathways that include the
(hidden) Pathways current compound.
#mzCloud Results Search mzCloud Displays the number of matching compounds found by the
Node mzCloud search for the calculated molecular weight.

Use the related mzCloud Results table to investigate the matching

compounds.

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Table 138. Compounds table columns listed in alphabetical order (Sheet 2 of 10)
Column Node Description
#mzVault Results Search mzVault Displays the number of matching compounds found by the
mzVault search for this molecular weight.

Use the related mzCloud Results table to investigate the matching

compounds.
#Similarity Results Apply mzLogic Displays the number of similarity results from the Apply mzLogic
(hidden) node.
#Spectra with MSn (n>2) Search mzCloud Displays the number of spectra with MS level > 2 that match the
Hit mzCloud result for this compound.

Available when the Search MSn Tree parameter in the Search

mzCloud node is set to True. (The default setting in the templates
provided with the application is True. The default setting in the
Search mzCloud on the Workflow Nodes page is False.)
# Usable QC Apply QC Displays the number of usable QC samples.
Correction
Annotation Source Assign Compound Indicates the match status for the selected compound from the
Annotations search nodes in the processing workflow. The expanded column
heading displays the annotation sources.

The Assign Compound Annotations node determines the validity

of the annotations from the Predict Compositions node and the
search nodes in the processing workflow.

Possible states for each annotation source:

• ( ) Green—Full Match—The current formula and structure
annotations match the best available item from the particular
source (online database or local mass list).
• ( ) Gray—No Results—Retrieved no data from the particular
source.
• ( ) Orange—Not the Top Hit—Current compound
annotation matches one of the hits, but not the top one.
• ( ) Orange—Partial Match—Only the formula for the
current compound annotation matches the items retrieved
from the particular source.
• ( ) Orange—Unused—Retrieved items from the particular
source, but did not assign any annotations.
• ( ) Red—Invalid mass—The best available item from the
particular source has a molecular weight that does not match
the molecular weight of the compound within the specified
mass tolerance.
• ( ) Red—No match—The particular source does not have an
item that matches the current annotations for the compound.

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Table 138. Compounds table columns listed in alphabetical order (Sheet 3 of 10)
Column Node Description
Annot. ΔMass [Da] Assign Compound Displays the mass difference in daltons between the experimental
(hidden) Annotations mass and the annotated mass.
Annot. ΔMass [ppm} Assign Compound Displays the mass difference in ppm between the experimental
Annotations mass and the annotated mass.
Annotation MW Assign Compound Displays the molecular weight of the matched compound from the
(hidden) Annotations specified annotation source.
Area (one subcolumn for Group Compounds Displays an area column for each input file.
each input file) (hidden if
the analysis includes study To display the areas for each input file, click the expand icon to the
groups) right of the column name.

Area (Max.) Group Compounds Displays the maximum chromatographic peak area from all of the
input files for compounds with the same retention time and
molecular weight (within the user-specified RT and mass
tolerances).
Avg. Exchange Analyze Labeled Average number of atoms exchanged for compound detected in
Compounds input file.
Background (hidden) Mark Background Displays a selected or clear check box that indicates whether the
Compounds compound was also found in the Blank sample above the
user-specified Sample/Blank or Blank/Sample level.
• Selected—Indicates that the compound is a background
compound.
• Clear—Indicates that the compound is not a background
compound.
BioCyc Pathways Map to BioCyc Displays whether the current compound is present in the named
(hidden) Pathways pathway.

To display the pathway names, click the expand icon to the right of
the column name.
Calc. MW Group Compounds Displays the calculated molecular weight of the neutral compound.
Checked Group Compounds Selecting this check box specifies that the compound is a selected
item.

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Table 138. Compounds table columns listed in alphabetical order (Sheet 4 of 10)
Column Node Description
Class Coverage Compound Class Displays the class coverage score for the compound by individual
Scoring compound classes. Expand the header to display the names of the
compound class libraries.

Color-coded cells:
• Light green to dark green for values from 0.00 to 100.00 or
gray
• Gray / N/A means no MS2 spectra are available for the
compound or there are 0 matched and 0 unmatched centroids
in the MS2 spectra.

At a value of 0.00, the node found no fragment structures or

m/z values in common with items in the compound class library. At
a value of 100%, the compound matches all the items in the
compound class library.

Scores range from 0.00 to 100.00

FISh Coverage (hidden) N/A Displays the FISh Coverage score for a custom annotation.
Formula Assign Compound Displays the predicted chemical formula for the neutral
Annotations compound. For the analysis to predict and display a chemical
formula for all compounds in the table, the processing workflow
must include the Predict Compositions node and the Assign
Compound Annotations node. When the processing workflow
includes any of the search nodes, the Assign Compound
Annotations node assigns the formula by using the specified
priority for the data sources. The default priority for the data
sources is (1) mzCloud Search, (2) Predicted Compositions, (3)
Mass List Match, (4) ChemSpider Search.
You can use the Fill Gaps node or the Apply Missing Value Imputation node to fill gaps for missing chromatographic
peaks. Both nodes generate a Gap Fill Status column and a Gap Status column; however, the indicators and tooltip
descriptions for the two nodes differ.
Gap Fill Status (hidden) Fill Gaps Indicates whether and how the analysis filled the gap.

( ) Green—No Gap to Fill.

( ) Blue—The analysis filled the gap in one of three ways: Filled

by Spectrum Noise, Filled by Simulated Peak, or Filled by Trace
Area.

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Table 138. Compounds table columns listed in alphabetical order (Sheet 5 of 10)
Column Node Description
Gap Status (hidden) Fill Gaps Indicates whether chromatographic peak for the compound was
completely missing or whether some of the user-specified ions were
not detected.

( ) Purple—Missing Ions—Indicates some missing ions (but not a

full gap).

( ) Gray—Full Gap—Indicates a full gap.

( ) Green—No Gap—Indicates a compound without any gap.

Gap Fill Status (hidden) Apply Missing Indicates whether and how the analysis filled the gap.
Value Imputation
( ) Green—No Gap to Fill.

( ) Orange—The analysis filled the gap in one of three ways:

Imputed by Group Median, Imputed by Low Area Value, or
Imputed by Random Forest.
Gap Status (hidden) Apply Missing Indicates whether chromatographic peak for the compound was
Value Imputation missing.

( ) Gray—Indicates a full gap.

( ) Green—No Gap—Indicates a compound without any gap.

KEGG Pathways Map to KEGG Displays whether the current compound is present in the named
(hidden) Pathways KEGG pathway.

To display the pathway names, click the expand icon to the right of
the column name.

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Table 138. Compounds table columns listed in alphabetical order (Sheet 6 of 10)
Column Node Description
Labeling Status (per file) Analyze Labeled The Analyze Labeled Compounds Node evaluates the measured
Compounds isotope pattern versus the fitted isotope pattern (for the expected
isotopologues) to determine the presence of contaminating masses.
It also evaluates the distribution of the measured exchange rates for
the expected isotopologues.

These flags indicate the following states:

• ( ) Red—Contaminating Mass—The average exchange for
the unlabeled sample is above the 0.1 threshold.
• ( ) Orange—Low Pattern Fit—The measured pattern
significantly differs from the fitted pattern. The SFit value is
below the threshold of 20%, the Fitted Coverage value is below
the threshold of 60%, or the Measured Coverage value is below
threshold of 60%. To review these values, see the “Labeled
Features table.”
• ( ) Blue—Irregular Exchange—The isotopologue exchange
rates are discontinuous; for example, there is a significant
valley in the exchange rates profile. This might indicate an
incorrect analysis or a special type of kinetics. However, when
this is the typical behavior expected for your experiments,
consider changing the setting for Mark Irregular Exchanges in
the Analyze Labeled Compounds node to False.

• ( ) Green—No Warnings—The measured isotope patterns

and the exchange rates are within acceptable limits.
• ( ) Gray—Compound was not detected in this sample.
Mass Defect Calculate Mass Displays the calculated mass defect for the compound.
Defect

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Table 138. Compounds table columns listed in alphabetical order (Sheet 7 of 10)
Column Node Description
Mass List Matches Search Mass Lists Indicates the match status for each mass list.
• ( ) Green—Single match found
• ( ) Orange—Multiple matches found
• ( ) Gray—No matches found

Use the related Mass List Search Results table to investigate the
matching compounds.
Metabolika Pathways Map to Metabolika Displays whether the current compound is present in the named
(hidden) Pathways Metabolika pathways.

To display the pathway names, click the expand icon to the right of
the column name.
m/z Group Compounds Displays the m/z value of the leftmost isotope peak of the most
common adduct ion of for this compound across the input files
(area-weighted average)
MS Depth (hidden) Group Compounds Displays the maximum depth of the mass spectral tree that the
analysis assigned to the compound.

This column is not available when the input files do not have any
fragmentation scans.
MS2 Group Compounds Displays whether the analysis found data-dependent fragmentation
scans for the compound.
• ( ) Red—No MSn—There are no available MSn scans.
• ( ) Green—ddMS2 for preferred ion—There is at least one
data-dependent MS2 scan for the preferred adduct ion.
• ( ) Blue—ddMS2 for other ion—There is at least one
data-dependent MS2 scan, but the scans are not for the
preferred adduct ion.
• ( ) Orange—DIA only—Only data-independent [all ions
fragmentation (AIF)] scans are available.
mzCloud Best Match Search mzCloud Displays the best match score (from 0 to 100) from the mzCloud
identity search for the compound.

Use the related mzCloud Results table to investigate the matching

compounds.
mzCloud Best Match Search mzCloud Displays the confidence of the best match mzCloud result found
Confidence for this compound.

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Table 138. Compounds table columns listed in alphabetical order (Sheet 8 of 10)
Column Node Description
mzCloud Best Sim Match Search mzCloud Displays the best similarity score from the mzCloud similarity
search for the compound.

Available when the Similarity Search parameter for the Search

mzCloud node is set to Similarity Forward or Similarity Reverse.

Use the related mzCloud Results table to investigate the matching

compounds.
mzCloud Best Tree Match Search mzCloud Displays the best tree match in the mzCloud results found for this
compound considering all the submitted spectra with MS level ≥ 2.
mzCloud Library Search mzCloud Indicates the match status for the compound in the selected
Matches (hidden) mzCloud databases.

Possible states for each database:

• ( ) Green—Single match found
• ( ) Gray—No matches found
• ( ) Red—Multiple matches found
mzVault Best Match Search mzVault Displays the best match score from the mzVault identity search for
the compound.

Use the related mzVault Results table to investigate the matching

compounds.
Name Group Compounds When the processing workflow includes a search node, this column
displays the compound name from the best match in the searched
databases.
Norm. Areas Normalize Areas Displays the normalized peak areas for the compound in each
input file.
Pattern Matches Pattern Scoring Displays a filled rectangle when the compound matches the
specified isotope pattern. The color of the filled rectangle has no
specific meaning.

Use the related Matched Patterns table to investigate the matched

isotope pattern.
Peak Rating Group Compounds Displays the calculated peak rating for the compound.
PQF: FWHM2Base Group Compounds Displays the calculated peak quality factor for the ratio of the peak
width a half the maximum peak height versus the peak width at the
base of the detected compound’s chromatographic peak.
PQF: Jaggedness Group Compounds Displays the calculated peak quality factor for the jaggedness of the
detected compound’s chromatographic peak.

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Table 138. Compounds table columns listed in alphabetical order (Sheet 9 of 10)
Column Node Description
PQF: Modality Group Compounds Displays the calculated peak quality factor for modality of the
detected compound’s chromatographic peak.
PQF: Zig-Zag Index Group Compounds Displays the calculated peak quality factor for the zig-zag index of
the detected compound’s chromatographic peak.
QC Fill Status (hidden) Apply QC Indicates the status for each QC sample.
Correction
Possible states:
• ( ) Green—Filled by re-detected peak
• ( ) Gray—N/A
• ( ) Orange—Filled by matching ion
• ( ) Blue—Filled by simulated peak
Rel. Exchange [%] Analyze Labeled Average exchange relative to the maximum exchange rate.
Compounds
100 × Average Exchange/Max. Exchange
Reference Ion Group Compounds Displays the most common adduct ion for this compound across
the input files
RT [min] Group Compounds Displays the retention time of the chromatographic peak for the
compound.
RT Tolerance [min] Group Compounds Displays the retention time tolerance specified in the Group
(hidden) Compounds node.
Structure (hidden) Group Compounds Displays the structure of the compound.
or structure
proposal The structure field is populated, the searches return a structure, or
you edit the annotations.
Tags – Use this column to add custom tags to the result table items. You
can filter the result table by these tags. See “Custom color-coded
tags for result table entries.”
The following three columns appear in the related Compounds table for the main KEGG Pathways table. Each
column contains an ordered list for the same KEGG compounds—that is, the first item in the KEGG Compound
IDs column corresponds to the first item in the KEGG Compound Names column and the first item in the KEGG
Compound Formula column, and so on.
KEGG Compound Map to KEGG Displays a list of the KEGG compound IDs in ascending order
IDs Pathways from left to right.
KEGG Compound Map to KEGG Displays a list of the KEGG compound names.
Names Pathways
KEGG Compound Map to KEGG Displays a list of the KEGG compound formulas.
Formulas Pathways

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Table 138. Compounds table columns listed in alphabetical order (Sheet 10 of 10)
Column Node Description
The following two columns appear in the related Compounds table for the main KEGG Pathways table and the
search results tables.
Max. ΔMass [Da] Displays the maximum mass difference between the measured mass
for the compound in the Compounds table and the theoretical
mass of the compound, in daltons.
Max. ΔMass [ppm] Displays the maximum mass difference between the measured mass
for the compound in the Compounds table and the theoretical
mass of the compound, in parts per million.
This column appears in related Compounds table for the main mzCloud Search Result table.
Scan Number Search mzCloud Displays the scan number of the scan that matches the reference
scan in the mzCloud database.
This column appears in the related Compounds table for the main mzVault Results table.
ΔRT [min] Search mzVault Displays the difference between the measured retention time of the
compound and the retention time of the mzVault library entry in
minute.

Compounds per File table

Use the Compounds per File table to review the compounds detected in each input file.

Table 139 describes the columns in the Compounds per File table.
Table 139. Compounds per File table (Sheet 1 of 2)
Column Description
#Adducts Displays the number of adduct ions.
Area (All Ions) Displays the chromatographic peak area in counts * minutes for
(hidden) the summed peaks of all the adduct ions in this input file.
Area (Reference Ion) Displays the chromatographic peak area in counts * minutes in the
XIC trace for the most common adduct ion across the input files.
Calc. MW Displays the calculated molecular weight of the neutral
compound.
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.

Clear: False or Selected: True

File ID (hidden) Displays the study file ID.

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Table 139. Compounds per File table (Sheet 2 of 2)

Column Description
FWHM [min] Displays the width of the chromatographic peak at its half-height.
Use this value to determine the best RT tolerance for peak
grouping.
Intensity (Max.) Displays the chromatographic peak height at the apex in intensity
(hidden) counts.
Max #MI Displays the number of matching isotope peaks.
Reference Ion Displays the ion definition of the reference ion.
RT [min] Displays the retention time at the chromatographic peak apex for
the reference ion (displayed in the Reference Ion column) in this
input file.
Study File ID (hidden) Displays the study file ID.
Tags Use this column to label the entries with custom tags that you
created by using the Custom Tags Filter view. You can filter the
result table on these tags.

Related Topics
• Shortcut menu commands for the result tables
• Show or hide table columns

Features per File table

Use the Features per File table to review the features detected in the input files.

The Detect Compounds Node adds the Features per File table to the result file.

Table 140 describes the columns in the Features per File table.
Table 140. Features per File table (Sheet 1 of 3)
Column Description
# Good Peaks (hidden) Number of chromatograms peaks (one or more for each isotopic
ion for the feature) that pass the peak quality factor thresholds
specified in the Detect Compounds node under Isotope Pattern
Detection.
#MI Displays the number of matching isotopes for the unknown
compound ion.
# Poor Peaks (hidden) Displays the number of chromatographic peaks that do not pass
the peak quality factor thresholds specified in the Detect
Compounds node under Isotope Pattern Detection.

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Table 140. Features per File table (Sheet 2 of 3)

Column Description
Area Displays the area of the reference isotopic chromatographic peak
for this feature in this input file.
Charge Displays the charge on the ion.
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
File ID Displays the integer that the application assigned to the input file.
FWHM [min] Displays the peak width at its half-height in minutes.
Intensity (hidden) Displays the intensity of the ion.
Ion Displays the ion definition of the molecular ion adduct.
m/z Displays the mass-to-charge ratio of the ion.
Molecular Weight Displays the neutral mass of the unknown ion based on the
measured m/z value (in daltons).
Parent Area [%] Displays the chromatographic peak area of the current peak as a
percentage of the total chromatographic peak area for the parent
compound (which is the compound selected in the Compounds
per File table) per input file.
PQF: FWHM2B Displays the calculated peak quality factor for the ratio of the peak
width a half the maximum peak height versus the peak width at
the base of the detected feature’s chromatographic peak.
PQF: Jaggedness Displays the calculated peak quality factor for the jaggedness of
the detected feature’s chromatographic peak.
PQF: Modality Displays the calculated peak quality factor for modality of the
detected feature’s chromatographic peak.
PQF: Zig-Zag Index Displays the calculated peak quality factor for the zig-zag index of
the detected feature’s chromatographic peak.
Processing Node No Displays the number of the workflow node in the processing
(hidden) workflow. These numbers are hidden in the Workflow Tree area
on the Workflows page of an analysis if you kept the default
selection of Hide Node Numbers on the Workflow Editor Settings
view of the Configuration page.

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Table 140. Features per File table (Sheet 3 of 3)

Column Description
Ref. Isotope Idx Displays the isotope index of the reference peak (most intense
(hidden) isotope) that the analysis used to create the XIC trace and report
the chromatographic peak area for this feature.

The isotope index is 0, 1, 2, and so on where 0 equals the A0

isotope in the isotope pattern.

Available when the Use Most Intense Isotope parameter is set to

True in the Detect Compounds node.
Ref. m/z (hidden) Displays the mass of the reference peak (m/z value of the most
intense isotope) used to create the XIC trace and report the
chromatographic peak area for this feature.

Available when the Use Most Intense Isotope Only parameter is

set to True.
RT [min] Displays the retention time in minutes of the chromatographic
peak that contains the unknown compound ion.
Study File ID Displays the study file ID (F#) of the input file.
Tags Use this column to label the entries with custom tags that you
created by using the Custom Tags Filter view. You can filter the
result table on these tags.

Filled Gaps table

For LC studies, use the Filled Gaps table to review the chromatographic peaks (Full Gap or
Missing Ion) that the Fill Gaps node finds. The Filled Gaps table is a related table for the
compound that you select in the Compounds table.

By default, the Filled Gaps table is hidden. To display the table, click the Select Table
Visibility icon, , select the Filled Gaps check box, and click OK.

Table 141 describes the columns in the Filled Gaps table.

Table 141. Filled Gaps table (Sheet 1 of 3)
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Ion Description Displays a description of the adduct where M is the neutral
compound.
Charge Displays the charge of the ion.

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Table 141. Filled Gaps table (Sheet 2 of 3)

Column Description
Exp. m/z Displays the m/z value for the adduct ion found in the other input
files. This value is based on the adduct type and the compound’s
molecular weight.
Exp. RT [min] Displays the average retention time of the adduct ion found in the
other input files.
Exp. Left RT [min] Displays the average peak start time of the detected
chromatographic peaks for the adduct ion in all the input files
included in the analysis.
Exp. Right RT [min] Displays the average peak end time of the detected
chromatographic peaks for the adduct ion in all the input files
included in the analysis.
Exp. FWHM [min] Displays the average peak width at the peak’s half height (full
width at half maximum) for the adduct ion in all the input files
included in the analysis.
Area Displays the area of the chromatographic peak found by the Fill
Gaps node.
Fill Status Indicates the gap status for the chromatographic peak detected or
redrawn by the Fill Gaps node are as follows:
• ( ) Green (Filled by Re-detected Peak)—The
chromatographic peak was detected with the PPD algorithm
(set to a lower threshold than in the Detect Compounds
node).
• ( ) Green (Filled by Matching Ion)—The gap was replaced
with a chromatographic peak for a matching ion.
• ( ) Blue (Filled by Spectrum Noise)—The gap was replaced
with a chromatographic peak based on the spectrum noise
level.
• ( ) Blue (Filled by Simulated Peak)—The gap was replaced
with a chromatographic peak that was simulated with a
Gaussian fit algorithm.
• ( ) Blue (Filled by Trace Area)—The gap was filled by the
trace area. The trace area is the area under the curve within
the retention time range defined by the chromatographic peak
detected in other files for analysis. The analysis uses the
retention time at the peak apex and the start and end points
for the detected chromatographic peak to determine the area
under the curve for missing peaks.

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Table 141. Filled Gaps table (Sheet 3 of 3)

Column Description
File ID Displays the integer that the application assigned to the input file.
Study File ID Displays the study file ID (F#) of the input file.

Labeled Features table

Table 142 describes the columns in the Labeled Features table. The labeled features are the
labeled adduct ions.
Table 142. Labeled Features table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to label the entries with custom tags that you
created by using the Custom Tags Filter view. You can filter the
result table on these tags.
Ion Displays the ion definition of the molecular ion adduct.
Charge Displays the charge on the ion.
Molecular Weight Displays the molecular weight of the unknown compound.
m/z Displays the mass-to-charge ratio of the ion.
RT [min] Displays the retention time in minutes of the chromatographic
peak that contains the unknown compound ion.
FWHM [min] Displays the width of the chromatographic peak for the adduct
ion at its half-height in minutes.
Intensity (hidden) Displays the intensity of the ion.
Area Displays the area of the chromatographic peak that contains the
unknown compound ion.
Parent Area [%] Displays the chromatographic peak area of the current peak as a
percentage of the total chromatographic peak area for the parent
compound (compound selected in the Compounds per File table)
per input file.
Max. Exchange Displays the maximum number of atoms considered for
isotopologue evaluation.
Avg. Exchange Displays the average number of atoms exchanged for the ion.
Rel. Exchange [%] Displays the relative number of atoms exchanged versus the
maximum number of exchangeable atoms for the feature’s
elemental composition.

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Table 142. Labeled Features table (Sheet 2 of 2)

Column Description
Exchange Rate [%] Displays the exchange rate for individual isotopologues.
#MI Displays the number of matching isotopes for the unknown
compound ion.
SFit [%] Displays the spectral similarity score between the measured and
theoretical isotope pattern.
Fitted Cov. [%] Displays the how well the intensities of the fitted isotope pattern
match those of the theoretical isotope pattern.
Measured Cov. [%] Displays the how well the intensities of the measured isotope
pattern match those of the theoretical isotope pattern.
File ID Displays the integer that the application assigned to the input file.
Study File ID Displays the study file ID (F#) of the input file.

Labeled Compounds per File table

Table 143 describes the columns in the Labeled Compounds per File table. The related table
displays details about the selected compound in the higher-level table. To view the compound
name for a component in the main Labeled Compound per File table, open its related
Compounds table.
Table 143. Labeled Compounds per File table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to label the entries with custom tags that you
created by using the Custom Tags Filter view. You can filter the
result table on these tags.
Molecular Weight Displays the molecular weight of the unknown compound.
RT [min] Displays the retention time in minutes of the chromatographic
peak that contains the unknown compound ion.
FWHM Displays the width of the chromatographic peak for the adduct
ion at its half-height in minutes.
Max. #MI Displays the maximum number of matching isotope peaks.
#Adducts Displays the number of adducts (features).
Area Displays the area of the chromatographic peak that contains the
unknown compound ion.

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Table 143. Labeled Compounds per File table (Sheet 2 of 2)

Column Description
Max. Exchange Shows the maximum number of exchangeable atoms that the
analysis considered.
Avg. Exchange Displays the average number of atoms exchanged for the ion.
Rel. Exchange [%] Displays the relative number of atoms exchanged versus the
maximum number of exchangeable atoms.
Status The Analyze Labeled Compounds Node evaluates the measured
isotope pattern versus the fitted isotope pattern (for the expected
isotopologues) to determine the presence of contaminating
masses. It also evaluates the distribution of the measured exchange
rates for the expected isotopologues.

For information about the status flags, see “Labeling Status (per
file).”
Exchange Rate [%] Displays the contribution of individual isotopologues to the final
measured pattern.
File ID Displays the integer that the application assigned to the input file.
Study File ID Displays the study file ID (F#) of the input file.

Similar Compounds Related table

Use the Similar Compounds table to review the compounds that the application connected to
a selected compound in the Compounds table.

The Similar Compounds table is generated by the Generate Molecular Networks node. See
“Generate Molecular Networks node.”

Table 144 describes the columns in the Similar Compounds table.

Table 144. Similar Compounds table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in
the result table and in reports after you apply result filters.
Tags Use this column to label the entries with custom tags that
you created by using the Custom Tags Filter view. You can
filter the result table on these tags.

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Table 144. Similar Compounds table (Sheet 2 of 2)

Column Description
Direction Displays the direction in which the transformation was
applied, and defines which compound is a substrate and
which is a product.

Forward—The selected compound acts as a substrate to

which the transformation was applied. The connected similar
compound is a product of the transformation.

Reverse—The selected compound is a product of the

transformation. The connected similar compound acts as a
substrate to which the transformation was applied.
Mass Shift [Da] Displays the difference between the measured molecular
weights of the two compounds.
Composition Change Displays the difference between the elemental compositions
of the two compounds.
Transformations Displays the name of assigned transformation pathway—that
is, this column lists the names of the individual steps.
Displays “Isomer” when the elemental composition of the
substrate and product compounds are identical.
Transformation Mass [Da] Displays the total theoretical mass of the assigned
transformation steps in Daltons.
# Fragments Displays the number of fragments available for the selected
compound.
MSn Score Displays the final spectral similarity score between the two
compounds as the average of the forward and reverse
coverages.
Forward Cov. [%] Displays the relative number of matched centroids in the
product compound’s MSn spectra.
Forward Matches Displays the number of matched centroids in the product
compound’s MSn spectra.
Reverse Cov. [%] Displays the relative number of matched centroids in the
substrate compound’s MSn spectra.
Reverse Matches Number of matched centroids in the substrate compound’s
MSn spectra.

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Compound Identification result tables

For information about the result tables for the compound identification workflow nodes, see
these topics:
• ChemSpider Results table
• Mass List Search Results table
• mzCloud Results table
• mzCloud Results Hits table
• mzVault Results table
• mzVault Results Hits table
• Predicted Compositions table

ChemSpider Results table

Use the ChemSpider Results table to review the compounds found in the ChemSpider
databases. The Search ChemSpider Node creates the ChemSpider Results table.

Y To open the ChemSpider information for a specific ChemSpider hit

Click the link in the CSID column.

The ChemSpider web page for the selected hit opens in your default web browser.

Table 145 describes the columns in the ChemSpider Results table.

Table 145. ChemSpider Results table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to add custom tags to the result table items. You
can filter the result table by these tags. See “Custom color-coded
tags for result table entries.”
Name Displays the name of the compound hit in the ChemSpider
database.
Structure Displays the molecular structure of the compound.
Formula Displays the chemical formula of the compound.
Molecular Weight Displays the molecular weight of the compound to five decimal
places.
CSID Displays the ChemSpider identification number.

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Table 145. ChemSpider Results table (Sheet 2 of 2)

Column Description
#References Displays the number of references for the compound in the
ChemSpider database.
Additional hidden columns
SMILES (hidden) Displays the compound’s molecular structure by using short
ASCII strings. SMILES stands for simplified molecular input line
entry system.
InChi (hidden) Displays the international chemical identifier for the compound.
#Data Sources Displays the number of ChemSpider data sources that include the
(hidden) compound.
#PubMed References Displays the number of PubMed references for the compound.
(hidden) You can use a PubMed reference to access the scientific literature.
#RSC (hidden) Displays the number of Royal Society of Chemistry references for
the compound.
Additional columns in the related ChemSpider Results table
Compound Match Indicates the match status between the current item and the
assigned compound annotation.

( ) Green—Full Match

( ) Orange—Partial Match

( ) Red—No Match
ΔMass [Da] Displays the mass difference in daltons between the search mass
and the mass of the matching compound in the ChemSpider
database.
ΔMass [ppm] Displays the mass difference in ppm between the search mass and
the mass of the matching compound in the ChemSpider database.
SFit[%] Displays the spectral similarity score from the Apply Spectral
Distance node.

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Mass List Search Results table

Use the Mass List Search Results table to review the compounds in the selected mass lists that
match the compounds detected by the Detect Compounds node.

The Search Mass Lists Node creates the Mass List Search Results table.

The main Mass List Search Results table displays all of the compounds in the selected mass
lists that match the compounds detected by the untargeted analysis. The related Mass List
Search Results table lists information about the compound selected in the main Compounds
table.

Table 146 describes the columns in the Mass List Search Results table.
Table 146. Mass List Search Results table (Sheet 1 of 2)
Column Description
Tags Use this column to add custom tags to the result table items. You
can filter the result table by these tags. See “Custom color-coded
tags for result table entries.”
Formula Displays the elemental composition of the compound in the mass
list.
Molecular Weight Displays the molecular weight of the compound in the mass list.
RT [min] Displays the chromatographic retention time (when available) of
the compound in the mass list.
Structure Displays the structure (when available) of the compound in the
mass list.
Name Displays the name of the compound in the mass list.
Miscellaneous These columns display additional information about the
annotations compound in the mass list.
Reference List Name Displays the name of the mass list that contains the matching
compound.
Additional columns in the related Mass List Search Results table
Compound Match (LC Indicates the match status between the current item and the
studies only) assigned compound annotation.
• ( ) Green—Full Match
• ( ) Orange—Partial Match
• ( ) Red—No Match
Max. ΔMass [Da] Displays the maximum mass difference between the measured
mass for the compound in the Compounds table and the
theoretical mass of the compound, in daltons.

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Table 146. Mass List Search Results table (Sheet 2 of 2)

Column Description
Max. ΔMass [ppm] Displays the maximum mass difference between the measured
mass for the compound in the Compounds table and the
theoretical mass of the compound, in parts per million.
SFit[%] (LC studies Displays the spectral similarity score from the Apply Spectral
only) Distance node.

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mzCloud Results table

Use the mzCloud Results table to view the results of an mzCloud search.

The Search mzCloud Node creates the mzCloud Results table.

Selecting a row in the mzCloud Results table displays a mirror plot with the selected
fragmentation scan on the top and the matched reference scan from the mzCloud database on
the bottom. The centroids for the matching fragments are displayed as green sticks with a
green circle at the end. Red circles on the x-axis indicate the m/z values of the missing
fragments.

In the collapsible spectrum tree pane to the left of the spectrum plot, the coverage bars
indicate whether the matching library spectrum is from an identity hit or a similarity hit.
Figure 147. Mirror plot with annotations for a matching spectrum in the mzCloud Results table

Coverage bar—dark blue for an identity hit and light blue for a similarity hit
Reference spectrum
from the mzCloud mass
Query spectrum from a sample spectral database
(Scan #2176 in input file F1)

Tip To automatically annotate the matching fragments in the mirror plot, you must set
the following advanced parameter in the Search mzCloud node to True—Annotate
Matching Fragments. By default, this parameter is hidden and set to False.

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Figure 148. Mass Spectrum view with an annotated mirror plot

Scan information

Table 147 describes the columns in the mzCloud Results table.

Table 147. mzCloud Results table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to add custom tags to the result table items. You
can filter the result table by these tags. See “Custom color-coded
tags for result table entries.”
Structure Displays the structure of the matching compound.
Name Displays the compound name in the mzCloud database.
Formula Displays the elemental composition formula of the matching
compound.
Molecular Weight Displays the molecular weight of the matching compound.
Best Match Displays the match value (0 to 100%) between the best
fragmentation scan for a compound (across the input files) and
the matching mzCloud spectrum (mzCloud ID). The related
Compounds table lists the scan number of the best fragmentation
scan.

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Table 147. mzCloud Results table (Sheet 2 of 2)

Column Description
Best Sim. Match Displays the best match score for a library spectrum to a
fragmentation scan across the input files. The related Compounds
tables lists the scan number of the similar fragmentation scan.
mzCloud ID Displays the mzCloud ID (Database-Number) for the matching
compound. Clicking this link opens the mzCloud database to the
matching compound’s reference spectrum.
KEGG ID Displays the KEGG ID for the compound in the KEGG database.
Compound Class Displays the mzCloud compound classes that include the
compound.
mzCloud Library Displays the name of the database where the search found the
matching spectrum.
Additional columns in the related mzCloud Results table
Compound Match Indicates the match status between the current item and the
assigned compound annotation. For color-coding information, see
“Annotations Source column in a compounds table.”
ΔMass [Da] Displays the difference between the theoretical mass of the
matching compound and the observed mass of the unknown
compound in daltons.
ΔMass [ppm] Displays the difference between the theoretical mass of the
matching compound and the observed mass of the unknown
compound in parts per million.
Match Displays the match value (0–100%) between the specified scan
number from the input files and the matching spectrum in the
mzCloud database.

mzCloud Results Hits table

The mzCloud Results Hits table is a related table for the mzCloud Results table.

Table 148 describes the columns in the mzCloud Results Hits table.
Table 148. mzCloud Results Hit table (Sheet 1 of 2)
Column Description
Confidence Displays the confidence of the match.
Intensity Threshold Displays the relative intensity threshold for the search spectrum.
Library Spectrum ID Displays the spectrum ID of the library spectrum.

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Table 148. mzCloud Results Hit table (Sheet 2 of 2)

Column Description
Match Displays the match quality of this search spectrum to the library
spectrum.
Name Displays the compound name in the mzCloud database.
Scan # Displays the scan number from the input files that contains the
best matching fragmentation spectrum.
Tree Match Displays the tree match value (0–100%) between the specified
scan number from the input files and the matching spectrum in
the mzCloud database.
Type Displays the match type: Identity or Similarity.

mzVault Results table

Use the mzVault Results table to review the results of an mzVault search.

The Search mzVault node creates the mzVault table.

Table 149 describes the columns in the mzVault Results table.

Table 149. mzVault Results table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to label the entries with custom tags that you
created by using the Custom Tags Filter view. You can filter the
result table on these tags.
Structure Displays the structure of the matching compound.
# Related Compounds Displays the number of unknown compounds with the same
putative elemental composition but different retention times.
mzVault ID Displays the ID number of the matching compound in the
mzVault library.
Name Displays the name of the matching compound.
Formula Displays the elemental composition formula of the matching
compound.
Molecular Weight Displays the molecular weight of the matching compound.
Best Match Displays the match value (0–100%) between the best
fragmentation scan for a compound (across the input files) and
the matching mzVault spectrum. The related Compounds table
lists the scan number of the best fragmentation scan.

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Table 149. mzVault Results table (Sheet 2 of 2)

Column Description
mzVault Library Displays the name of the mzVault library where the analysis found
a matching compound.
ChemSpider ID Displays the ChemSpider ID number for the matching
compound. Clicking this link opens the ChemSpider database to
the compound’s record.
Compound Class Displays the mzVault compound class that includes the
compound.
mzCloud ID Displays the mzCloud ID for the matching compound in the
mzCloud database. Clicking this link opens the mzCloud database
to the compound’s record.
KEGG ID Displays the KEGG ID for the matching compound in the
KEGG database. Clicking this link opens the KEGG database to
the compound’s record.
Additional columns in the related mzVault Results table
Compound Match Indicates the match status between the current item and the
assigned compound annotation. For color-coding information, see
“Annotations Source column in a compounds table.”
ΔMass [Da] Displays the difference between the theoretical mass of the
matching compound and the observed mass of the unknown
compound in daltons.
ΔMass [ppm] Displays the difference between the theoretical mass of the
matching compound and the observed mass of the unknown
compound in parts per million.
Scan Number Displays the scan number from the input files that contains the
best matching spectrum.
Match Displays the match value (0–100%) between the specified scan
number from the input files and the matching spectrum in the
mzVault database.

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mzVault Results Hits table

The mzVault Results Hits table is a related table for the mzVault Results table.

Table 150 describes the columns in the mzVault Results Hits table.
Table 150. mzVault Results Hit table
Column Description
Intensity Threshold Displays the relative intensity threshold for the search spectrum.
Match Displays the match quality of this search spectrum to the library
spectrum.
Name Displays the compound name in the mzVault library file.
Scan # Displays the scan number from the input files that contains the
best matching fragmentation spectrum.

Predicted Compositions table

Each compound in the Compounds table has a related Predicted Compositions table.

Use the Predicted Compositions table to review the possible chemical formulas for the
selected compound in the Compounds table. The Predicted Compositions tables lists the
possible chemical formulas based on the compound’s molecular weight.

The Predict Compositions Node creates the Predicted Compositions table.

Table 151 describes the columns in the Predicted Compositions result table.
Table 151. Predicted Compositions table (Sheet 1 of 3)
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to add custom tags to the result table items. You
can filter the result table by these tags. See “Custom color-coded
tags for result table entries.”
Compound Match Displays whether the predicted composition matches the currently
assigned compound annotation.

( ) Red—No Match

( ) Green—Full Match
Formula Displays the predicted elemental composition.
Molecular Weight Displays the molecular weight.

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Table 151. Predicted Compositions table (Sheet 2 of 3)

Column Description
ΔMass [Da] Displays the difference between the theoretical mass and the
measured mass in daltons.
ΔMass [ppm] Displays the difference between the theoretical mass and the
measured mass in ppm.
RDBE Displays the rings and double bonds equivalent value for the
predicted composition.
H/C Displays the ratio of hydrogen to carbon atoms in the predicted
composition.
Rank Displays the rank order of each composition.
#Matched Iso. Displays the number of matching isotopes.
#Missed Iso. Displays the number of isotopes that were missing in the
measured isotope pattern as compared to the theoretical pattern
for the predicted composition.
#Matched Fragments When the Use Fragments Matching algorithm is turned on in the
Predict Compositions node, this column displays the number of
centroids (m/z values) in the best MS2 scan that match possible
fragments (mass values from a subset of the elemental
compositions in the predicted composition).
SFit [%] Displays the spectral similarity score between the theoretical and
the measured isotope pattern as a percentage.

The SFit [%] score = (1–SD) × 100

SD (hidden) Displays the spectral distance score. A lower SD score corresponds
to a higher SFit [%] score.

Range: 0 to 1
Pattern Cov. (%) Displays the summed intensity of the matching isotope peaks in
the measured MS1 spectrum relative to the summed intensity of
the theoretical isotope pattern.

Provides a quantitative measure of how well the measured isotope

pattern matches the theoretical isotope pattern.
Note Because the base peak (leftmost peak) is typically
responsible for most of the pattern intensity, even a small
decrease in the percent coverage might be important. For
example, a missing peak for an isotope with two 13C atoms
might cause only a small decrease in the summed intensity of the
measured isotope pattern.

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Table 151. Predicted Compositions table (Sheet 3 of 3)

Column Description
MS Cov. (%) Displays the summed intensity of matching isotope peaks in the
measured pattern relative to the summed intensity of all the peaks
in the measured pattern.
IMPORTANT Low values for all of the candidates might indicate
an overlapping pattern rather than a lack of good matches.
MSMS Cov. (%) Displays the summed intensity of the matched fragment peaks
relative to the summed intensity of all the fragment peaks in the
selected fragmentation scan.
Note Low values for all of the candidates might indicate a
contaminating compound within the isolation window for the
fragmentation scan.

Pathway Mapping result tables

For information about the result tables for the Pathway Mapping nodes, see these topics:
• BioCyc Pathways table
• BioCyc Results table
• KEGG Pathways table
• Metabolika Pathways table
• Metabolika Results table

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BioCyc Pathways table

Use the BioCyc Pathways table to review all the mapped pathways in the result file.

The Map to BioCyc Pathways node creates the BioCyc Pathways table. The columns that are
available in the main BioCyc Pathways table and the related BioCyc Pathways table depend on
which nodes provide data to the Map to BioCyc Pathways node.

In an LC processing workflow, the Group Compounds node, the Group Expected

Compounds node, or both nodes connect to the Map to BioCyc Pathways node. And the
Map to BioCyc Pathways node connects to the Apply Spectral Distance node and the Apply
mzLogic node when the processing workflow includes these nodes. The Group Compounds
node creates the Compounds table, and the Group Expected Compound node creates the
Expected Compounds table.

For more information, see “BioCyc Pathways view.”

Table 152 describes the columns in the BioCyc Pathways main table. The BioCyc Pathways
table lists all the BioCyc pathways that include at least one of the compounds in the main
compounds table.
Table 152. BioCyc Pathways table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in
the result table and in reports after you apply result filters.
Tags Use this column to add custom tags to the result table items.
You can filter the result table by these tags.
Pathway Name Displays the names of the mapped Metabolika pathways that
include matching structures (by formula, mass, or both) for
at least one compound in the Compounds table.
#Mapped Compounds Displays the number of detected compounds (in the
Compounds table) mapped onto the BioCyc pathway.
#Mapped Expected Displays the number of expected compounds (in the
Compounds Expected Compounds table) mapped onto the BioCyc
pathway.
#Matched Compounds Displays the number of compounds in the pathway that map
to the Compounds table.
#Matched Expected Displays the number of compounds in the pathway that map
Compounds to the Expected Compounds table.
Total #Matched Displays the number compounds in the pathway that map to
Compounds the Compounds table, the Expected Compounds table, or
both tables.
#Compounds in Pathway Displays the total number of compounds in the pathway.

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Table 152. BioCyc Pathways table (Sheet 2 of 2)

Column Description
Additional columns in a BioCyc Pathways table for a compound in the main compounds table
BioCyc Compound IDs Displays BioCyc compound ID.
(related table)
BioCyc Compound Names Displays the BioCyc compound name.
(related table)
BioCyc Compound Formula Displays the BioCyc compound formula.
(related table)

BioCyc Results table

Use the BioCyc Results table to review the compounds found in the mapped BioCyc database.

The Map to BioCyc Pathways node creates the BioCyc Results table.

Table 153 describes the columns in the BioCyc Results table.

Table 153. BioCyc Results table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to add custom tags to the result table items. You
can filter the result table by these tags. See “Custom color-coded
tags for result table entries.”
Structure Displays the molecular structure of the compound.
Name Displays the compound name in the BioCyc database.
Formula Displays the chemical formula of the compound.
Molecular Weight Displays the molecular weight of the compound to five decimal
places.
Additional columns in the related BioCyc Results table for a compound
Compound Match Indicates the match status between the current item and the
assigned compound annotation.
Max. ΔMass [Da] Displays the maximum mass difference between the measured
mass for the compound in the Compounds table and the
theoretical mass of the compound, in daltons.
Max. ΔMass [ppm] Displays the maximum mass difference between the measured
mass for the compound in the Compounds table and the
theoretical mass of the compound, in parts per million.

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Table 153. BioCyc Results table (Sheet 2 of 2)

Column Description
BioCyc ID Displays the BioCyc identification number for the compound.
BioCyc DB Displays the name of the BioCyc database that mapped the
compound.
mzLogic Score Displays the mzLogic score provided by the Apply mzLogic node.
(LC studies)
SFit[%] Displays the spectral similarity score from the Apply Spectral
(LC studies) Distance node.

KEGG Pathways table

Use the main KEGG Pathways table to review all of the mapped pathways that include
compounds detected across the input file set.

The Map to KEGG Pathways Node creates the KEGG Pathways table.

Table 154 describes the columns in the main KEGG Pathways table and the KEGG Pathways
table for a compound. The KEGG Pathways table lists all the KEGG pathways that include at
least one of the compounds detected by the untargeted search.
Table 154. KEGG Pathways table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to add custom tags to the result table items. You
can filter the result table by these tags. See “Custom color-coded
tags for result table entries.”
Pathway ID Displays the identification number of the mapped KEGG
pathway.
Pathway Name Displays the name of the mapped KEGG pathway that includes at
least one compound in the Compounds table.
#Referenced Compounds (LC studies) Displays the number of detected compounds in the Compounds
table that are referenced in the identified KEGG pathway.

Available when the workflow includes the Group Compounds

node.
#Referenced Expected Compounds (LC studies) Displays the number of compounds in the Expected Compounds
table that are referenced in the identified KEGG pathway.

Available when the workflow includes the Group Expected

Compounds node.

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Table 154. KEGG Pathways table (Sheet 2 of 2)

Column Description
#Identified Compounds (LC studies) Displays the number of different KEGG compound IDs
identified for the compounds in the Compounds table.

Available when the workflow includes the Group Compounds

node.
#Identified Expected Compounds (LC studies) Displays the number of different KEGG compound IDs
identified for the compounds in the Expected Compounds table.

Available when the workflow includes the Group Expected

Compounds node.
#All Identifications Displays the number of unique identifications for all compound
categories (for the compounds in the Expected Compounds table
and the Compounds table) related to a specific pathway.

Available when the workflow includes the Group Expected

Compounds node and the Group Compounds node
#mzCloud Results (LC studies) Displays the number of compounds in the identified KEGG
pathway that the mzCloud search identified.

Available when the workflow includes the Search mzCloud node.

Additional columns in the KEGG Pathways table for a compound in a main compounds table
KEGG Compound IDs Displays a list of the KEGG compound IDs in ascending order
from left to right.
KEGG Compound Names Displays a list of the KEGG compound names.
KEGG Compound Formulas Displays a list of the KEGG compound formulas.
Max. ΔMass [Da] Displays the maximum mass difference between the measured
mass for the compound in the compounds table and the
theoretical mass of the compound, in daltons.
Max. ΔMass [ppm] Displays the maximum mass difference between the measured
mass for the compound in the compounds table and the
theoretical mass of the compound, in parts per million.

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Metabolika Pathways table

Use the main Metabolika Pathways table to review all of the mapped pathways that include
compounds detected across the input file set. Use the related Metabolika Pathways tables to
review the results for specific compounds.

The Map to Metabolika Pathways node creates the Metabolika Pathways table.

Table 155 describes the columns in the Metabolika Pathways table. The main Metabolika
Pathways table lists all the Metabolika pathways that include at least one of the compounds in
any of the main compounds tables (Compounds table, Expected Compounds table, or both).
The related table displays the search results for the selected compound in the main
compounds table.
Table 155. Metabolika Pathways table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in
the result table and in reports after you apply result filters.
Tags Use this column to add custom tags to the result table items.
You can filter the result table by these tags.
Pathway Name Displays the names of the mapped Metabolika pathways that
include matching structures (by formula, mass, or both) for
at least one compound in the Compounds table.
#Mapped Compounds Displays the number of detected compounds (in the
Compounds table) mapped onto the Metabolika pathway.
#Mapped Expected Displays the number of expected compounds (in the
Compounds Expected Compounds table) mapped onto the Metabolika
pathway.
#Matched Compounds Displays the number of compounds in the pathway that map
to the Compounds table.
#Matched Expected Displays the number of compounds in the pathway that map
Compounds to the Expected Compounds table.
Total #Matched Displays the number compounds in the pathway that map to
Compounds the Compounds table, the Expected Compounds table, or
both tables.
#Compounds in Pathway Displays the total number of compounds in the pathway.
Additional columns in a Metabolika Pathways table for a compound in the main compounds
table
Metabolika Compound IDs Displays Metabolika compound ID.
(related table)

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Table 155. Metabolika Pathways table (Sheet 2 of 2)

Column Description
Metabolika Compound Displays the Metabolika compound name.
Names (related table)
Metabolika Compound Displays the Metabolika compound formula.
Formula (related table)

Metabolika Results table

Use the Metabolika results table for a specific compound to review the match between the
putative compound in your experimental data and the mapped compounds. This table is
empty when the compound in the main compounds table has zero associated Metabolika
pathways.

The Map to Metabolika Pathways node creates the Metabolika Results table.

Table 156 describes the columns in the Metabolika Results table.

Table 156. Metabolika Results table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to add custom tags to the result table items. You
can filter the result table by these tags. See “Custom color-coded
tags for result table entries.”
Structure Displays the molecular structure of the compound.
Name Displays the compound name in the Metabolika database.
Formula Displays the chemical formula of the compound.
Molecular Weight Displays the molecular weight of the compound to five decimal
places.
Compound Match Displays whether the Metabolika pathway structure is a full or
partial match for the selected compound.

( )—Full Match

( )—Partial Match

( )—No Match

Available for compounds in the Compounds table from an LC

study.

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Table 156. Metabolika Results table (Sheet 2 of 2)

Column Description
mzLogic Score Displays the normalized score from the Apply mzLogic node for
the structure based on the mzCloud similarity matches (Apply
mzLogic node).

Available for compounds in the Compounds table when the

processing workflow includes the Apply mzLogic node.
Original mzLogic Displays the score from the Apply mzLogic node for the structure
Score (hidden) based on the mzCloud similarity matches.

Available for compounds in the Compounds table when the

processing workflow includes the Apply mzLogic node.
Max. ΔMass [Da] Displays the maximum mass difference between the measured
mass for the compound in the compounds table and the
theoretical mass of the compound, in daltons.
Max. ΔMass [ppm] Displays the maximum mass difference between the measured
mass for the compound in the compounds table and the
theoretical mass of the compound, in parts per million.
SFit[%] Displays the spectral similarity score from the Apply Spectral
Distance node.

Available when the processing workflow includes the Apply

Spectral Distance node.

Compound Scoring tables

For information about the result tables for the unknown compound scoring nodes, see these
topics:
• Compound Class Matches table
• Matched Patterns table
• Neutral Losses table

Compound Class Matches table

The Compound Class Matches table is related to the Compounds table. Use the Compound
Class Matches table to review the compounds classes that match the compound selected in the
Compounds table.

The Compound Class Scoring node adds the Class Coverage column to the Compounds table
and creates the Compound Class Matches table, which is related to the Compounds table.

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Table 157 describes the columns in the Compound Class Matches table.
Table 157. Compound Class Matches table
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to add custom tags to the result table items. You
can filter the result table by these tags. See “Custom color-coded
tags for result table entries.”
Name Displays the name of the library that contains the matching
structure.
Description Displays the user-specified description of the library.
FISh Coverage Displays the FISh coverage score (see “FISh scoring for proposed
structures.” ).
Class Coverage Displays the number of matching centroids in the best
fragmentation scan divided by the total number of fragments in
the selected compound class libraries.
# Matched Fr. Displays the number of library fragments that match the centroids
in the best fragmentation scan for a compound.
# Missed Fr. Displays the number of library fragments that do not match the
centroids in the best fragmentation scan for a compound.

Figure 149 shows an annotated fragmentation scan of a detected compound. By comparing

the m/z values of the centroids in the fragmentation scan against a compound class library
with 11 structures, the application annotated 6 centroids in the fragmentation scan with
matching structures from the library. The legend in the Mass Spectrum view lists the search
library, the Class Coverage score, and the FISh Coverage score.

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Figure 149. Fragmentation scan and compound class match result for a detected compound

#Matched fragments

Matched Patterns table

The Matched Patterns table is related to the Compounds table. Use the Matched Patterns
table to review how well the isotopic pattern matches the compound selected in the
Compounds table.

The Pattern Scoring node adds the Matched Patterns table to the result file.

Table 158 describes the columns in the Matched Patterns table.

Table 158. Matched Patterns table (Sheet 1 of 2)
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to add custom tags to the result table items. You
can filter the result table by these tags. See “Custom color-coded
tags for result table entries.”
Name Displays the name or chemical formula of the compound.

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Table 158. Matched Patterns table (Sheet 2 of 2)

Column Description
SFit [%] Displays the spectral fit for the isotope pattern to the chemical
formula.
SD Displays the spectral distance score.
Pattern Coverage [%] Displays the summed intensity of the matching isotope peaks in
the measured MS1 spectrum relative to the summed intensity of
the theoretical isotope pattern.

Provides a quantitative measure of how well the measured isotope

pattern matches the theoretical isotope pattern.
Note Because the base peak (leftmost peak) is typically
responsible for most of the pattern intensity, even a small
decrease in the percent coverage might be important. For
example, a missing peak for an isotope with two 13C atoms
might cause only a small decrease in the summed intensity of the
measured isotope pattern.
#Matched Iso. Displays the number of matching isotopes for the unknown
compound.
File ID Displays the integer that the application assigned to the input file.
Study File ID Displays the study file ID (F#) of the input file.

Neutral Losses table

When the processing workflow for an analysis includes the Search Neutral Losses node, the
result file includes the main Neutral Losses table and a related Neutral Losses table for each
detected compound.

For more information, see Neutral loss detection and visualization.

Table 159 describes the columns in the main and related Neutral Losses tables.
Table 159. Neutral Losses table (Sheet 1 of 2)
Column Description
Main table
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Tags Use this column to add custom tags to the result table items. You
can filter the result table by these tags. See “Custom color-coded
tags for result table entries.”

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Table 159. Neutral Losses table (Sheet 2 of 2)

Column Description
Name Displays the name of the neutral loss fragment. This name
corresponds to the name of the neutral loss in the Neutral Losses
view.
Formula Displays the formula of the neutral loss fragment.
Molecular Weight Displays the molecular weight of the neutral formula.
#Compounds Displays the number of compounds where the application
detected the specified neutral loss in their fragmentation spectra.
Related table for a specific compound
Name Displays the name of the neutral loss.
Formula Displays the elemental composition of the neutral loss.
Molecular weight Displays the neutral loss shift, in daltons, between the precursor
ion and the fragment ion produced by the specified neutral loss.
#Compounds Displays the number of compounds where the application
detected the named neutral loss in their fragmentation scans.
Scan# Displays the scan number where the application detected the
specified neutral loss.
Precursor Mass Displays the mass of the precursor ion that underwent the
specified neutral loss.
Charge Displays the charge of the fragment produced by the specified
neutral loss.
Expected Mass Displays the expected mass (m/z value) of the fragment produced
by the specified neutral loss.
ΔMass [Da] Displays the difference between the mass of the expected fragment
produced by the specified neutral loss to the experimental mass of
the fragment in the specified fragmentation scan, in daltons.
ΔMass [ppm] Displays the difference between the mass of the expected fragment
produced by the specified neutral loss to the experimental mass of
the fragment in the specified fragmentation scan, in parts per
million.

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Statistical Methods table

Statistical Methods table

For LC studies, when the analysis includes any of the following nodes, the analysis result
includes the Statistical Methods table:
• Align Retention Times (ChromAlign) node
• Group Compounds node
• Fill Gaps node
• Apply Missing Value Imputation node
• QC Correction nodes
• Normalize Area node
• Differential Analysis node

Table 160 describes the columns in the Statistical Methods table.

Table 160. Statistical Methods table
Column Description
Checked Use this column to select the rows that you want to display in the
result table and in reports after you apply result filters.
Method Description Displays a description of the statistical methodology.
Node ID Displays identification number for the workflow node in the
processing workflow.
Node Name Displays the name of the processing workflow node that applied
the specified statistical methodology.
Node Workflow ID Displays the identification number of the workflow node.
Processing Step Displays the processing step where the analysis applied the
specified statistical methodology.

Differential analysis columns

When the analysis includes sample groups and group ratios and the processing workflow
includes the Differential Analysis node, the following columns appear in the Compounds
table and the Expected Compounds table:
• Group Areas
• Group CV(%)
• Ratio
• Log2 Fold Change

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Differential analysis columns

• P-value
• Adj. P-value.

In addition, the following columns appear in the Merged Features table, Group Areas, Ratio,
and Log2 Fold Change. The background colors of the table cells provide visual information
about the numeric values in these columns.

Table 161 describes the columns from a differential analysis.

Table 161. Differential analysis columns (Sheet 1 of 3)
Column Description
Group Areas Displays the median chromatographic peak area for the compound in
the sample group. To display the group names, click the expand icon
to the right of the column heading.

When the compound is not found, the cells have a gray background.
The Differential Analysis node bins the group areas in the current
result file on the Log10 scale, with one bin for each order of
magnitude (1e4, 1e5, 1e6, and so on), and uses a different background
color for each bin. The values in the lowest bin have a pale-yellow
background. The values in the highest bin have a green background.

Color-coding:
• Lowest values:
• Highest values:
Note When a result table includes the Group Areas column, the
Area column is hidden, by default.
Group CV(%) Displays the coefficient of variation for the groups. Groups with a high
degree of variation (20% or greater) have a red background.

Color-coding:
( ) Values equal to or greater than 20 have a red background.

( ) Values from 0 to 19 have a white background.

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Table 161. Differential analysis columns (Sheet 2 of 3)

Column Description
Ratio Displays the area ratio or ratios for the generated ratios.

A ratio of 0 (0/X) has a dark purple background ( 0.000 ). An

undefined ratio (X/0) (labeled as Infinity) has an orange background
( Infinity ).

The cells for compounds with defined ratios greater than 0 have the
following background colors:
• Compounds with ratios between 0 and 0.5 are divided into five
equal bins. The background color for the table cells is a
progressively darker blue hue as the ratio approaches zero.
• Compounds with ratios greater than 2 are divided into five equal
bins. The background color for the tables cells is a progressively
darker red hue as the ratio increases.
0.5 2
0 < Ratio < 0.5 Ratio ≥ 2

Log2 Fold Change Displays the fold change (ratio) in the log base 2 scale.

A log2 fold change of Infinity has an orange background ( Infinity ).

When the ratio is 0 (0/X) or –Infinity in the Log2 format, the
background color is a dark purple (–Infinity ).

The cells for compounds with log2 fold change values between
– infinity and infinity have the following background colors:
• Compounds with log2 fold change values more negative than –
1.00 are divided into five equal bins. The background color for
the table cells is a progressively darker blue hue as the value
becomes more negative.
• Compounds with log2 fold change values greater than 1.00 are
divided into five equal bins. The background color for the table
cells is a progressively darker red hue as the value increases.
Log2 Fold Change Log2 Fold Change
negative –1 1 positive

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Differential analysis columns

Table 161. Differential analysis columns (Sheet 3 of 3)

Column Description
P-value Displays the p-value for the sample group calculated by running the
Tukey HSD test (post hoc) after an analysis of variance (ANOVA) test.

The p-value is a number between 0 and 1.

Given the following hypotheses:

• Null hypothesis—There is no difference between the sample
groups for the variable tested.
• Alternate hypothesis—There is a difference between the sample
groups for the variable tested.

You can interpret the p-value as follows:

• A low p-value means that you can reject the null hypothesis with a
low probability of error that the alternate hypothesis is true.
• A high p-value means that you can accept the null hypothesis with
a low probability of error that the alternate hypothesis is true.
Adj. P-Value (Differential Analysis node) Displays the adjusted p-value.

The application adjusts p-values in cases of multiple testing. Multiple

testing of a null hypothesis leads to higher probabilities of rejecting
this null hypothesis by chance, and therefore the application corrects
the whole set of hypotheses (for example, all detected compounds) as a
function of the set size (for example, a set of 10 000 compounds has a
stronger correction than one of only 1000). The application performs
this correction by using the Benjamini-Hochberg algorithm for the
false discovery rate.
P-value and Adj. Color-binning for p-values and adjusted p-values:
P-value
• 1–0.05 [ ] Red
• 0.05–0.01 [ ] Orange
• 0.01–0.005 [ ] Yellow
• 0.005–0.001 [ ] Yellow green
• <0.001 [ ] Green

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Descriptive statistics columns

Descriptive statistics columns

The Descriptive Statistics post-processing node adds the columns described in Table 162 to
the compounds tables (Compounds table and Expected Compounds table). The descriptive
statistics columns are hidden by default.
Table 162. Descriptive statistics columns
Column Description
Min. Area Displays the minimum peak area for the compound in the sample
set.
Q1 Area Displays the lower boundary of the first quartile (25%) area for
the compound in the sample set.
Median Area Displays the median area for the compound (MW × RT) in the
sample set.
Q3 Area Displays the upper boundary of the third quartile (75%) area for
this compound in the sample set.
Mean Area Displays the calculated average area for the compound
(MW × RT) in the sample set.
Area SD Displays the standard deviation of the peak areas for the
compound (MW × RT) in the sample set.
Area CV [%] Displays the coefficient of variation of the area for the compound
(MW × RT) in the sample set.

QC Correction columns
Table 163 describes the columns that the Apply QC Correction node (in combination with
QC samples) adds to the various compounds tables.
Table 163. QC correction columns (Sheet 1 of 2)
Column Description
Norm. Area (hidden) Displays the normalized areas of the QC corrected
compounds per input file.

When a compound does not pass any of the QC correction

filters, the area cell for the compound is empty. You can
view the uncorrected chromatographic peak area for the
compound in the corresponding Areas column.
# Usable QC Displays the number of usable QC samples. See “Using
quality control samples to compensate for batch effects.”

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Annotations Source column in a compounds table

Table 163. QC correction columns (Sheet 2 of 2)

Column Description
RSD QC Areas [%] Displays the relative standard deviation of the peak areas
for the compound across the QC samples before area
correction.
RSD Corr. QC Areas [%] Displays the relative standard deviation of the peak areas
for the compound across the QC samples after area
correction.
QC Fill Status Displays a status rectangle for each QC sample.

Possible states:

( ) Green—Filled by re-detected peak

( ) Gray—N/A

( ) Orange—Filled by matching ion

( ) Blue—Filled by simulated peak

Annotations Source column in a compounds table

The Annot. Source column in the Compounds table for an LC study indicates the match
status for each compound from the search nodes in the processing workflow. The expanded
column heading displays the annotation sources.

For LC data, the Assign Compound Annotations node determines the validity of the
annotations from the annotation sources that are selected in the Assign Annotations node
when the processing workflow includes these annotation sources. You can select up to six
compound identification and pathway mapping sources in the Assign Annotations node

The Annot. Source column indicates the match status for the selected compound from the
compound identification nodes and pathway mapping node in the processing workflow. The
expanded column heading displays the annotation sources.

Tip To sort by the annotation source, do the following:

1. Click the expand icon to display the vertical headings of the subordinate columns.
2. Select the heading of the subordinate column that you want to sort by.
The selected subordinate column heading appears in bold text with an asterisk at the
top of the vertical text.
3. Click the Annot. Source column heading to sort the table rows.

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Peak Rating columns

Table 164. Match states from the annotation source nodes in a processing workflow
Possible states Meaning
( ) Green—Full Match The current formula and structure annotations match
the best available item from the particular source
(online database or local mass list).
Gray—No Results Retrieved no data from the particular source.
Orange—Not the Top Hit Current compound annotation matches one of the
hits, but not the top one.
Orange—Partial Match Only the formula for the current compound
annotation matches the items retrieved from the
particular source.
Orange—Unused Retrieved items from the particular source, but did not
assign any annotations.
Red—Invalid mass The best available item from the particular source has
a molecular weight that does not match the molecular
weight of the compound within the specified mass
tolerance.
Red—No match The particular source does not have an item that
matches the current annotations for the compound.

Peak Rating columns

For information about how the Compound Discoverer application calculates the peak rating
for a chromatographic peak, see “Chromatographic peak rating filter.”

An analysis that includes the following workflow nodes generates a Peak Rating column in
each of the following result tables.
• The Group Compounds node generates the Peak Rating column in the Compounds
table.
• The Group Expected Compounds node generates the Peak Rating column in the
Expected Compounds table.
• The Differential Analysis node generates the (recalculated) Peak Rating column in the
GC CI Compounds table.

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Peak quality factor (PQF) columns in the result tables

Table 165. Color-coding in the Peak Rating data column

Color Calculated peak rating (0 to 10)
Gray N/A

Orange 0 to 2.5

Yellow >2.5 to 5.0

Yellow green >5.0 to 7.5

Green > 7.5 to 10.0

Peak quality factor (PQF) columns in the result tables

For information about how the Compound Discoverer application calculates the peak quality
factors for a chromatographic peak, see “Peak quality factors.”

The following result tables include PQF columns:

• Compounds table
• Compounds per File table
• Features per File table
• Expected Compounds table
• Expected Features per File table
Table 166. Color-coding for the four peak quality factors
Peak Quality Factors
Color FWHM to base Jaggedness Modality Zig-Zag Index
Gray N/A N/A N/A N/A

Dark Green 0.0 to 0.8 0.0 to 0.1 0.0 to 0.02 0 to 0.05

Yellow 0.8 to 0.9 0.1 to 0.4 0.02 to 0.3 0.05 to 0.2

Orange 0.9 to 1.0 0.4 to 1.0 0.3 to 1.0 0.2 to 1.0

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Create and print reports

The following topics describe how to create, preview, and print reports:
• Reporting workflow
• Generate a report with an existing report template
• Create new report templates
• Edit existing report templates
• Reference information for the report template page
• Select the paper type, print width, page orientation, and watermark for a report template
• Preview and print a report

When you open a report template for editing, it opens as a tabbed page with a workspace area
on the left. You can use the standard report templates provided with the application or you
can create your own custom report templates.

Note The following reporting features are new in the Compound Discoverer 3.3
application:
• The name of the study and the file name of the result file (analysis result)—By
default, these items appear in the upper-middle of the page header section and
cover-page section of the report.
• mzCloud mirror plot—You can now add an mzCloud mirror plot to a report
template. See “Add mzCloud mirror plots to a report template.”

Reporting workflow
The following flowchart shows the reporting workflow (Figure 150 and Figure 151).

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Reporting workflow

Figure 150. Reporting workflow (page 1)

Open a result file.

Filter the data to display only the

table rows of interest.

Sort the table rows in the order of

interest and save the result file.

Can you use an existing No Can you use an existing No

report template as is? report template with minor
modifications?

Yes Yes

From the Reporting menu, From the Reporting menu, From the Reporting menu,
choose Create Report choose Edit Report Template choose Create Report Template.
and select a report template. and select a report template.
The Customize Report dialog box
The report resolution page opens. The report template page opens. opens.

Review the resolved report. Make the appropriate selections

and click OK.
The report template page opens.

Close the page.

No
Does the template display
the data correctly?

Yes Next page

Print the report.

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Generate a report with an existing report template

Figure 151. Reporting workflow (page 2)

Previous
page

Edit the report template.

To resolve the data and preview the report, click

the Preview Report icon, , to open the
Report Preview dialog box.
Or, click the Print Report icon, , to open the
Report Print dialog box.

Does the template display No To return to the report template

the data correctly? page, close the dialog box.

Yes

To print the report, click the Print icon, .

To save the report template with a new name,

close the dialog box to return to the report
template page and click the Save As icon, .

Generate a report with an existing report template

You can use one of the report templates provided with the application or one of your own
custom report templates to produce reports that display items of interest in a result file.

For details, see these topics:

• Report templates provided with the application
• Preview and print a report by using an existing report template

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Report templates provided with the application

The Compound Discoverer application comes with several report templates. The report
templates reside in the following folder:
drive:\ProgramData\Thermo\Compound Discoverer 3.3\Common
Templates\ReportTemplates

For LC studies, the application comes with the nine defined report templates.
Table 167. LC report templates provided with the application (Sheet 1 of 2)
Report template name Description
Compounds No Graphs A4 Generates single row for each visible compound in the
Compounds table. Reports the structure, name, and
formula when available. Reports the calculated molecular
weight and group areas.
Compounds with Graphs A4 Generates a single page for each visible compound in the
Compounds table. Reports the structure, name, and
formula when available. Reports the calculated molecular
weight and group areas. The report includes a
chromatogram plot, an MS1mass spectrum plot, and an
MS2 spectrum plot.
Expected Compounds No Graphs A4 Generates a single row for each visible compound in the
Expected Compounds table. Reports the parent
compound, formula, calculated molecular weight,
retention time, dealkylations, transformations,
composition change, FISh coverage, and group areas.
Expected Compounds per File No Graphs A4 Generates a single row for each visible compound in the
Expected Compounds table. Reports the parent
compound, formula, calculated molecular weight,
retention time, ions and the m/z values of the ions,
composition change, chromatographic peak area, and
study file ID.
Expected Compounds per File with Graphs A4 Generates a separate page for each visible compound in
the Expected Compounds per File table. Includes the
following graphs: MS1 spectrum, chromatogram, and
MS2 spectrum.
Expected Compounds with Structures No Graphs A4 Generates a single row for each visible compound in the
Expected Compounds table. Reports the parent
compound, formula, calculated molecular weight,
composition change, retention time, FISh coverage, and
group areas. Reports the structure and name when
available.

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Table 167. LC report templates provided with the application (Sheet 2 of 2)

Report template name Description
Expected Compounds with Structures with Graphs A4 Generates a separate page for each visible compound in
the Expected Compounds table. Reports the parent
compound, formula, calculated molecular weight,
composition change, retention time, FISh coverages, and
group areas. Reports the name when available. Includes
the following graphs: chromatogram, MS1 spectrum, and
MS2 spectrum with fragment annotations.
Expected Compounds with Graphs A4 Generates a separate page for each visible compound in
the Expected Compounds table. Reports the parent
compound, formula, calculated molecular weight,
retention time, dealkylations, transformations,
composition change, FISh coverage, and group areas.
Reports the name and structure when available. Includes
the following graphs: chromatogram, MS1 spectrum, and
MS2 spectrum with fragment annotations.
Compounds with Graphs and mzCloud Mirror Plot Generates a single page (or more depending on the
number of mzCloud matches the analysis found for the
compound) for each visible compound in the
Compounds table. Reports the structure, name, and
formula when available. Reports the calculated molecular
weight. The report includes a chromatogram plot, an
MS1 mass spectrum plot, and mirror plots.

Preview and print a report by using an existing report template

Y To preview and print a report by using an existing report template

1. Open a result file. See “Open, close, and update result files.”
In the application window, the reporting menu commands and the reporting toolbar
icons ( ) become available.
2. Determine which main table you want to include in the report and filter the data in this
table as appropriate. See “Filter the data for data reduction.”
For LC studies, you can use the report templates provided with the application with one
of these tables as described in the template name: Compounds table, Expected
Compounds table, or Expected Compounds per File table.
3. To select an existing report template, choose Reporting > Create Report from the menu
bar or click the Create Report icon, .
The Open Report Design Template dialog box opens to the Report Templates folder.

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To select an appropriate report template, you must know what data the report template is
designed to resolve. Typically, a report template resolves the filtered data from one of the
main tables and one or more of the graphs associated with the table. A report template
can also resolve data from one or more related tables. The predefined report templates
resolve the data in the Compounds table or the Expected Compounds table.
4. Select the appropriate report template and click Open.
The report resolution page opens with the thumbnail pane on the right and a report
preview on the left.
The tab format for the report resolution page is as follows:
Report Template Name
As the application resolves the data with the report template, the following icon displays
the progress.

When the data is resolved, the progress icon disappears, and the application begins
rendering the report pages. The current page/estimated pages box lists the progress.
If the selected template does not contain ReportInfo items, the application displays the
pages as it renders them. If the selected template contains a ReportInfo item, the
application does not display the rendered pages until it has rendered all of the report
pages. ReportInfo items include the time stamp in the upper left and the page number at
the center bottom of the defined report templates.
If the report contains too many pages, the application cancels the report generation and
the following message box appears.

5. If the application cancels the report generation, repeat step 2 to step 4. This time, reduce
the number of reported items by modifying the filters.
6. Review the contents of the report.
7. On the report resolution page, click the Print icon, , in the toolbar to print the
report.
The Print dialog box opens.

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8. Select the appropriate printer and the page range that you want to print.
The report templates that come with the application default to printing on A4 paper.
9. If you are not printing on A4 paper, change the printer setting.
10. Click OK to print the report.

Create new report templates

This topic describes how to create a new report template by using the Customize Report
dialog box where you do the following:
• Select the data to be included in the report:
– Columns of interest in the main table
– Graphs associated with the main table
– Columns of interest in any of the related tables
– Graphs associated with any of the selected related tables
• Change the appearance of the tables:
– Transpose the column orientation from left to right to top to bottom
– Add Separator lines below the column headings
– Indent the related tables below the main table
– Select background colors for the table headers and table rows
• Select the paper type (PaperKind parameter), page orientation, and logo image

For details, see these topics:

• Create a new report template by using the Customize Report dialog box
• Add, remove, or modify the color schemes for a report template
• Customize Report dialog box parameters

Create a new report template by using the Customize Report dialog box
When you create a new report template by using the Customize Report dialog box, the
application automatically adds a date-and-time stamp on the left side of the report header, the
Compound Discoverer logo on the right side of the report header, and the page number in the
report footer. By default, the application displays information from the currently selected
main result table on A4 paper in the portrait orientation with the data columns listed left to
right. You can select a different main table, add related tables and graphs (chromatogram,
mass spectrum, mirror plot), and change the paper type, page orientation, and logo image.

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Y To create a report template by using the Customize Report dialog box

1. Open a result file. See “Open, close, and update result files.”
2. Do one of the following:
• From the menu bar, choose Reporting > Create Report Template.
• In the toolbar, click the Create a New Report Template icon, .
The Customize Report dialog box opens in front of the New Report Template page.
Figure 152. Customize Report dialog box for the Compounds table

3. In the Reported Table list at the top of the dialog box, select the main table for the report
template.
A list of data items for the selected table appears. By default, the Columns list is
expanded, and the Graphs and Related Tables lists are collapsed.
4. To select the columns for the main table, any of the associated graphs, and any of the
main table’s related tables, do the following:
a. Under the selected table name, click each expand icon, , to open these sections:
• Columns
• Graphs
• Related Tables
b. In the expanded sections, select the check box for each column, graph, or related
table (and associated columns) that you want to include in the generated reports.

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5. To add a separator line above the column heading row for each result table, select the
Draw Lines check box.

(Default layout for the main result table)

Column 1 label Column 2 label Column 3 label Column 4 label Column 5 label
Data text box Data text box Data text box Data text box Data text box
(Related table)
Column 1 label Column 2 label Column 3 label Column 4 label Column 5 label
Data text box Data text box Data text box Data text box Data text box

Tip For result tables with a large number of data columns, transpose the columns by
selecting the Transpose Data check box. Otherwise, you might need to resize the data
columns to fit the page.

6. To transpose the tabular data from columns to rows, do the following:

a. Select the main result table and the related tables for the report.
b. In the data item list, select the table that you want to transpose as follows:
• To transpose the columns in the main table, select the main table name (the first
data item) in the Customize Report dialog box.
• To transpose the columns in a related table, select the check box to the left of the
related table name and click the table name to make sure that it is highlighted in
blue.
c. Select the Transpose Data check box.

Note Selecting another table clears the Transpose Data check box.

Each selected data column appears as a two-column row in the report template. The first
column displays the column heading and the second column displays the data from a
table row.

(Default layout for the main table)

Column 1 label Column 2 label Column 3 label
Data text box Data text box Data text box
(Transposed layout for the main table)
Column 1 label Data text box
Column 2 label Data text box
Column 3 label Data text box

7. To indent a related table, do the following:

a. Select the related table in the expanded list of data items.

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b. In the Indenting box, type the indentation value from 0.00 to 1.00 inch.

(Default layout for the main result table)

Column 1 label Column 2 label Column 3 label Column 4 label Column 5 label
Data text box Data text box Data text box Data text box Data text box
______________________________________________________________
(Related table indented by 1 inch)
Column 1 label Column 2 label Column 3 label Column 4 label
Data text box Data text box Data text box Data text box

8. To select a color scheme for a report table, do the following:

a. In the report item list, select the table of interest, for example, the main table or one
of the related tables.
b. In the Color Scheme list, select one of the available color schemes.
Each scheme consists of two colors: the first color for the background of the table
headers and the second color for the background of the table rows. The default color
scheme is Transparent/Transparent.
9. Under General Settings, do the following:
• In the PaperKind list, select the default paper size for the report.
• In the Orientation list, select the page orientation.
• Next to the Logo Image box, click the browse icon, . Then, in the Open Image
File dialog box, select the graphic file for the logo image and click Open.
10. To apply the settings and close the Customize Report dialog box, click OK.
Your selections appear on the report template page. The tab format for the report
template page is as follows:
Main Result Table
11. To save the template with a different name, click the Save As icon ( ) in the upper-left
corner of the report template page.
For information about editing the report template, see “Edit existing report templates.”

Figure 153 shows a report template for selected columns in the Compounds per File table and
two associated graphs. The default report template uses the Compound Discoverer
application icon. You can select a different image and resize its picture container as
appropriate.

Note The Customize Report dialog box automatically adds the file name and study name
fields to the page header section of the report template.

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Figure 153. Report template with data from the Compounds per File table
Date-and-time stamp (automatically added) Logo image’s Default
picture logo image
Selected main table name container

Selected
columns

Selected
graphs

Page number (automatically

added)

Note The Customize Report dialog box automatically adds the file name and study name
fields to the page header section of the report template.

Add, remove, or modify the color schemes for a report template

In the Customize Report dialog box, follow this procedure to modify, add, or remove the
color schemes for the report tables.

Y To modify the current color scheme or to add or remove color schemes from the list

1. Open the Customize Report dialog box. See “Create new report templates.”
2. Select the main result table and the related tables for the report.
3. Click Modify.
Two color selection lists appear below the Color Scheme list. The list on the left changes
the background color for the column headings. The list on the right changes the
background color for the data columns.

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4. From the color lists, select one or two background colors, and then click Add.

The application displays the effect of the color scheme in the data item list, adds the new
color scheme to the Color Scheme list, and makes the Remove button available.

Note Accepting the settings in the Customize Report dialog box adds the new color
scheme to the ColorScheme.xml file that is located in the following folder:
C:\Users\Public\Public Documents\Thermo\Compound Discoverer 3.3
\Common Templates\ReportTemplates

If you remove the new color scheme before you click OK at the bottom of the
Customize Report dialog box to accept the settings, the application does not add the
new color scheme to the ColorScheme.xml file.

5. To change the color selection, do one or both of the following:

• If you do not want to apply the new color scheme to the currently selected table, click
Reset.
The application undoes the color selections, applies the default color scheme
(Transparent/Transparent), and closes the color lists. When you click OK to accept
the settings and close the Customize Reports dialog box, the application adds the new
color scheme to the ColorScheme.xml file.

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• If you do not want to keep the new color scheme, click Remove.
The application undoes the color selections, leaves the color lists open, and removes
the color scheme from the Color Scheme list.

Customize Report dialog box parameters

Table 168 describes the parameters in the Customize Report dialog box.
Table 168. Customize Report dialog box parameters (Sheet 1 of 3)
Parameter Description
Reported Table Lists the main tables in the result file.
Columns Lists the columns for the selected main table.
Graphs Lists the graphs for the selected main table.
Related Tables Lists the tables related to the selected main table.
Columns Lists the columns for the selected related table.
Graphs Lists the graphs for the selected related table.
Related Tables Lists the second-level related tables for the selected related table.
Appearance
Draw Lines Specifies whether the application draws a line above the table
column headers.

Default: Selected
Transpose Data Specifies the layout of the data in the result table columns.

The default layout (check box cleared) matches the result table
layout, with columns displayed from left to right and rows
displayed from top to bottom. Select this check box to transpose
the columns to rows.

Default: Cleared
Tip When you select a table item in the data item list, the
application automatically clears the Transpose Data check box.
For each table that you want to transpose, select the table name
and make sure that it is highlighted in blue. Then select the
Transpose Data check box.
Indenting Specifies the indentation of the selected related table data from the
left edge of the page, from 0.00 to 1.00 inch.

Default: 0.00 in.

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Table 168. Customize Report dialog box parameters (Sheet 2 of 3)

Parameter Description
Color Scheme
Color Scheme Specifies the color scheme for the selected table.

Each color scheme consists of two colors. The first color is the
background of the column headings. The second color is the
background of the table rows.

You can modify the Color Scheme list by adding or removing

color schemes.

Default: Transparent/Transparent
Note Accepting the settings in the Customize Report dialog box
adds the new color schemes to the ColorScheme.xml file that is
stored in the same folder as the common report templates.
General Settings
PaperKind Specifies the size of the paper for printing the report. Select the
appropriate paper size before sending the report to the printer.

Default: A4
Orientation Specifies the orientation of the report, either Portrait or
Landscape.

Default: Portrait
Logo Image Specifies the logo image to appear by default in the upper-right
corner of each report page.

The default size of the picture container for the logo is

1.823 × 0.492 in. (width × height). When the selected image is
larger than the picture container, the container clips the image.
You can edit the properties of the picture container in the report
template.
Buttons
Reset Resets the color scheme to the default scheme.
Modify Opens two color selection lists.
Add Selecting colors in one or both of the color selection lists (below
the Color Scheme list) makes this button available.

Applies the new color scheme to the selected table and adds the
new color scheme to the Color Scheme list.
Remove Removes the selected color scheme from the Color Scheme list.

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Table 168. Customize Report dialog box parameters (Sheet 3 of 3)

Parameter Description
OK Applies the selected settings to the new report template.
Cancel Cancels your selections and closes the dialog box.

Edit existing report templates

Use the report template page to modify a report template. The report template page shows the
items that you selected using the Customize Report dialog box or the items in the existing
report template that you selected. Some of the items appear as containers (a rectangular box)
where you can add text, images, or data graphs.

Note You can open more than one report template page in the application window.

Tip For reference information about the toolbars, shortcut menus, and so on, see
“Reference information for the report template page.” For information about changing
the paper type and page orientation, see “Select the paper type, print width, page
orientation, and watermark for a report template.”

To modify a report template, follow these procedures as applicable:

• Open a report template for editing
• Add a cover page to a report template
• Change the logo image for a report template
• Change the format of the date and time field in a report template
• Add items in the Section Reports pane to a report template
• Add a rich text box to a report template
• Add main table columns to a report template
• Add data graphs to a report template
• Add mzCloud mirror plots to a report template
• Add related table columns to a report template
• Edit the properties of subreport columns in a report template
• Move a subreport column to the main table of a report table
• Modify the properties of a section report item
• Add page breaks to a report template
• Delete a pair of workspace sections on the report template page

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• Resize the sections of a report template

• Add, align, and transpose columns in a report template by using the shortcut menu
commands
• Add a border to an item by using the Format Border command

Figure 154 shows the Compounds No Graphs template on the report template page.
Figure 154. Report template page

Click this square to display the report Upper Item list

template properties (page orientation and toolbar
paper type) in the Properties pane.

Sizing bar Lower toolbar Properties pane for the

paper size, page orientation,
and watermarks

Open a report template for editing

The Compound Discoverer application comes with several report templates.

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Y To open a report template

1. Open a result file. See “Open, close, and update result files.”
2. From the application window, do one of the following:
a. Choose Reporting > Create Report Template from the menu bar, or click the
Create a New Report Template icon, , in the toolbar.
The Customize Report dialog box opens.
b. Make the appropriate selections and click OK.
The report template page opens as a tabbed document. The tab format is as follows:
Main Result Table Name

Add a cover page to a report template

By default, the cover page is not visible in the report templates that you create by using the
Customize Report dialog box.

The default items on the cover page are as follows:

• Name of the main result table
• Date and time stamp
• Logo

Y To display and edit the cover page of a report template

1. Open the report template that you want to edit. See “Open a report template for editing.”
The report template opens as a tabbed page in the application window. Typically, the
cover page section is closed.

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2. (Optional) To view the items in the cover page section that you might want to edit, drag
down the sizing handle to the left of PageHeader. Then, edit the items as applicable.

Sizing handle next to the beginning of the

page header section

3. To add the cover page to the report, do the following:

a. Click the cover page title bar to select it.
The properties for the cover page appear in the Properties pane.
Figure 155. Cover page properties

Cover page
properties

b. In the properties pane, select True for Visible in the Behavior section.

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Change the logo image for a report template

Y To change the logo image in a report template

1. Open the report template. See “Open a report template for editing.”
The report template opens as a tabbed page in the application window.
2. Select the logo image container.
The picture properties appear in the Properties pane.

Note The Compound Discoverer icon is the default logo for the common templates
and the templates that you create with the Customize Reports dialog box.

3. In the Data area, click the browse icon, , to the right of the Image property. You might
have to click the row to make the browse icon appear.

The Open dialog box opens with a setting of All image files for the file type.
4. Browse to the folder where you stored the logo of interest, select the logo, and click
Open.
The selected image appears in the container.
5. Modify the Layout properties as appropriate.

Change the format of the date and time field in a report template
The templates that come with the application include a DateTimeInfo field (date and time
stamp) in the Cover Page section and the Page Header section.

Y To change the format of the date-and-time field

1. Open the report template. See “Open a report template for editing.”
The report template opens as a tabbed page in the application window.
2. Select the DateTimeInfo item.
The properties for this item appear in the Properties pane.

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Figure 156. Output Format box for the Date Time Info field in the report templates

3. Under Appearance, click the OutputFormat box to make the browse icon appear. Then
click the browse icon.
The Output Format dialog box opens.
Figure 157. Output Format dialog box

4. Select the format of interest.

5. Click OK to accept the setting.

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Add items in the Section Reports pane to a report template

You can add any of the items in the Section Reports pane to a report template. See “Section
report items for a report template.”

Y To add an item to the template

1. Open the report template. See “Open a report template for editing.”
The report template opens as a tabbed page in the application window.
2. From the Section Reports pane to the right of the workspace area, drag an item to the
appropriate location on a workspace section of the page.
Some of the items appear as containers (boxes) where you can add text or images.
3. Select the item to open its properties below the Section Reports pane.
4. Edit the properties of the item as necessary.

Add a rich text box to a report template

A rich text box contains fixed text that is not dynamically populated from the contents of the
result file.

Y To add rich text box to a report template

1. Open a report template for editing. See “Open a report template for editing.”
2. From the Section Reports pane to the right of the workspace area, drag the RichTextBox
item to the appropriate location on a workspace section of the page.
3. Do one of the following:
• Type text in the rich text box.
• Click the Load File link below the properties pane to open the Open dialog box.
Then, select the file type (RTF, TXT, HTML, or HTM), browse to the file location,
select the file, and click Open. Figure 158 shows the properties for the rich text box
and the Load File link below the properties pane.

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Figure 158. Properties for the rich text box

Add main table columns to a report template

Use the Add Field shortcut menu command or the Add Items icon in the upper toolbar to add
data fields from a result table to the report template.

Y To add a main table column to the report template

1. Open the report template. See “Open a report template for editing.”
The report template opens as a tabbed page in the application window.
2. Depending on the orientation of the table columns, do the following:
• If the result table columns are arranged horizontally from left to right, go to step 3.
• If the result table columns are arranged vertically from top to bottom, go to step 5.
3. To add a main table column to a column set that is arranged horizontally, do either of the
following:
• To place the new column to the right of the current column set, select the
PageHeader bar.
• To place the new column to the right of a specific column, select the column heading.

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4. Do one of the following:

• Right-click the PageHeader bar or a specific column heading, and then choose Add
Field > Data Column from the shortcut menu.
–or–
a. Click the PageHeader bar or a specific column heading.
b. In the toolbar, click the Add Items icon, , to open a list of data column
selections.
The available items in the list include the unused data columns in the current main
table. The data columns that are already in the template are unavailable and grayed
out.
c. Select an available data column from the list.
The new data column appears to the right of the selected column or the current
column set. If there is a gap to the right of the selected column or to the right of the
column set, the new column fills the gap. If there is no space to the right of the
selected column or to the right of the column set, the new column shares the space
with the selected column or the last column in the column set.
5. To add a main table column to a column set that is arranged vertically, do the following:
a. Use the sizing bar to display all of the data column rows.
b. Right-click the Label column (heading) of the two-column row that is above where
you want to add the new two-column data row, and choose Add Field > Data
Column.
The new two-column data row appears below the selected two-column row.

Add data graphs to a report template

You can add the following data graphs to a report template from a compounds table—MS1
Spectrum, MS2 Spectrum, Chromatogram Trace.

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Y To add a data graph that is associated with the main table to the report template

1. Open the report template. See “Open a report template for editing.”
The report template opens as a tabbed page in the application window.
2. Do one of the following:
• Right-click the DetailSection_Main_Table_Name bar and choose the Add Field >
Data Graph of interest from the shortcut menu.
–or–
a. Click the DetailSection_Main_Table_Name bar.
b. In the toolbar, click the Add Items icon, , to open a list of data graphs and
related table column and graph selections.
The available items in the list include the data graphs associated with the current
main table and the related tables and graphs for the current main table.
c. Select an available data graph from the list.

The new data graph appears below the right of the last graph currently in the template.

Add mzCloud mirror plots to a report template

When the processing workflow includes the Search mzCloud node, you can add mirror plots
to the report template.
• Add the mirror plots for each mzCloud hit for a compound to a report
• Create a report template for the mzCloud Results table that includes a mirror plot

Add the mirror plots for each mzCloud hit for a compound to a report

Y To add an mzCloud mirror plot for a to a report template

1. Add a sub report for the mzCloud results table to the details section as follows:
a. Click the DetailSection_Main_Table_Name bar to select it.
b. In the toolbar, click the Add Items icon, , and choose mzCloud Results > Name
(or any table columns that you want to report). See Figure 159.

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Figure 159. Menu selections for the mzCloud Results table

The SubReport_mzCloud_Results report appears in the DetailSection area.

Sub Report

2. Double-click SubReport_mzCloud_Results.
The DetailSection mzCloud_Results area appears below the bottom toolbar. See
Figure 160.

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Figure 160. Detail section for the mzCloud Results table selections

Detail section for the

mzCloud Results table

3. Right-click DetailSection_mzCloud_Results and choose Add Field > MS2 Spectrum.

The MS Spectrum data field appears in the detail section for the related mzCloud Results
table.

Create a report template for the mzCloud Results table that includes a mirror plot

Y To create a report template for the mzCloud hits in the mzCloud Results table

1. From the application menu bar, choose Reporting > Create Report Template.
The Customize Report Dialog box opens.
2. In the Reported Table list, select mzCloud Results.

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3. Under Columns select the check boxes for the table columns you want to include in the
report.
4. Expand Graphs and select the MS2 Spectrum check box.

Note The MS2 Spectrum under Graphs for the mzCloud Results table is a mirror
plot of the best MS2 spectrum for the compound and its best match spectrum from
the mzCloud mass spectral database.

5. Make the appropriate selections for the appearance, color scheme, paper kind,
orientation, and logo image.
For example, select the Draw Lines and Transpose Data check boxes. And, select
Landscape for the paper orientation. See Figure 161.
Figure 161. Customize Report box for the mzCloud Results table

Mirror Plot

6. Click OK.
The template appears on the report designer page. The default print width for the
landscape orientation on A4 paper is 10.993 inches. See Figure 162.

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Figure 162. Report designer page with a report template for the mzCloud Results table

7. Modify the report template as appropriate.

• In the Page Header section, add labels to the left of the Result File container and the
Study File container by dragging the Label item from the Section Reports area at the
right of the report designer page, aligning it to the left of the left of the data field
container, and then typing the appropriate text in the Label container.
• Expand the vertical size of the Detail Section for the mzCloud Results table. Then,
do the following:
• Move the Structure data field and the container for the structure image to the
right of the other table columns. Then enlarge the size of the container for the
structure image.
• Adjust the widths of the Name, Formula, Molecular Weight, Best Match, and
mzCloud columns on the left as appropriate.
• In the Page Footer section, center the Page Number In container.
By default, the x axis location of the page number is 3.948 inches and the print width
for the page is 10.993 inches. To center the page number, change the location of the
page number under the Layout property to 5.5 inches.

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Figure 163. Modified report template for the mzCloud Results table

File name and Structure image Mirror Plot

Study labels

8. To preview the report, click the Preview Report icon, .

Figure 164 shows the report review.

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Figure 164. Preview for the mzCloud Results table report

9. To save the report, do the following:

a. In the toolbar at the top of the report designer page, click the Save As icon, .
The Save Report Template As dialog box opens.
b. Select the directory location, change the file name as appropriate, and click Save.

Add related table columns to a report template

When you add table columns from a related table to a report template, a subreport item
appears in the report template.

Y To add a column from a related table to a report template

1. Open the report template. See “Open a report template for editing.”
The report template opens as a tabbed page in the application window.

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2. Do one of the following:

• Right-click the DetailSection_Main_Table_Name bar and choose Add Field >
Related Table Name > Column of Interest.
Figure 165. Using the shortcut menus to select a column from a related table

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• Select the DetailSection_Main_Table_Name bar. Then, in the toolbar, click the

Add Items icon, , select an available related table from the first list, and then
select a table column from the second list.
Figure 166. Using the Add Items list to select a column from a related table

Note The available items in the first list include the data graphs associated with
the current main table and the related tables for the current main table. When
you select a related table from the first list, the second list includes the available
columns for that table.

3. If the DetailSection is collapsed, click the expand icon to open the section.

Expand icon

The added table column appears at the bottom of the DetailSection (data area). The
application automatically adds a line above the column heading.

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Figure 167. Expected Compounds per File table with the ΔMass [ppm] column from the related
Expected Features per File table

Line above the

related table
column

Column from the related table

Edit the properties of subreport columns in a report template

Y To edit the properties of subreport columns

1. Open the report template. See “Open a report template for editing.”
The report template opens as a tabbed page in the application window.
2. To open the subreport editor area, do one of the following:
• Double-click the Subreport_Related_Table_Name box.
–or–
a. Select the Subreport_Related_Table_Name box.
The Edit Sub-Report icon, , becomes available.
b. Click the Edit Sub-Report icon.

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The TextBox item for the related table column appears in a separate section. The
container for the item is sized to the full width of the page.
Figure 168. Report template page with the subreport section open

Column heading for the

ΔMass [ppm] column Subreport section with the container for
the ΔMass [ppm] data item sized to the
full page width

3. To change the properties of the TextBox item in the subreport section, select it.
The properties for the selected item appear in the properties pane to the right of the
workspace.
4. Make changes as necessary in the properties pane, or click the property dialog link below
the properties pane to open the TextBox dialog box and make similar changes.
5. To close the subreport section, click the Close Sub-Report icon in the report designer
toolbar.

Move a subreport column to the main table of a report table

Y To move a subreport column up to the set of main table columns

1. Open the report template. See “Open a report template for editing.”
The report template opens as a tabbed page in the application window.

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2. Resize the column heading container for the subreport column. Then, move it to an
appropriate location in the set of labels for the main table columns.
3. Resize the Subreport_Related_Table_Name container. Then, move it to the appropriate
location in the Detail Section.
4. Double-click the Subreport_Related_Table_Name container that you moved to the Detail
Section.
The DetailSection_Related_Table_Name appears below the bottom toolbar.
5. In the related table’s Detail Section, resize the containers for the data items from the
related table.
Figure 169 shows a report template for the Expected Compounds per File table with an
additional column from the related Expected Features per File table.
Figure 169. Related table column moved up to the main table
Column heading for the
related table column

Subreport container moved to the

main table’s Detail Section

Detail Section for the related table with a

resized container for a data item

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Modify the properties of a section report item

On the report template page, you can edit the position and size of an item by using the mouse
or the properties pane on the right. You can also edit other properties for an item from the
properties pane or the specific dialog box for the item.

Y To modify the properties of a section report item

1. Open the report template. See “Open a report template for editing.”
The report template opens as a tabbed page in the application window.
2. Select the item.
The properties for the selected item appear in the properties pane, at the bottom right of
the report template page. For information about the properties of each item, see
“Property settings for the sections and items in a report template.”
3. Do any of the following:
• To move the item to another position, do either of the following:
– Move the item by dragging it (or you can use the arrow keys on the keyboard).
– In the Properties pane, under Layout, expand Location, and then change the X
and Y values.
• To resize the container for the item, do either of the following:
– Resize the item by dragging the handle points of the container.
– In the Properties pane, under Layout, expand Size, and then change the Width
and Height values.
• To change other properties for the item, do either of the following:
– Modify the properties in the Properties pane.
– Click the Property Dialog link at the bottom right of the report template page,
and then modify the property in the item-specific dialog box.

Note For the RichTextBox item, in addition to the Property Dialog link, you can
click the Load File link to load text from a file. See “Add a rich text box to a report
template.”

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Add page breaks to a report template

Y To add a page break between reported result table rows

1. Open the report template. See “Open a report template for editing.”
The report template opens as a tabbed page in the application window.
2. On the report template page, drag the PageBreak item from the Section Reports pane to
the bottom of the Detail Section of the report template.

Delete a pair of workspace sections on the report template page

Note The report template page pairs these sections together:
• Cover Page and Appendix
• Page Header and Page Footer

When you select one of the paired sections to delete, the application removes both
sections. You cannot delete one section without deleting the other, and you cannot delete
the Detail Section section.

Y To delete a pair of workspace sections

1. Open the report template. See “Open a report template for editing.”
The report template opens as a tabbed page in the application window.
2. Select one of the workspace sections by clicking the section header or by clicking within
the section area.
3. From the shortcut menu, choose Delete.

Resize the sections of a report template

Use the sizing bar to the left of the workspace to resize each workspace section vertically,
except for the Appendix section. See “Workspace sections and sizing bar on the report
template page.”

Tip Make sure to enlarge the workspace section enough to hold all of the items that you
want to add to that section of the template.

The size of a section on the report template page is not necessarily the same as its size in
the generated report.

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Y To vertically resize a workspace section

1. Open the report template. See “Open a report template for editing.”
The report template page opens as a tabbed page in the application window.
2. Do any of the following:
• For the CoverPage, PageHeader, DetailSection, and PageFooter sections, do the
following
– In the sizing bar, drag the sizing handle.
– To vertically enlarge a workspace section, drag down the handle that is aligned
with the header of the subsequent section. To reduce a workspace section, drag
the handle up.
• To enlarge the Appendix section, drag it down by the bottom edge of the report
template page. To reduce this workspace section, drag the bottom edge up.

Add, align, and transpose columns in a report template by using the shortcut menu
commands
See the following table for information about using the shortcut menu for the report template
page to modify a report template.
Table 169. Using the shortcut menu commands on the report template page (Sheet 1 of 2)
Task Do the following
Open the shortcut Right-click the report template page.
menu for the report
template page.
Add an item to a Right-click the section bar of a section area and choose Add Field > Item of Interest.
section of the report
template.

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Table 169. Using the shortcut menu commands on the report template page (Sheet 2 of 2)
Task Do the following
Align a column 1. In the PageHeader section, right-click the column heading (Label item) that you want
heading to its to align with its associated data field (TextBox item).
associated data field.
The Align Columns icon becomes available.
Align Columns icon

Selected Aligned data field

column header (TextBox item)
(Label item)
2. From the shortcut menu, choose Align Fields.
Transpose the data 1. Right-click a column heading (Label) or a column data field (TextBox) and choose
fields (columns to row Transpose Data Fields.
or rows to columns)
2. To undo the change, if necessary, right-click a column heading (Label) or a column data
field (TextBox) and choose Transpose Data Fields.

Add a border to an item by using the Format Border command

You can add a border or modify the current border of any item in the workspace area of a
report template.

Y To add a border to an item

1. Open the report template that you want to edit.

2. Right-click the item of interest in the workspace of the report template and choose
Format Border.
The Format Border dialog box opens.

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Figure 170. Format Border dialog box with the selection of a coral, double-line border

3. To set up the border, click one of the icons in the Presets area or select the line style in the
Line Styles area, and click the appropriate sides of the square in the Preview area.

Reference information for the report template page

For information about the editing tools on the report template page, see these topics:
• Workspace sections and sizing bar on the report template page
• Report template page toolbars
• Shortcut menu commands for the report template page
• Section report items for a report template
• Property settings for the sections and items in a report template
• Open the property dialog box for a workspace section or a specific report item

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Workspace sections and sizing bar on the report template page

Figure 171 shows the five workspace sections, the sizing bar on the left, and the icon that
opens the page orientation and paper type options in the upper-left corner.
Figure 171. Workspace sections, sizing bar, and icon that opens the page size options
Click this square to display the report template properties
(page orientation and paper type) in the Properties pane.

Sizing
bar

Resizing the Appendix area

By default, the workspace on the report template page has five sections. Table 170 lists these
sections, from top to bottom.

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Table 170. Default workspace sections (Sheet 1 of 2)

Workspace section Description
Cover Page Appears as the first page of a report with the following property
selections:
• True—For the Visible parameter in the Behavior section of
the properties pane.
Default: False
• After—For the NewPage parameter in the Data section of the
properties pane.
Default: After. See “NewPage.”

To display the Cover Page section without a page break between it

and the next section, select True for the Visible parameter and
None for the New Page parameter.

Use this section to add nonrepeating information, such as the

report title, date-and-time stamp, and company logo.
Page Header Adds items to the top of each report page. The standard templates
include a Label item with the main table name, a TextBox item
with a time stamp, and a Picture item with a company logo. The
column headings (Label items) appear here when you add table
columns to the report.
Detail Section Adds data from the result file, such as the repeating items
(TextBox item) of a main table or the data graphs for each table
(concatenated with the row.
selected Main_Table
name)
Page Footer Adds information to the footer of each report page, for example,
the page number.

Report templates created with the Customize Reports dialog box

automatically include a page number at the bottom of each page.
The page number is a TextBox item.

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Table 170. Default workspace sections (Sheet 2 of 2)

Workspace section Description
Appendix Adds information to an appendix section of the report.

An Appendix section appears after the last page of a report, with

the following property settings:
• True—For the Visible parameter in the Behavior section of
the properties pane
Default: False
• Before—For the NewPage parameter in the Data section of
the properties pane
Default: Before

To display the Appendix section without a page break between it

and the previous section, select True for the Visible parameter and
None for the NewPage parameter.

Report template page toolbars

Table 171 describes the toolbars on the report template page.

For more information about the report template page, see “Edit existing report templates.”
Table 171. Toolbars on the report template page (Sheet 1 of 4)
Icon Description
Top toolbar
Save Active Item—Saves the report template using the same file
name.

By default, the template file name is the same name as the main
table that you selected in the Customize Report dialog box. See
“Create new report templates.”
Save As—Saves the report template using a different file name.

Preview—Opens the Report Preview dialog box. See “Preview and

print a report.”
Print—Opens the Report Print dialog box.

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Table 171. Toolbars on the report template page (Sheet 2 of 4)

Icon Description
Edit Sub-Report—Enlarges a selected subreport so that you can
edit it.

Selecting a subreport item makes this icon available. When you

click this icon, the report designer opens the subreport in a
separate Detail Section workspace section. You can zoom in on this
temporary section or zoom out of it. Increasing the size of this
temporary section does not affect the report template page.
Note Related tables that you select in the Customize Report
dialog box appear as subreports on the report template page.
Close Sub-Report—Closes the separate subreport workspace
section.

Clicking anywhere in the separate subreport workspace makes this

icon available.
Align Columns—Aligns the Label (column heading) and Textbox
(data) containers for the selected column or columns.

Selecting a report column makes this icon available.

Add Items—Opens a list of items that you can add to the currently
selected section of the report template.

Clicking within a workspace section or the section header makes

this icon available. The list of items varies depending on the
selected section:
• CoverPage and DetailSection sections: You can add related
table columns or graphs that are not currently in the template.
• PageHeader section: You can add main table columns that are
not currently in the template. The column heading appears in
the PageHeader section as a Label item, and the container for
the column data appears in the DetailSection as a TextBox
item.
Cut—Deletes the selected item without confirmation.

Copy—Copies the selected item.

Paste—Pastes the selected item.

Delete—Deletes the selected item after you click OK in the

confirmation dialog box.

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Table 171. Toolbars on the report template page (Sheet 3 of 4)

Icon Description
Zoom Out—Reduces the magnification of the page.

Zoom In—Increases the magnification of the page.

Magnification box—Displays the magnification percentage.

Actual Size—Displays the page at 100% magnification.

Changing the magnification by using the Zoom In and Zoom Out

icons or by typing a value in the magnification box makes this icon
available.
Bottom toolbars
Dimension Lines—Displays dimension lines ( ) as you
resize an item by using the mouse.
Hide Grid—Clears the grid on the page.

Show Dots—Shows the main grid lines and the small dots within
the grid.
Show Lines—Shows the main grid and the smaller lines within the
grid.
Snap Lines—When you move an item on the page, blue alignment
lines appear. When the selected item (Item 1 below) is horizontally
aligned with another item, two vertical lines bracket the aligned
items. When the selected item is vertically aligned with another
item, two horizontal lines bracket the aligned items.

Item 2

Item 1 Item 3

Snap to Grid—When you move an item on the page, this mode

automatically snaps it to the smaller grid lines.
Select Mode—Use this mode to select items on the page.

To select multiple items, press the SHIFT key while you select the
items.

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Table 171. Toolbars on the report template page (Sheet 4 of 4)

Icon Description
Pan Mode—When the page is zoomed in, use this mode to move
to a different part of the page.
Magnification bar—Move the slider to the left to zoom out and to
the right to zoom in. The magnification percentage appears to the
left of the slider.

Shortcut menu commands for the report template page

Table 172 describes the shortcut menu commands for the report template page.
Table 172. Report template page shortcut menu (Sheet 1 of 2)
Command Description
Add Field Adds the item that you choose to the selected workspace section.
Align Fields Aligns a column header or subreport with the associated data.

This command becomes available when you select a column

header or a subreport.
Transpose Data Fields Transposes the data from columns to rows or from rows to
columns.

This command becomes available when you select a column

header.
Note The Insert Section command is available if the template does not already include a
Report Header/Footer section or a Page Header/Footer section.
Insert Section > Report Inserts the ReportHeader and ReportFooter sections.
Header/Footer
Insert Section > Page Inserts the PageHeader and PageFooter sections.
Header/Footer
Copy Copies the selected item.
Paste Pastes the selected item.
Cut Removes the selected item without confirmation.
Delete Deletes the selected item after you click OK in the confirmation
dialog box.
Bring to Front Moves the selected item to the front, on top of other surrounding
items.
Send to Back Moves the selected item to the back, beneath all other surrounding
items.

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Table 172. Report template page shortcut menu (Sheet 2 of 2)

Command Description
Format Border Opens the Format Border dialog box where you can change an
item’s border layout, line style, and color.
Properties Highlights the (Name) property in the properties pane of the
report template page.

Section report items for a report template

The Section Reports pane to the right of the workspace on the report template page contains
all of the different items that you can add to the report template.
Figure 172. Section Reports pane of the report template page

Table 173 describes the items in the Section Reports pane.

Table 173. Items in the Section Reports pane (Sheet 1 of 3)
Item Description
Label A text label that you can add to the report. For example, the File
Name and Study Name labels in the Page Header section of the
report templates provided with the application are labels.
TextBox A text box that is usually used to group multiple items together.
The application uses the TextBox item to display the repeating
tabular data in the result file.
IMPORTANT Use the Rich Text Box item rather than the
TextBox item to add fixed (non-dynamic) text to the report’s
cover page.
CheckBox A check box that you can select or clear.

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Table 173. Items in the Section Reports pane (Sheet 2 of 3)

Item Description
RichTextBox A text box that you can populate by typing text in the box or by
loading text from a file. Use the Load File link below the
properties pane on the right to select and open a text file.
Shape A geometric shape such as a rectangular or square box (with either
square or rounded corners), an ellipse, or a circle.

Tip When you add this item, by default, it appears as a

rectangular box with square corners. To change to a different
shape, modify the Style property under Appearance in the
properties pane.
Picture A container for a graphic.
Line A straight line.
PageBreak A break to push the subsequent content to the next page. To place
reported table rows on separate pages, add a page break at the
bottom of the DetailSection.
Barcode A bar code. For information about setting up the Barcode
properties, refer to the ActiveReports User Guide on the company
website for Grape City.

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Table 173. Items in the Section Reports pane (Sheet 3 of 3)

Item Description
ReportInfo A variable that the application automatically replaces with
real-time data in the generated report. Use the ReportInfo item to
show the current page number or to add a date-and-time stamp.
Select the page number or date-and-time stamp from the
FormatString list under Appearance in the Properties pane.

CrossSectionLine A line that can span across multiple workspace sections on the
report template page.
Note You cannot add this item to the Detail Section workspace
section. However, you can add it to another section (for
example, the Page Header section) and have it span across the
Detail Section section.
CrossSectionBox A box that can span across multiple workspace sections on the
report template page.
Note You cannot add this item to the Detail Section workspace
section. However, you can add it to another section (for
example, the Page Header section) and have it span across the
Detail Section section.

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Property settings for the sections and items in a report template

On the report template page, the properties pane to the bottom right of the workspace
includes all of the property settings that you can use to format a workspace section or an item
in the report template. The settings vary depending on the selected workspace section or item.

If it is available, click the expand icon, , to open the settings for a particular property or the
collapse icon, , to close the settings.

The properties pane contains these property groups, from top to bottom:
• Appearance properties
• Behavior properties
• Data properties
• Design properties
• Layout properties
• Miscellaneous properties

IMPORTANT The Summary properties are not functional.

Tip To open a report template for editing, see “Open a report template for editing.”

For information about opening the properties dialog box for a report item, see “Open the
property dialog box for a workspace section or a specific report item.”

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Appearance properties
Table 174 describes the Appearance properties for report template items.
Table 174. Appearance properties in the Properties pane (Sheet 1 of 3)
Property Description
AnchorBottom (For the Line item only) Specifies whether the line is anchored to
the bottom of the workspace section.

Selections:
• False—Does not anchor the line to the bottom of the
workspace section.
• True—Anchors the line to the bottom of the workspace
section.
Alignment (For the Label, TextBox, ReportInfo, and Barcode items) Specifies
the horizontal alignment of the text within the container.

(For the Barcode item) Specifies the horizontal alignment of the

caption text that is associated with the bar code. You enable the
caption text by setting the CaptionGrouping and CaptionPosition
properties.
BackColor Specifies the background or fill color.
BarHeight (For the Barcode item only) Specifies the height of the bar code.
CaptionGrouping (For the Barcode item only)

Selections:
• False—Does not enable a text caption to be associated with
the bar code.
• True—Enables a text caption.
CaptionPosition (For the Barcode item only) Sets the position of the caption
container relative to the bar code symbol.

Selections:
• None—Hides the caption.
• Above—Sets the position above the symbol.
• Below—Sets the position below the symbol, as in the figure
above.
CharacterSpacing (For the Label and TextBox items) Specifies the spacing between
the characters in the text, in points.

Default: 0

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Table 174. Appearance properties in the Properties pane (Sheet 2 of 3)

Property Description
ClassName Specifies the name of the class for a particular format.

Default: Normal
Font (For the Label, TextBox, and CheckBox items) Specifies the name
of the font and other font characteristics such as the style, size,
effects, and script. Clicking the browse icon, , opens the Font
dialog box where you can specify the font characteristics. Clicking
the expand icon, , expands the settings.
Font > Specifies the GDI character set to use. For a list of valid values,
GdiCharSet refer to the GdiCharSet Property in the Microsoft Developer
Network (MSDN) Library.
Font > Specifies that the font is derived from a GDI vertical font.
GdiVerticalFont
ForeColor (For the Label, TextBox, and CheckBox items) Specifies the font
color.
FormatString (For the ReportInfo item only) Specifies the format of the
generated content as a page number or a date-and-time string.
LineColor Specifies the color of a line or border.
LineSpacing Specifies the spacing between multiple lines of content, in points.
LineStyle Specifies the style of a line or border.
LineWeight Specifies the thickness of a line or border, in pixels.
NarrowBarWidth (For the Barcode item only) Specifies the width of the narrow bars
in the bar code (a value of 1.0 equals 0.864 points).
Tip At a thicker width for the narrow bars, the entire bar code
might be too large for the container. In this case, enlarge the size
of the container to see the entire bar code.
NWRatio (For the Barcode item only) Specifies the ratio of the width of the
wide bars relative to the width of the narrow bars in the bar code.
The larger the ratio, the thicker the wide bars appear.
Tip At a thicker width for the wide bars, the entire bar code
might be too large for the container. In this case, enlarge the size
of the container to see the entire bar code.

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Table 174. Appearance properties in the Properties pane (Sheet 3 of 3)

Property Description
OutputFormat (For the TextBox item only) Specifies the format settings for
custom content, or for a number, currency, date, time, or
percentage. Clicking the browse icon, , for this property opens
the OutputFormatDialog box (see Figure 157 on page 583) where
you can change the settings.

Do not change the OutputFormat settings for data fields from a

result table column.
PictureAlignment (For the Picture item only) Specifies the alignment of the selected
image with respect to the container. For proper alignment, the
container must be larger than the image.

Selections: TopLeft, TopRight, Center, BottomLeft, and

BottomRight
QuietZone (For the Barcode item only) Specifies the left, right, top, and
bottom margins of the quiet zone for the bar code, in inches.
Rotation (For the Barcode item only) Specifies the rotation of the bar code
within the container.
Tip At a rotation of 90 or 270 degrees, the entire bar code might
be too large for the container. In this case, enlarge the size of the
container to see the entire bar code.
Style Specifies the format settings such as color, alignment, font,
geometric shape, or bar code properties.
SupplementOptions (For the Barcode item only) Specifies the supplement options (2-
or 5-digit add-ons for EAN/UPC bar codes).
TextJustify (For the Label and TextBox items) Specifies how to distribute the
text when you set the Alignment property to Justify.
VerticalAlignment (For the Label and TextBox items) Specifies the vertical alignment
of the text within the container.

Selections: Top, Middle, and Bottom

VerticalText Specifies the vertical alignment for the text.
• False—Does not render the text according to the vertical
layout settings.
• True—Renders the text according to the vertical layout
settings.
WrapMode Specifies that a long line of text wraps to the beginning of the next
line to fit in the container.

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Behavior properties
Table 175 describes the Behavior properties for report template items.
Table 175. Behavior properties in the Properties pane (Sheet 1 of 3)
Behavior property Description
Angle Specifies the slope of the text within the container, in degrees.
AutoReplaceFields (For the RichTextBox item only) Specifies whether the data in the
container is automatically replaced with the data from the data
source as specified by the Data Field property selection.
• False—Does not automatically replace the fields of the object
with the fields in the data source that are assigned to the
current workspace section.
• True—Automatically replaces the fields of the object with the
fields in the data source that are assigned to the current
workspace section.
AutoSize (For the Barcode item only) Specifies whether the barcode item
stretches to fill its container.

Selections: True or False

CanGrow Specifies whether the container or section can increase in height to
fit its contents.

Selections: True or False

CanShrink Specifies whether the container or section can decrease in height
to fit its contents.

Selections: True or False

CheckAlignment (For the CheckBox item only) Specifies the alignment of the check
box in the container.
Checked (For the CheckBox item only) Specifies whether the CheckBox
item appears with or without a check mark in the report.

Selections:
• False—Shows the check box selected.
• True—Shows the check box cleared.
CheckSumEnabled (For the Barcode item only) Specifies whether the application
computes and includes a checksum in the bar code.

Selections: True or False

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Table 175. Behavior properties in the Properties pane (Sheet 2 of 3)

Behavior property Description
ColumnDirection (For the Detail Section workspace section only) Specifies whether
to display the data columns in the down-and-across direction or
the across-and-down direction, for a multi-column
(newspaper-style) report.

Selections: DownAcross or AcrossDown

Enabled (For the PageBreak item only) Specifies whether the PageBreak
item is enabled.

Selections: True or False

KeepTogether (For the Detail Section and Appendix workspace sections only)
Specifies whether the contents of the current section prints on a
single page. This property does not shrink items to fit; rather, it
acts like a page break between reported table rows.

Selections: True or False

MultiLine (For the Label, TextBox, ReportInfo, and RichTextBox items
only) Specifies whether the report template displays only the
content that fits on one line or displays all the lines that fit in the
container.

Selections: True or False

PrintAtBottom (For the Appendix workspace section only) Specifies where the
design items in the Appendix section are printed.

Selections:
• False—Places the Appendix design items immediately after
the DetailSection and before the page footer information.
• True—Places the Appendix design items at the bottom of the
current page just above the page footer information.
RepeatToFill (For the Detail Section workspace section only)

False—Does not repeat content to fill the report page.

True—Repeats content to fill the report page.

RightToLeft (For the Label, TextBox, and ReportInfo items) Specifies whether
the text is aligned with the right side of the container. Also
supports locales that use right-to-left fonts.

Selections: True or False

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Table 175. Behavior properties in the Properties pane (Sheet 3 of 3)

Behavior property Description
ShrinkToFit Specifies whether the font size of the text within the selected
container shrinks to fit the container. If the WrapMode property
under Appearance is set to WordWrap, the application first wraps
the text to fit the container and then shrinks the text to fit the
container.

Selections: True or False

Visible Specifies whether the selected item appears in the report. By
default, the Cover Page and Appendix sections are set to False, and
therefore, do not appear in the report.

Selections: True or False

Data properties
Table 176 describes the Data properties.
Table 176. Data properties in the Properties pane (Sheet 1 of 3)
Data property Description
ColumnCount (For the Detail Section workspace section only) Specifies the
number of columns in the report, similar to a newspaper layout.

Default: 1

When the template contains data columns that match the layout
of the main table (data columns displayed from left to right), use
the default value of 1 (ColumnCount = 1) for the number of
columns.
Tip Increasing the number of columns per page works with
transposed data columns (transposed from rows to columns).
CountNullValues (For the Textbox item only)

False—Does not include null values as zeros in the summary

fields.

True—Includes null values as zeros in the summary fields.

ColumnSpacing (For the Detail Section workspace section only) Specifies the space
between columns (newspaper style) in a multi-column report.
Culture (For the Textbox item only) Formats the report data based on the
selected culture from a particular country or region.

Default: Inherit

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Table 176. Data properties in the Properties pane (Sheet 2 of 3)

Data property Description
DataField Specifies the data source (main table column, related table
column, or data graph) for the content.
IMPORTANT For best results, do not manually modify the
content of this box; that is, do not select from the associated
dropdown list or type text in the box.

To change an item to another item, delete the current item.

Then, add a new item as described in these topics:
• Add main table columns to a report template
• Add data graphs to a report template.
Description (For the Picture item only) Not implemented.
Hyperlink Sets to a URL address for a specific location. The application
automatically converts this URL to a hyperlink in the HTML or
PDF exported reports.
Image (For the Picture item only) Opens the Open dialog box where you
can find and select the image file. The default file types for the
search are image files.
MaxLength (For the Rich Textbox item only) Specifies the maximum number
of characters to be displayed.
NewColumn (For the Detail Section workspace section only) Specifies where a
new column is printed. The default number of report columns is
1. The standard report templates contain only one column and
the Customize Reports dialog box creates reports with one
column. In this context, a column is a formatting option, not a
table column from a result table.

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Table 176. Data properties in the Properties pane (Sheet 3 of 3)

Data property Description
NewPage Specifies whether a page break is inserted before, after, or both
before and after the section.

Default settings:
• CoverPage—After
• DetailSection—None
• Appendix—Before

CoverPage section:
• None—No page break between the cover page and the next
section.
• Before—No effect.
• After—Adds a page break between the cover page and the
next section.
• BeforeAfter—Adds a page break between the cover page and
the next section.

DetailSection:
• None—No page break between the table rows.
• Before—Adds a page break between each table row.
• After—Adds a page break between each table row.
• BeforeAfter—Adds a page break between each table row.

Appendix section:
• None—No page break.
• Before—Adds a page break before the Appendix section.
• After—No effect.
• BeforeAfter—Adds a page break before the Appendix section.
Tag Displays information associated with an object on the page.
IMPORTANT Do not modify or delete the Tag property.
Text For a Label item, you can type text here. For the column headings,
this box displays the column heading text. For the TextBox item,
this box displays the name of the data source (table column in the
result file).
Title (For the Picture item only) Not implemented.

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Design properties
Table 177 describes the Design property.
Table 177. Design properties in the Properties pane
Design property Description
(Name) Displays the internal name of an object on the report template
page, used by the application to uniquely identify each individual
object.

Layout properties
Table 178 describes the Layout properties.
Table 178. Layout properties in the Properties pane (Sheet 1 of 2)
Layout property Description
End (For the CrossSectionLine and CrossSectionBox items only)
Specifies the X and Y coordinates of the end of the line or the
bottom-right corner of the box, based on the rulers at the top and
left side of the report template page.
Height (For a workspace section only) Specifies the height of the section,
based on the ruler to the left of the template workspace.
Location Specifies the X and Y coordinates of the upper-left corner of an
object, based on the rulers at the top and to the left of the
template workspace.
Padding Specifies the values in points for the space to the left, top, right,
and bottom of the textual content within the container.
Radius (For the CrossSectionBox item only) Specifies the percentage
value for the roundness of the corners of the box. The default
value of 0 creates corners with no rounding. A value of 100 creates
top and bottom sides that look like half circles.
RoundingRadius (For the Shape item only) Specifies the percentage value for the
roundness of the corners when you select RoundRect (rectangle
with rounded corners) for the Style property.
Size Specifies the width and height of an object on the page, in inches.
SizeMode (For the Picture item only) Specifies how the report designer sizes
the image to fit in the container.

Selections:
• Clip—Clips images that are larger than the container.
• Stretch—Stretches images to fit the container.
• Zoom—Decreases the image size to fit the container.

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Table 178. Layout properties in the Properties pane (Sheet 2 of 2)

Layout property Description
Start (For the CrossSectionLine and CrossSectionBox design items
only) Specifies the X and Y coordinates of the start of the line or
the top-left corner of the box, based on the rulers at the top and to
the left of the template workspace.
X1 (For the Line item only) Specifies the coordinate of the left end of
a line, based on the horizontal ruler at the top of the report
template page.
X2 (For the Line item only) Specifies the coordinate of the right end
of a line, based on the horizontal ruler at the top of the report
template page.
Y1 (For the Line item only) Specifies the coordinate of the left end of
a line, based on the vertical ruler to the left of the template
workspace.
Y2 (For the Line item only) Specifies the coordinate of the right end
of a line, based on the vertical ruler to the left of the template
workspace.

Miscellaneous properties
Table 179 describes the Miscellaneous properties.
Table 179. Miscellaneous properties in the Properties pane (Sheet 1 of 2)
Miscellaneous property Description
Code128 (For the Barcode item only) When you select Code_128_x for the
Style property in the Appearance area, use this property to define
the code.
Code49 (For the Barcode item only) When you select Code49 for the Style
property in the Appearance area, use this property to define the
code.
DataMatrix (For the Barcode item only) When you select the DataMatrix
option for the Style property in the Appearance area, use this
property to define the code.
PDF417 (For the Barcode item only) When you select Pdf417 for the Style
property in the Appearance area, use this property to define the
code.

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Table 179. Miscellaneous properties in the Properties pane (Sheet 2 of 2)

Miscellaneous property Description
QRCode (For the Barcode item only) When you select QRCode for the
Style property in the Appearance area, use this property to define
the code.

A QR code (quick response code) is a matrix (2D) barcode.

Because smartphones can convert QR codes to URLs, QR codes
can provide quick access to websites.
RssExpandedStacked (For the Barcode item only) When you select
RssExpandedStacked for the Style property in the Appearance
area, use this property to define the code.

Open the property dialog box for a workspace section or a specific report item
The reporting feature for the application includes a property dialog box for each item in the
Section Reports pane. Using this dialog box, you can modify the formatting parameters for a
selected item on the report template page. The available properties vary depending on the
selected workspace section or item. Most of these parameters are similar to the properties
listed in the properties pane, although some have slightly different names.

Y To open the property dialog box for an item

1. Select the item of interest in the workspace.

The properties pane for the selected item appears.
Figure 173. Properties pane for a label item

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Select the paper type, print width, page orientation, and watermark for a report template

2. At the bottom-right corner of the report template page, click the Property Dialog link.
The property dialog box for the selected object opens (Figure 174).
Figure 174. Property dialog box for the Label item

Note For the RichTextBox item, in addition to the Property Dialog link, you can click the
Load File link to load text from a file into the box. See “Add a rich text box to a report
template.”

The parameters in the property dialog boxes have equivalent parameters in the properties
pane.

Select the paper type, print width, page orientation, and watermark
for a report template
On the report template page, you can add a watermark, change the print width and the
orientation of the report template (portrait or landscape), and select the type of paper that you
want the printer to use.

See the following topics:

• Open the property settings for a report template
• Add a watermark to a report template
• Change the print width of a report template
• Change the page orientation of a report template
• Change the page orientation of a report template
• Change the paper size for the printer

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Open the property settings for a report template

Y To open the property settings for the report template

1. Open a report template for editing. See “Open a report template for editing.”
2. Click the unfilled square in the upper-left corner (above the vertical sizing bar) of the
report template page.
Figure 175. Square in upper-left corner of the report template grid
Opens the report template properties in the Properties pane

The watermark properties appear in the Appearance group, and the orientation and paper
size properties appear in the Miscellaneous group.
Figure 176. Report template properties (in the Properties pane)

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Select the paper type, print width, page orientation, and watermark for a report template

Add a watermark to a report template

By default, the Watermark property for a report template is set to None.

Y To add a watermark to a report template

1. Open the property settings for the report template. See “Open the property settings for a
report template.”
2. Under Appearance, click the browse icon, , to the far right of the Watermark property.
The Open dialog box opens with the file type setting for all image files.
3. Find and select the image file of interest and click Open.
4. In the WatermarkAlignment list, select the appropriate alignment.
5. In the WatermarkPrintOnPages box, type the page number of the page where you want
the watermark to appear.
6. In the WatermarkSizeMode list, select whether you want to clip the image if it is larger
than the container, stretch the image to fit the container, or reduce the image size to fit
the container.

Change the print width of a report template

Y To change the print width of a report template

1. Open the property settings for the report template. See “Open the property settings for a
report template.”
2. Under Behavior, type a numeric value in the PrintWidth box.

Tip When you change the page layout from portrait (IsLandscape = False) to landscape
(IsLandscape = True) or landscape to portrait, the numeric value in the PrintWidth box
automatically updates, but the grid ruler does not update.

To update the grid ruler, type the print width in the PrintWidth box.

Change the page orientation of a report template

Y To change the page orientation of the report template

1. Open the property settings for the report template. See “Open the property settings for a
report template.”
2. Under Misc, select True for Landscape or False for Portrait in the IsLandscape list.

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Change the paper size for the printer

Y To change the paper size used by the printer

1. Open the property settings for the report template. See “Open the property settings for a
report template.”
2. Under Misc, select the appropriate paper size from the PaperKind list.
To open the list to the paper size of interest, type the first letter of the paper-size name.
For example, if you want to change the size from A4 to Letter, type an L in the box. If the
paper size does not appear in the box, continue typing the next letter of its name. The
application cycles through the paper sizes that begin with this letter or letters.

Preview and print a report

This topic describes how to work with the Report Preview and Report Print dialog boxes and
the report resolution page.

You can print all of the report pages from the report resolution page or the Report Print dialog
box. You can print up to five pages from the Report Preview dialog box.

Perform these tasks as applicable:

• Preview a report for up to five rows in the main result table
• Preview a report for all the visible rows in the main result table
• Open the Report Resolution page
• Find a text item in a resolved report
• Copy a portion of a report to the Clipboard
• Export the contents of a report to an external document
• Print a report
• Report preview toolbar
• Page thumbnails pane

Preview a report for up to five rows in the main result table

To preview a report, use the Report Preview dialog box to preview up to five rows.

Y To open the Report Preview dialog box

1. Open a report template for editing. See “Open a report template for editing.”
2. In the toolbar on the report template page, click the Preview Report icon, .

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The application opens the Report Preview dialog box and resolves the current result file
with the current template on the report template page. The Page Thumbnails pane
displays up to five resolved pages.
A red line in the right page margin indicates that the print width does not fit on the
selected page size, and the printer will print an empty page with every report page it
prints, unless you resize the template. See “Change the print width of a report template.”

Preview a report for all the visible rows in the main result table
To preview a report for all the visible rows in the selected main result table, use the Report
Preview dialog box.

Y To open the Report Print dialog box

1. Open a report template. See “Open a report template for editing.”

2. In the toolbar on the report template page, click the Print Report icon, .
The application opens the Report Print dialog box and resolves the current result file with
the current template on the report template page. The Page Thumbnails pane displays all
of the report pages.

Open the Report Resolution page

Y To open the report resolution page

1. Open a result file.

2. Select an existing report template as follows:
a. Choose Reporting > Create Report from the menu bar or, click the Create Report
icon, .
The Open Report Design Template dialog box opens to the Report Templates folder.
b. Select the appropriate report template and click Open.
The application resolves the current result file with the selected template. The Page
Thumbnails pane displays all of the report pages.

Find a text item in a resolved report

Y To find a text item in a resolved report

1. On the report template page, resolve the report by clicking the Print Report icon, , or
the Preview Report icon, .
2. In the toolbar of the Report Print dialog box or the Report Preview dialog box, click the
Find icon, .

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The Find dialog box opens.

3. In the Find What box, type the text that you want to find.
Figure 177. Find dialog box with a text entry

4. Select the appropriate check boxes.

• To match whole words only, select the Match Whole Word Only check box.
• To match the case—uppercase or lowercase, select the Match Case check box.
5. Click Find Next or Find Prev.

Copy a portion of a report to the Clipboard

Y To copy a portion of a report to the Clipboard

Do one of the following:

a. To copy a specific item to the Clipboard, click the Selection Mode icon, , in the
Report Preview toolbar.
b. Click the item that you want to copy, and then click the Copy icon, .
–or–
a. To copy a rectangular portion of the report to the Clipboard, click the Snapshot
Mode icon, .
b. Drag the cursor across the area of interest.

Export the contents of a report to an external document

Y To export the contents of a report to an external document

1. Open the report resolution page or the Report Print dialog box.
2. In the toolbar, choose Export > File Type, where the File Type is one of the following:
• Text—text file
• PDF—portable document format file
• RTF—rich text format file
• Excel—Microsoft spreadsheet

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• HTML—web page that opens in a browser

• Printing a report

Print a report
After you review the items in your Compound Discoverer result file and reduce the number of
table rows to report to a reasonable number, open an existing report template or create a new
report template, resolve the template, and then print a report.

Y To print a report for the visible table rows in a result file

1. Open the result file of interest. See “Open, close, and update result files.”
2. Review and filter the data. See “Filter the data for data reduction.”
3. Do one of the following:
a. From the menu bar, choose Reporting > Create Report.
The Open Report Design Template dialog box opens.
b. Select an appropriate template and click Open.
The report resolution page opens.
–or–
• From the report template page, open the Report Print dialog box by clicking the
Print Report icon, .
4. In the toolbar, click the Print icon, .
The Print dialog box opens.
5. Select the appropriate printer and the page range that you want to print.
6. Click OK to print the report.

Report preview toolbar

The Report Preview and Report Print dialog boxes and the report resolution page share a
common toolbar. Table 180 describes the icons in the toolbar, from left to right.
Table 180. Report preview icons (Sheet 1 of 3)
Icon Description
Toggle Sidebar—Opens and closes the Page Thumbnails pane. See “Page
thumbnails pane.”
Print—Opens the Print dialog box where you select the appropriate print
options and send the report to the selected printer.

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Preview and print a report

Table 180. Report preview icons (Sheet 2 of 3)

Icon Description
Copy—Copies the selected item to the Clipboard. Clicking the Selection
Mode icon makes the Copy available.
Find—Opens the Find dialog box where you can search for a particular
word or phrase in the report.
Zoom Out—Reduces the magnification of the report view. The current
zoom box displays the magnification.
Zoom In—Increases the magnification. The current zoom box displays the
magnification.
Current zoom—Use to change the on-screen magnification of the report
by selecting or typing a percentage from 10 to 800 in this box, and then
pressing ENTER.
Fit Width—Sizes the width of the report to the screen width. The current
zoom box displays the magnification.
Fit Page—Sizes the current report page to the screen width and height,
while maintaining the aspect ratio. The current zoom box displays the
magnification.
Single Page View—Fits the current report page to the full-screen view and
removes the scroll bar. To view the report pages, you must use the First
Page, Previous Page, Next Page, and Last Page icons or the Page
Thumbnails pane.
Continuous View—Changes the magnification to 100% and makes the
scroll bar available so that you can scroll through the document.
Multipage view—Changes the display to the selected multi-page view.

First Page—Displays the first page of the report.

Previous Page—Displays the previous page of the report.

Current Page—Indicates the current page and the estimated number of

pages in the report.
Next Page—Displays the next page of the report.

Last Page—Displays the last page of the report.

Backward—Displays the previously selected page in the report.

Selecting pages as you browse makes the Backward icon available.

Forward—Displays the next selected page in the report.

Clicking the Backward icon makes the Forward icon available.

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Preview and print a report

Table 180. Report preview icons (Sheet 3 of 3)

Icon Description
Pan Mode—Use the hand cursor to drag the page on the screen.

Selection Mode—Use to copy a report item to the Clipboard.

Snapshot Mode—Use to copy a rectangular area to the Clipboard.
Export—Use to export the contents of the report to an external document
of one of these types: Text, PDF, RTF, Excel, or HTML.

Page thumbnails pane

The Page Thumbnails pane appears to the left of the page preview in the Report Preview and
Report Print dialog boxes and the report resolution page. Each thumbnail represents a page in
the report. The Report Preview dialog box resolves up to five pages of data. The Report Print
dialog box resolves all of the data. In the Report Print dialog box, click a page thumbnail to
jump to that page.

Table 181 describes the icons in the Page Thumbnails pane, from top left to bottom right.
Table 181. Page Thumbnails pane icons
Icon Description
Enlarge—Enlarges the size of the thumbnails.

Reduce—Reduces the size of the thumbnails.

Thumbnails Pane—Displays the Page Thumbnails pane.

Search Results—Displays the Search Results pane where you can search for
a particular word or phrase in the report. The found instances appear in
the list of results.

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 12

Manage the lists and libraries

To modify the lists and libraries that you use to process mass spectral data and identify
compounds in the Compound Discoverer application, see the following topics:
• Lists & Libraries manager
• Expected Compounds view
• Generate an Xcalibur inclusion list
• Adducts view
• Ion Definitions view
• Transformations view
• Neutral Losses view
• Mass Lists view
• Spectral Libraries view
• Metabolika Pathways view
• Edit new and existing Metabolika pathways
• Compound Classes view
• Load a structure from a structure file
• Find a structure in the ChemSpider database
• Structure drawing tools and commands
• Copy and paste InChi strings and MOL strings

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Lists & Libraries manager

Lists & Libraries manager

Clicking the Lists & Libraries Manager icon, , in the application toolbar opens the Lists &
Libraries manager as a tabbed page. The buttons in the left pane open the individual views,
and the buttons across the top of the page perform various tasks.

Not all the task buttons are available for every view. The Edit button is unavailable for the
Spectral Libraries view, and the Replace button is visible only for the Mass Lists, Spectral
Libraries, and Metabolika Pathways views.

Each view in the Lists & Libraries Manager page includes a table. For information about
freezing panes, hiding and showing columns, freezing rows, sorting, and filtering the
application tables, see “Common operations for manipulating data tables.”

Expected Compounds view

The Expected Compounds view of the Lists & Libraries page contains a list of the expected
(parent) compounds for targeted analyses in LC studies. See Figure 178.

Tip To open the Expected Compounds view, choose Lists & Libraries > Expected
Compounds from the application menu bar.

In a targeted analysis, the Generate Expected Compounds node generates a list of expected
compounds by using the parent compounds and transformations that you specify. The Find
Expected Compounds node then searches for these compounds in the raw data files that you
submit for analysis.

The initial expected compounds list contains omeprazole, the targeted compound used in the
Compound Discoverer Metabolism Tutorial.

Note To run a targeted processing workflow that includes the Generate Expected
Compounds node, the Create FISh Trace node, or both of these nodes, you must first add
the compounds of interest to the Expected Compounds list.

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 12 Manage the lists and libraries
Expected Compounds view

Figure 178. Expected Compounds view on the Lists & Libraries page
Button bar Filters row

To modify the expected compounds list, see these topics:

• Expected Compounds view parameter descriptions
• Delete, import, or export expected compounds
• Add and edit expected compounds with the Compound Editor

For information about generating an Xcalibur inclusion list, see “Generate an Xcalibur
inclusion list.”

Expected Compounds view parameter descriptions

This table describes the buttons and columns in the Expected Compounds view of the
Libraries & Lists page.
Table 182. Expected Compounds view parameters (Sheet 1 of 2)
Feature Description
Buttons
New Opens the Compound Editor for adding new compounds to the
Expected Compounds list.
Edit Opens the Compound Editor for editing the selected compound.

Selecting a compound makes this button available.

Delete Deletes the selected compound.

Selecting a compound makes this button available.

Import Opens the Open dialog box for selecting an XML or SDF file.
Export All Opens the Save As dialog box for exporting the entire Expected
Compounds list as an XML file.

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Expected Compounds view

Table 182. Expected Compounds view parameters (Sheet 2 of 2)

Feature Description
Generate Inclusion List Opens the Generate Xcalibur Inclusion List dialog box for
creating and exporting a list of compounds to include in an
inclusion list for data acquisition. The application creates the
inclusion list by generating a list of expected compounds by using
the dealkylation and dearylation reactions, the transformation
reactions, and the adduct ions that you specify. The application
saves the list as a text file with the name and path that you specify.
Filters row

Use this row to filter the table as appropriate. See “Filter the tables on a study page or a list
or library view.”
Columns
Name Displays the user-specified compound name.
Description Displays the user-specified description.
Elemental Displays the elemental composition that the application
Composition determines from the compound’s structure.
Molecular Weight Displays the molecular weight that the application calculates from
the compound’s elemental composition.
Structure Displays the structure created by using the drawing tools or by
importing a structure file.

Delete, import, or export expected compounds

You can perform the following tasks directly from the Expected Compounds view of the Lists
& Libraries page.
Table 183. Expected Compounds view tasks (Sheet 1 of 2)
Task Procedure
Delete a compound. Select the compound in the expected compounds list and click
Delete. Then, click Yes at the prompt.
Import compounds Click Import, select the XML or SDF file of interest, and click
from an XML file or Open. Then, click OK at the prompt.
and SDF file.
The application only imports new entries; it does not import
entries that are already in the expected compounds list. After the
application imports the new compound entries, it provides a tally
of the number of imported compounds versus the number of
skipped compounds.

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Expected Compounds view

Table 183. Expected Compounds view tasks (Sheet 2 of 2)

Task Procedure
Export compounds to 1. Click Export All.
an XML file or an SDF
2. Select a folder, name the file, and click Save.
file.
The application exports the list to the selected file type: XML
or SDF.
3. At the prompt, click OK.

Add and edit expected compounds with the Compound Editor

Use the Compound Editor dialog box to create new compound entries or edit existing entries
in the Expected Compounds view.

Note Similar Compound Editor dialog boxes open from the Mass List and Metabolika
Pathways editors. For information about using the structure drawing tools, see “Structure
drawing tools and commands.”

Y To add a new compound or edit an existing compound

1. Open the Expected Compounds view on the Library & Lists page.
2. Do one of the following:
• To edit the definition of a compound, double-click the entry or select the entry and
click Edit.
The Compound Editor dialog box opens with information for the selected entry.
• To add a compound to the Expected Compounds list, click New.
The Compound Editor dialog box opens. As indicated by the red borders you must
name the compound and enter its elemental composition to save it.

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 12 Manage the lists and libraries
Expected Compounds view

Figure 179. Compound Editor dialog box for a new compound

Click to locate and

open a structure file.

Drawing area

Opens the ChemSpider application

3. To enter or edit the elemental composition of the compound, do any of the following:
• Draw or edit the structure in the drawing area. See “Structure drawing tools and
commands.”
• Paste an InChi or MOL string from the Clipboard.
• Open a structure file. See “Load a structure from a structure file.”
• Click ChemSpider to find the structure. See “Find a structure in the ChemSpider
database.”
The application automatically populates the Elemental Composition and Molecular
Weight boxes with read-only values. To change the elemental composition and the
molecular weight, you must modify the chemical structure in the drawing area.
4. In the Name box, type the name of the compound.
5. (Optional) In the Description box, type a description for the compound.
6. Click Save.
The dialog box closes and the new compound or the edited information for the existing
compound appears in the expected compounds list.

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 12 Manage the lists and libraries
Generate an Xcalibur inclusion list

Generate an Xcalibur inclusion list

An Xcalibur inclusion list is a text file that contains the formulas and m/z values of the adduct
ions (found in the survey scan) that you want the mass spectrometer to fragment and acquire
data-dependent scans for during data acquisition.

Note The application creates the inclusion list from the parent compounds (compounds
in the Expected Compounds list), transformations, and adduct ions that you select. A
parent compound is the beginning compound in a set of metabolic reactions.

Tip For instructions on how to export inclusion and exclusion lists from the result tables
of a result file, see “Export an Xcalibur inclusion or exclusion list from a compounds
table.”

Y To generate an Xcalibur inclusion list from the Expected Compounds view

1. From the application menu bar, choose Lists & Libraries > Expected Compounds.
2. If the parent compounds of interest are not in the list, add them. See “Add and edit
expected compounds with the Compound Editor.”
3. Select the parent compounds that you want to add to the Xcalibur inclusion list.
4. In the command bar of the Expected Compounds view, click Generate Inclusion List.
The Generate Xcalibur Inclusion List dialog box opens.
Figure 180. Generate Xcalibur Inclusion List dialog box

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Generate an Xcalibur inclusion list

5. Browse to the folder where you want to store the TXT file that this dialog box generates,
and name the file.
6. Do one of the following:
• Click Load Settings, select the inclusion settings file that includes all the parameter
settings for generating the inclusion list, and then click Open.
• Specify all the reactions that you want to use to generate the inclusion list, and select
the adduct ions to generate.

Note For information about the parameters in the Dealkylation/Dearylation,

Transformations, and Ionization areas of the dialog box, see “Generate Expected
Compounds node.”

Tip If you expect to use these parameter settings for generating other inclusion
lists, click Save Settings and save the settings to an inclusion settings file
(.inclSet).

7. Click Generate.
8. At the prompt, verify the directory and file name for the inclusion list file, and then click
OK.
The application generates a list of adduct ions by using the user-specified parent
compounds, and transformations, and ions. It exports the generated TXT file to the
user-specified folder.
The TXT file includes two columns. The first columns lists the formulas and the second
column lists the m/z values of the ions that you want the mass spectrometer to include in
a targeted DDA experiment. You can import the information in this file into the
instrument method for your LC/MS system.
Figure 181. Xcalibur inclusion list for caffeine and its metabolites

Note The Generate Xcalibur Inclusion List dialog box retains the new parameter settings
until you change them.

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 12 Manage the lists and libraries
Adducts view

Adducts view
Use the Adducts view of the Lists & Libraries page to define the expected adducts in your
samples. Adducts are part of the ion definition–that is, to create a new ion definition that uses
an adduct that is not currently in the adducts list, you must first add the adduct to the adducts
list.

Tip To open the Adducts view, choose Lists & Libraries > Adducts from the application
menu bar.

The adducts list provided with the application contains 20 adducts. You can modify this list.
Figure 182. Adducts view

Adducts list

To modify the adducts list, see these topics:

• Adducts view parameter descriptions
• Delete, import, and export adducts
• Add and edit adducts with the Adduct Editor

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Adducts view

Adducts view parameter descriptions

This table describes the buttons and table columns in the Adducts view of the Lists &
Libraries page.
Table 184. Adducts view parameters
Feature Description
Buttons
New Opens the Adduct Editor for defining an adduct.
Edit Opens the Adduct Editor for editing the selected adduct.

Selecting an adduct makes this button available.

Delete Deletes the selected adduct.

Selecting an adduct makes this button available. You cannot delete

the following adducts: H, Na, K.
Import Opens the Open dialog box for selecting an XML file.
Export All Opens the Save As dialog box for exporting the entire adducts list
to an XML file.
Filters row

Use this row to filter the table as appropriate. See “Filter the tables on a study page or a list
or library view.”
Table columns
Name Displays the specified name of the adduct.
Adduct Mass Displays the mass that the application calculates from the specified
elemental composition.
Elemental Displays the specified elemental composition of the adduct.
Composition
Charge Displays the specified charge of the adduct.

Delete, import, and export adducts

You can perform the following tasks directly from the Adducts view of the Lists & Libraries
page.
Table 185. Adducts view tasks (Sheet 1 of 2)
Task Procedure
Delete an adduct Select the adduct in the adducts list and click Delete. Then, click
Yes at the prompt. You cannot delete the H, Na, or K adducts.

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Adducts view

Table 185. Adducts view tasks (Sheet 2 of 2)

Task Procedure
Import adducts from 1. Click Import.
an XML file
2. In the Open dialog box, locate the file, and click Open.
A message opens with a tally of the number of imported
adducts versus the number of skipped adducts. The
application only imports new entries; it does not import
entries that are already in the list.
3. At the prompt, click OK.
Export a list of adducts 1. Click Export All.
to an XML file
2. Select a folder, name the file, and click Save.
The application exports the list to an XML file.
3. At the prompt, click OK.

Add and edit adducts with the Adduct Editor

Use the Adduct Editor dialog box to define additional adducts, which are part of the ion
definition.

Y To add or edit adducts

1. From the application menu, choose Lists & Libraries > Adducts.
2. In the Adducts view, do one of the following:
• To edit the definition of an adduct, double-click the entry or select the entry and
click Edit.
The Compound Editor dialog box opens with information for the selected entry.
• To add an adduct to the list, click New.
The Adduct Editor dialog box opens. As indicated by the red borders, you must name
the adduct and enter its elemental composition to save it.

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Ion Definitions view

Figure 183. Adduct Editor dialog box for a new entry

3. Define the new adduct or modify the existing adduct as follows:

• In the Name box, select New and type a name for the adduct or keep or modify the
name of the existing adduct.
• In the Elemental Composition box, enter the elemental composition of the new
adduct or keep or modify the elemental composition of the existing adduct.
The editor validates the entry.
• In the Charge box, enter the charge that the new adduct adds to the ion definition or
keep or modify the charge of the existing adduct.
Range: –10 to +10
4. Click Save.
The new or modified adduct appears in the list.

Ion Definitions view

The Ion Definitions view of the Lists & Libraries page contains a list of adduct ions.

The application uses the entries in the Ion Definitions list in the following workflow nodes:
Detect Compounds and Generate Expected Compounds.

Tip To open the Ion Definitions view, choose Lists & Libraries > Ion Definitions from
the application menu bar.

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Ion Definitions view

To modify the ion definitions list, see these topics:

• Default list of ion definitions
• Delete an ion definition
• Import ion definitions from an XML file
• Export the ion definitions list to an XML File
• Add or edit ion definitions with the Ion Definition Editor

Ion Definition view parameters

Table 186 describes the parameters in the Ion Definitions view.
Table 186. Ion Definitions view parameters
Parameter Description
Filter row Use this row to filter the table as appropriate. See “Filter the tables
on a study page or a list or library view.”
Buttons
New Opens the Ion Definition Editor for editing the new ion
definition.
Edit Opens the Ion Definition Editor for editing the selected ion
definition.

Selecting an ion definition makes this button available.

Delete Deletes the selected ion definition.

Selecting an ion definition makes this button available.

Import Opens the Open dialog box for selecting an XML file.
Export All Opens the Save As dialog box for exporting the entire ion
definitions list to an XML file.
Table columns
Ion Definitions Displays the user-specified ion definition.
Adducts Total Mass Displays the difference between the exact mass of the neutral
molecule and the molecular ion adduct or the exact mass of the
neutral dimer and the ionized dimer.
Charge Displays the charge of the ion.
Weight Specifies the weighting factor for the ion definition when the ion
definition is added to the list of possible ions in the Ions list for
the Detect Compounds node.

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Ion Definitions view

Default list of ion definitions

The default list of ion definitions contains the most common adducts and dimers formed
when using the electrospray-mass spectrometry (ESI-MS) technique in either the positive or
negative ionization mode.

Table 187 lists the common adducts and dimers for the positive ionization mode.
Table 187. Common adducts and dimers in the positive ionization mode
Adducts Adducts
Ion definition Charge Ion definition Charge
total mass total mass
M+H–H2O –17.00329 1 M+H+Na 23.9965 2
M+H–NH3 –16.01927 1 M+H+MeOH 33.03349 1
M+H 1.00728 1 M+K 38.96316 1
2M+H 1.00728 1 2M+K 38.96316 1
M+2H 2.01455 2 M+H+K 39.97044 2
M+3H 3.02183 3 M+H+ACN 42.03383 1
M+NH4 18.03383 1 2M+H+ACN 42.03383 1
2M+NH4 18.03383 1 M+2H+ACN 43.0411 2
M+H+NH4 19.0411 2 M+Na+ACN 64.01577 1
M+Na 22.98922 1 2M+Na+ACN 64.01577 1
2M+Na 22.98922 1 M+H+DMSO 79.02121 1

Table 188 lists the common adducts and dimers for the negative polarity mode.
Table 188. Common adducts and dimers in the negative ion mode
Adducts Adducts
Ion definition Charge Ion definition Charge
total mass total mass
M–H –1.00728 –1 M–H+FA 44.9982 –1
2M–H –1.00728 –1 2M–H+FA 44.9982 –1
M–2H –2.01455 –2 2M–H+HAc 59.01385 –1
M–H–H2O –19.01784 –1 M–H+HAc 59.01385 –1
M+Cl 34.9694 –1 M–H+TFA 112.98559 –1
M–2H+K 36.94861 –1

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Ion Definitions view

Figure 184 shows the Ion Definitions view.

Figure 184. Ion Definitions view

Delete an ion definition

All the ion definitions are deletable.

Y To delete an ion definition

1. From the application menu bar, choose Lists & Libraries > Ion Definitions.
2. Select the ion definition and click Delete.
3. At the prompt, click Yes.

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Ion Definitions view

Import ion definitions from an XML file

Y To import a list of ion definitions from an XML file

1. From the application menu bar, choose Lists & Libraries > Ion Definitions.
2. Click Import.
3. Locate the file and click Open.
A message opens with a tally of the number of imported ion definitions versus the
number of skipped ion definitions. The application only imports new entries; it skips
entries that are already in the list.
4. At the prompt, click OK.

Export the ion definitions list to an XML File

Y To export the entire list of ion definitions to an XML file

1. From the application menu bar, choose Lists & Libraries > Ion Definitions.
2. Click Export All.
3. Select a folder, name the file, and click Save.
The application automatically adds the file name extension (.xml).
4. At the prompt, click OK.

Add or edit ion definitions with the Ion Definition Editor

Use the Ion Definition Editor dialog box to create new or edit existing ion definitions.

Y To add new ion definitions or edit existing ion definitions

1. From the application menu bar, choose Lists & Libraries > Ion Definitions.
2. Do one of the following:
• To add a new ion definition, click New.
The Ion Definition Editor dialog box opens. The Ion Definition box contains only
an M for the uncharged molecule. Because the ion definition must include at least
one additional component, a charge, or both, the box has a red border, and the Save
button is unavailable.

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Ion Definitions view

Figure 185. Ion Definition Editor dialog box

• To edit an existing ion definition, double-click it or select it and click Edit.

3. To edit the ion definition, do any of the following:
• Type the ion definition in the Ion Definition box.
• Under Available Adducts, use the arrows to add or subtract components. Or, type a
nonzero integer value for each component that you want to add or subtract.
4. In the Weight Factor box, type the weighting factor for the ion definition.
Range: 0 to 99

Note The Detect Compounds node uses the weight factor value for the ion
definitions. With the exception of the protonated molecule [M+H]+ in the positive
polarity mode and the deprotonated molecule [M–H]– in the negative polarity mode,
if you set the weight factor to 0, the Detect Compounds node does not look for the
specified adduct in the mass spectrum.

5. To save the changes, click Save.

The application calculates the ion’s charge and the mass difference between the uncharged
molecule and its adduct ion. The new ion definition appears in the list.

Table 189 describes the parameters in the Ion Definition Editor dialog box.

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Transformations view

Table 189. Ion Definition Editor parameters

Parameter Description
Ion Definition Displays the current ion definition. Valid ion definitions include the
neutral molecule, which is represented by M, and components from the
component list. A red border indicates an invalid ion definition.

As you edit the ion definition by using the component list, the application
automatically updates the ion definition.
Weight Factor Specifies the weighting factor for the ion definition.
Available Use this list to create custom ion definitions.
Adducts list

Transformations view
The Transformations view contains a table of possible transformations. The Generate
Expected Compounds node uses a selection of entries from this table and the information in
the expected compounds list to generate a table of expected transformations for a known
(parent) compound.

With the addition of the PFAS Chain Shortening transformation in the Compound
Discoverer SP2 release, the default Transformations list now contains 35 transformations.

Tip To open the Transformations view, from the application menu bar, choose Lists &
Libraries > Transformations.

To modify the transformations list, see these topics:

• Transformations view parameters
• Delete a transformation
• Import a list of transformations from an XML File
• Export the transformations list to an XML file

For details using the Transformation Editor to add or edit transformations, see “Add or edit
transformations with the Transformation Editor.”

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Transformations view

Figure 186. Transformations view with the default transformations list

Transformations view parameters

Table 190. Transformations view parameters (Sheet 1 of 2)
Parameter Description
Buttons
New Opens the Transformation Editor dialog box for creating new
transformations.
Edit Selecting an entry makes this button available.

Opens the Transformation Editor dialog box for editing the

selected transformation.

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Transformations view

Table 190. Transformations view parameters (Sheet 2 of 2)

Parameter Description
Delete Selecting an entry makes this button available.

Deletes the selected transformation from the library.

Import Opens a dialog box for selecting an XML file to import.
Export All Opens the Save As dialog box for saving the list as an XML
file.
Filter row Use this row to filter the table as appropriate. See “Filter the
tables on a study page or a list or library view.”
Columns
Name Displays the user-specified name for the entry.
Leaving Group Displays the user-specified elemental composition of the
leaving group for the transformation, if specified.
Arriving Group Displays the user-specified elemental composition of the
arriving group for the transformation, if specified.
Leaving Modification Displays the elemental composition difference between the
arriving group and the leaving group, if the transformed
compound contains fewer atoms than the original compound.
Arriving Modification Displays the elemental composition difference between the
arriving group and the leaving group, if the transformed
compound contains more atoms than the original compound.
ΔM [Da] Displays the difference in mass between the original
compound and the transformed compound in daltons.
Phase Displays the user-specified category for the transformation.
Max Occurrence Displays the user-specified value for the maximum number of
times that this transformation can occur in a sequence of
combinatorial transformations.

Delete a transformation
Y To delete an entry from the transformations list

1. Open the Transformations view.

2. Select the entry and click Delete.
3. At the prompt, click Yes.

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Transformations view

Import a list of transformations from an XML File

Y To import a list of transformations from an XML file

1. Open the Lists & Libraries > Transformations view.

2. Click Import.
3. Locate the file and click Open.
A message opens with a tally of the number of imported transformations versus the
number of skipped transformations. The application only imports new entries; it does not
import entries that are already in the library.
4. At the prompt, click OK.

Export the transformations list to an XML file

Y To export the entire transformations list to an XML file

1. Open the Lists & Libraries > Transformations view.

2. Click Export All.
3. Select a folder, name the file, and click Save.
4. At the prompt, click OK.

Table 190 describes the parameters in the Transformations view.

Add or edit transformations with the Transformation Editor

Use the Transformation Editor to add entries to or to edit entries in the transformations list.

Y To add a new transformation or edit an existing transformation

1. From the menu bar, choose Lists & Libraries > Transformations.
2. Do one of the following:
• To add a new transformation, go to step 3.
• To edit an existing transformation, go to step 4.
3. To add a transformation to the transformations list, do the following:
a. Click New.
The Transformation Editor dialog box opens. For details about the editor, see
“Transformation Editor dialog box.”
The empty Name, Arriving Group, and Leaving Group boxes have a red outline. You
must enter information in the Name box and in at least one of the group boxes.

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Transformations view

Figure 187. Transformation Editor dialog box

b. In the Name box, type alphanumeric text to identify the transformation.

The red outline disappears.
c. Define the transformation as follows:
• In the Arriving Group box, type alphanumeric text for the arriving group of the
transformation, if applicable.
Valid alphabetic characters include all of the naturally occurring elements in the
periodic table. The valid range of integers is from 1 to 100 000.
After you define the arriving group, the red outline remains until you place the
cursor in the Leaving Group box. If you leave the Arriving Group box empty, the
red outline remains until you define the leaving group.
• In the Leaving Group box, type alphanumeric text for the transformation’s
leaving group.
The red outline disappears when you select a phase from the Phase list or place
the cursor in the Maximum Occurrence box.
• In the Phase list, select Phase 1 or Phase 2 for a biotransformation, or select
Other for other transformation types.
• In the Maximum Occurrence box, type an integer from 1 to 10.
The Transformation Editor validates the entries from top to bottom.
After you make valid entries, the Save button becomes available.
d. Click Save.
The Transformation Editor dialog box closes and the new entry appears in the
transformations library.

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Transformations view

4. To edit an entry in the transformations list, do the following:

a. Select the entry and click Edit.
The Transformation Editor dialog box opens. The entry boxes are populated with the
information for the transformation that you selected in the transformations list.
Figure 188. Transformation Editor with information for an acetylation chemical reaction

b. Make the appropriate changes.

If the changes are invalid, the Save button becomes unavailable, the application
outlines the invalid entries in red, and the invalid entries temporarily appear in the
transformations library.
c. Click Save and, at the prompt, click Yes.

Transformation Editor dialog box

Table 191 describes the parameters in the Transformation Editor dialog box.
Table 191. Transformation Editor parameters
Parameter Description
Name Type alphanumeric text in this box.
Arriving Group Type the elemental composition of the arriving group in this box.
Leaving Group Type the elemental composition of the leaving group in this box.
Phase Select a phase from this list.

Selections: Phase I, Phase II, and Other

Maximum Occurrence Type the maximum number of times that this reaction can occur
in a set of combinatorial reactions.

Default: 1; range: 1 to 10

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Neutral Losses view

Neutral Losses view

Use the Lists & Libraries > Neutral Losses view to modify the list of neutral losses that you
can specify in an analysis that includes the Neutral Losses workflow node (for LC studies). See
“Search Neutral Losses node.”
Figure 189. Neutral Losses view

For more information, see these topics:

• Add, edit, delete, import, or export neutral loss entries
• Neutral Loss Editor
• Default neutral loss entries

Add, edit, delete, import, or export neutral loss entries

Table 192 describes the tasks that you can perform in the Neutral Losses view.

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Neutral Losses view

Table 192. Neutral Loss view tasks

Task Procedure
Add a neutral loss entry 1. Click New.
to the list.
The Neutral Losses Editor opens. See “Neutral Loss Editor.”
2. Do the following:
• Type a name in the Name box.
• Enter the elemental composition of the loss in the
Elemental Composition box.
3. Click Save.
By default, the new entry appears in the neutral loss list in
alphabetical order.
Edit an existing neutral 1. Select an entry and click Edit.
loss.
2. In the Neutral Loss Editor, edit the name, the elemental
composition, or both.
3. Click Save.
Delete neutral losses. 1. Select the entries that you want to delete.
Use the SHIFT key to select contiguous entries or the CTRL
key to select noncontiguous entries.
2. Click Delete.
Import defined neutral 1. Click Import.
losses.
2. Select the XML file that you want to import and click Open.
Export the neutral loss 1. Click Export All.
list to an XML file.
2. Browse to the folder where you want to store the file.
3. Name the file.
4. Click Save.

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Neutral Losses view

Neutral Loss Editor

From the Lists & Libraries > Neutral Losses view, use the Neutral Loss Editor to add and edit
neutral losses.

Tip To open the Neutral Loss Editor, click New in the Neutral Loss view or select an item
in the neutral loss list and click Edit.
Figure 190. Neutral Loss Editor

Table 193. Neutral Loss Editor

Parameter Description
Name Specifies the name of the elemental composition.

The Name box accepts alphanumeric and special characters.

Elemental Composition Specifies the elemental composition of the entry.

The Elemental Composition box accepts any of the chemical

symbols in the periodic table, D for deuterium, and T for
tritium. For each chemical element, enter the element and
the number of atoms for the element. Separate each element
with a space.
Delta Mass Displays the mass difference between the precursor ion and
the product ion as the result of the neutral loss of the
specified elemental composition.

The application calculates the delta mass as you enter the

elemental composition.
Save Saves the new entry or the edited entry to the neutral losses
table in the Neutral Losses view.

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Neutral Losses view

Default neutral loss entries

Table 194. Default neutral loss list (Sheet 1 of 2)
No. Name Elemental Comp. Delta Mass No. Name Elemental Comp. Delta Mass
1 Br Br 78.91384 36 Fatty_Acid_18.3 C18 H30 O2 278.22458
2 C2H3 C2 H3 27.02348 37 Fatty_Acid_20.4 C20 H32 O2 304.24023
3 C2H3O2 C2 H3 O2 59.01330 38 Fatty_Acid_22.5 C22 H34 O2 330.25588
4 C2H4N C2 H4 N 42.03437 39 Fatty_Acid_22.6 C22 H32 O2 328.24023
5 C2H5 C2 H5 29.03913 40 Gluconuric Acid C6 H10 O7 194.04265
6 C2H5O C2 H5 O 45.03404 41 Glucuronide C6 H8 O6 176.03209
7 C2H5OH C2 H6 O 46.04186 42 H H 1.00783
8 C2H6 C2 H6 30.04695 43 H2 H2 2.01565
9 C3H7 C3 H7 43.05478 44 H2C=CH2 C2H4 28.03130
10 C4H10 C4 H10 58.07825 45 H2C=O C H2 O 30.01056
11 C4H7 C4 H7 55.05478 46 H2O H2 O 18.01056
12 C4H8 C4 H8 56.06260 47 H2S H2 S 33.98772
13 C4H9 C4 H9 57.07043 48 HBr H Br 79.92616
14 CH2 C H2 14.01565 49 HCCH C2 H2 26.01565
15 H2C=O C H2 O 42.04695 50 HCl H Cl 35.97668
16 CH3 C H3 15.02348 51 HCN H Cl 27.01090
17 CH3CH=CH2 C3 H6 42.04695 52 Hexose C6 H10 O5 162.05282
18 CH3CO C2 H3 O 43.01839 53 Hexose-Hexose C12 H20 O10 324.10565
19 CH3COOH C2 H4 O2 60.02113 54 HF HF 20.00623
20 CH3O C H3 O 31.01839 55 HI HI 127.91229
21 CH3OH C H4 O 32.02621 56 HS HS 32.97990
22 CH4 C H4 16.03130 57 I I 126.90447
23 CH5O C H5 O 33.03404 58 NH3 H3 N 17.02655
24 Cl Cl 34.96885 59 NO NO 29.99799
25 CO CO 27.99491 60 NO2 N O2 45.99290
26 CO2 C O2 43.98983 61 OH HO 17.00274
27 CO3 C O3 59.98474 62 Pentose C5 H8 O4 132.04226
28 CONH2 C H2 N O 44.01364 63 Pentose-Hexose C11 H18 O9 294.09508
29 Deoxyhexose C6 H10 O4 146.05791 64 Pentose-Pentose C10 H16 O8 264.08452

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Mass Lists view

Table 194. Default neutral loss list (Sheet 2 of 2)

No. Name Elemental Comp. Delta Mass No. Name Elemental Comp. Delta Mass
30 F F 18.99840 64 Pyroglutamic Acid C5 H7 N O3 129.04259
31 Fatty_Acid_16:0 C16 H32 0 256.24023 66 S S 31.97207
32 Fatty_Acid_16:1 C16 H 30 02 254.22458 67 SO OS 47.96699
33 Fatty_Acid_18:0 C18 H36 02 284.27153 68 SO2 O2 S 63.96190
34 Fatty_Acid_18:1 C18 H34 02 282.25588 69 y-GluAlaGly-2H C10 H15 N3 O6 273.09609
35 Fatty_Acid_18:2 C18 H32 02 280.24023

Mass Lists view

Use the Mass Lists view to create a library of available mass lists to use with the Search Mass
Lists node—a processing workflow node that searches selected mass lists for matching
compounds.

Tip To open the Mass Lists view, choose Lists & Libraries > Mass Lists from the
application menu bar.

Figure 191. Mass Lists view

The application comes with 14 mass lists:

• Anita Lab 6549 Flavonoid Structure Database (with structures)
• Chemical List PFASSTRUCT-2022-04-20

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Mass Lists view

• EFS HRAM Compound Database

• Endogenous Metabolites database 4400 compounds
• Example Mass List
• Extractables and Leachables HRAM Compound Database (with structures) 2023 Update

Tip If you uninstall a previous version of Compound Discoverer 3.3 from your data
processing computer before you install the latest service pack, your mass list will
include the obsolete version of the Extractables and Leachables HRAM Compound
Database and the current 2023 update of this mass list. To delete the obsolete mass
list, select it and click Delete.

• FCCDB_2022
For more information, go to https://doi.org/10.5281/zenodo.3240108.
• GC Orbitrap Contaminants Library Compound Database
• GC Orbitrap Flavor and Fragrances Compound Database
• GC Orbitrap Metabolomics Library Compound Database
• LipidMaps Structure Database 2021-09-13
For more information, go to http://ncbi.nlm.nih.gov/pubmed/17098933.
• Natural Products Atlas 2021_08
• PFAS_NEG
• PFAS_NIST
For more information, go to https://data.nist.gov/od/id/mds2-2387.

Note The Example Mass List file, which contains four amino acids, is specifically
designed for the metabolomics tutorial for LC studies that you can access from the Help
menu.

The application can read the following file types:

• The following types of CSV files:
– CSV files with a molecular weight column that specifies the molecular weight to five
decimal places, an elemental composition column, or both of these columns
– CSV files created by exporting a ChemSpider Results table or a Compounds table as
plain text

Note The Export > As Plain Text shortcut menu command saves the data in the
result table to a CSV file (ChemSpider Results.csv or Compounds.csv).

– CSV files created by exporting data from the Thermo Scientific ToxID application

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Mass Lists view

– CSV files (MaConDa_version#_.csv) downloaded from the Mass Spectrometry

Contaminant Database
• Mass lists files (.massList) created by the Compound Discoverer application
• XML files created by exporting all the compounds in the Expected Compounds library
• SDF files

For information about creating, editing, importing, exporting, and replacing mass list files, see
these topics:
• Flowchart for creating and editing mass lists
• Delete or replace mass list files
• Import a mass list from a CSV file
• Import a mass list from a massList file, an XML file, or an SDF file
• Export a mass list file
• Mass Lists view parameters

Flowchart for creating and editing mass lists

Figure 192 shows a flowchart for creating a new mass list from scratch or editing the
compounds in an existing mass list.

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Mass Lists view

Figure 192. Flowchart for creating, importing, and editing mass lists within the application
To open the Mass Lists view, from
the application menu bar, choose
Lists & Libraries > Mass Lists.

Edit an
Create a new
No existing Yes
mass list?
mass list?

Yes No
In the Mass Lists view,
select a mass list and
click Edit.

Import a mass
list?

Yes
In the Mass Lists view, click New.

In the Mass Lists view, In the Mass Lists view, In the Mass Lists view,
In the Create New Mass List click Import and select a click Import and select click Import and select
dialog box, name the mass list and CSV file. an SDF file or an XML a mass list file.
click Create. file.
Then, define the essential The mass list appears
columns in the Define CSV as a new item in the
File Format dialog box and Mass Lists view.
click OK.

In the Edit ‘File Name.massList’ In the Edit ‘File Name.massList’

(No Compounds) dialog box, (# Compounds) dialog box, click New or
click New. select a compound and click Edit.
Repeat for each Repeat to add
new compound. or edit more
compounds.
In the Compound Editor dialog In the Compound Editor dialog box, define the
box, define the new compound new compound or edit the selected compound
and click Save. and click Save.

In the Edit ‘File Name.massList’ In the Edit ‘File Name.massList’

(No Compounds) dialog box, click (# Compounds) dialog box, click Save to
Save to save the new mass list. save the edited mass list.

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Mass Lists view

Delete or replace mass list files

Y To delete mass list files or replace a mass list file

Do either of the following in the Lists & Libraries > Mass Lists view:
• To delete mass list files, select the entries to delete and click Delete. Then, at the
prompt, click Yes.
• To replace a mass list file, select the entry and click Replace. Then, browse to the
appropriate folder, select a massList file, and click Open.

Import a mass list from a CSV file

You can import mass lists from CSV, massList, SDF, or XML files. Follow this procedure to
import a mass list from a CSV file.

Tip You can create CSV files by exporting compound entries as plain text from the
following result tables: Compounds, GC EI Compounds, or GC PCI Compounds.

Y To import a mass list from a CSV file

1. In the Lists & Libraries > Mass Lists view, click Import.
2. Locate the CSV file of interest and click Open.
The Define CSV Format dialog box opens.
Figure 193. Define DSV File Format for ‘Filename.csv’ dialog box

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Mass Lists view

Note When the column header in the CSV file matches the name of an essential
column, the application recognizes it in the Essential Columns area. A red border
around a column name indicates that you must define the column.

The OK button remains unavailable until you define the Name column and at least
one column that provides the compound’s mass.

3. Define the essential parameters in the Essential Columns area as follows:

• To define the column in the CSV file that contains the compound names, select the
column name from the Name list.
• To define the column in the CSV file that provides the compound masses, select the
column name from the Formula, Molecular Weight, or Structure lists.

Note Double (for decimal numbers) is the value type for the Molecular Weight
column.

• To define the column in the CSV file that provides the chromatographic retention
times of the compounds, select the column name from the Retention Time list.
4. Click OK.
The Edit ‘File Name.massList (# Compounds)’ dialog box opens.
5. To edit the mass list, see “Create and edit mass list files.”

Import a mass list from a massList file, an XML file, or an SDF file
You can import mass lists from CSV, massList, SDF, or XML files.

Y To import a mass list from a massList file, an XML file, or an SDF file

1. In the Libraries & Lists > Mass Lists view, click Import.
2. Locate the massList file, XML file, or SDF file and click Open.
The Edit ‘File Name.massList (# Compounds)’ dialog box opens.
3. To edit the mass list, see “Create and edit mass list files.”

Export a mass list file

Y To export a mass list file to a specified file directory

1. In the Libraries & Lists > Mass Lists view, select the file.
2. Click Export.
3. Select a folder for the file, rename the file if applicable, and click Save.

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Mass Lists view

Mass Lists view parameters

Table 195 describes the parameters in the Mass Lists view.
Table 195. Mass Lists view parameters (Sheet 1 of 2)
Parameter Description
Button
New Opens the Create Mass List dialog box for creating and naming a
new and empty mass list file. After you name the file and click
Create, the Edit ‘File Name.massList (# Compounds)’ dialog box
opens for adding compounds to the list.
Edit Opens the Edit ‘File Name.massList (# Compounds)’ dialog box
for editing the selected mass list.

Selecting a table row makes this button available.

Delete Deletes the selected file from the library.

Selecting a table row makes this button available.

Import Opens a dialog box for locating and opening a CSV, a massList, an
SDF, or an XML file that contains, at a minimum, a list of masses.

When you select a CSV file, the Define CSV File Format ‘File
Name.csv’ dialog box opens.
Export Opens the Save As dialog box for renaming and saving the selected
mass list file to another folder.
Replace Replaces the selected file with the replacement file. Use this
command when the replacement file has the same name as the
current file.

Selecting a table row makes this button available.

Table columns
Filename Displays the file name of the imported file.
Description User-editable field for adding descriptive information about the
mass list.
File Size Displays the file size of the imported file.
Uploaded Displays the date (month/day/year) and time (hour/minute) when
you added the file to the library in the following format:
MM/DD/YYYY HH:mm
Updated Displays the data and time when the file was updated.

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Mass Lists view

Table 195. Mass Lists view parameters (Sheet 2 of 2)

Parameter Description
Context Displays the source of the mass list—for example, Import from
CSV or Import from XML.
State Specifies whether the mass list is available, corrupted, or missing.

If you remove a mass list from the ServerFiles folder or edit a mass
list in the ServerFiles Folder, and then restart the application, the
mass list’s state changes to Missing or Corrupted, respectively.

Create and edit mass list files

Use the Edit ‘File Name.massList (# Compounds or No Compounds) dialog box to modify
the compounds list in a mass list. You can modify the mass list by adding, deleting, and
editing the compounds in the list.
Figure 194. Edit ‘File Name.massList’ (No Compounds) dialog box

Y To create a new mass list from scratch or edit the compounds in an existing or
imported mass list
1. From the application menu bar, choose Lists & Libraries > Mass Lists.
2. Do one of the following:
• To create a new mass list from scratch, click New. Then, in the Create New Mass List
dialog box, name the file and click Create.

The Edit File Name (No Compounds) dialog box opens with an empty mass list and
the new file name appears in the table in the Mass Lists view.

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Mass Lists view

• To import a mass list from an external .massList file or SDF file, click Import, select
the file, and click Open.
The Edit ‘File Name (# Compounds)’ dialog box opens with editable entries for the
selected mass list or an empty mass list.
• To edit an existing mass list file, select it and click Edit. Or, double-click it.
The Edit ‘File Name (# Compounds)’ dialog box opens with editable entries for the
selected mass list or an empty mass list.
3. To modify the opened mass list, perform any of the tasks in Table 196.

Note You can add, rename, and delete nonessential columns. If you add a column,
you cannot delete it until you save your changes and reopen the mass list for editing.

Table 196. Editing a mass list that is opened in the Edit ‘File Name’ dialog box (Sheet 1 of 2)
Task Procedure
Add a compound. Click New, and follow the instructions in “Add and edit mass
list compounds with the Compound Editor.”
Delete a compound. 1. Select the compound and click Delete.
2. At the prompt, click Yes.
Import compounds Click Import, locate the XML file, and click Open.
from an XML file.
Import compounds Click Import, locate the SDF file, and click Open.
from an SDF file.
Import compounds 1. Click Import, locate the CSV file, and click Open.
from a CSV file.
2. Define the essential columns as described in “Import a
mass list from a CSV file.”
3. Click OK.
Add a nonessential 1. Click Add Column.
column.
2. In the Add Column dialog box, do the following:
a. Name the column.
b. (Optional) Select the data type:
• String: Alphanumeric and special characters
• Double: Decimal numbers
• Integer: Integers
c. Click Add.

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Mass Lists view

Table 196. Editing a mass list that is opened in the Edit ‘File Name’ dialog box (Sheet 2 of 2)
Task Procedure
Rename a nonessential 1. Click Rename Column.
column.
2. In the Old Name list, select the column.
3. In the New Name box, type the new name.
4. Click Rename.
Delete a nonessential 1. Click Delete Column.
column.
2. In the Column list, select the column.
3. Click Delete.

4. Click Save to save the changes to the mass list.

Table 197 describes the buttons at the top of the Edit ‘File Name.massList’ (#Compounds)
dialog box.
Table 197. Edit ‘File Name.massList’ (# Compounds) dialog box parameters
Feature Description
Buttons
New Opens the Compound Editor dialog box for defining a new
compound.
Edit Opens the Compound Editor dialog box for editing the selected
compound in the mass list.

Selecting a compound makes this button available.

Delete Deletes the selected compound from the mass list.

Selecting a compound makes this button available.

Import Opens a dialog box for locating and opening a CSV, massList, or
XML file that contains, at a minimum, a list of masses.

When you select a CSV file, the Define CSV File Format ‘File
Name.csv’ dialog box opens.
Add Column Opens the Add Column dialog box for naming and defining an
additional table column.
Rename Column Opens the Rename Column dialog box for renaming a
nonessential column.
Delete Column Opens the Delete Column dialog box for deleting a nonessential
column.

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Mass Lists view

Add and edit mass list compounds with the Compound Editor
Use the Compound Editor dialog box to add entries to and edit entries in a mass list.

Note The application includes three similar Compound Editor dialog boxes. All three
dialog boxes include the same structure drawing tools, but their data entry fields differ.
The Compound Editor dialog box that opens for editing mass list compounds includes
the following data entry fields: Molecular Weight, Name, Formula, and RT [min].

Y To add a compound to or edit a compound in a mass list

1. From the Libraries & Lists > Mass Lists view, open the mass list for editing. See “Create
and edit mass list files.”
2. In the Edit ‘File Name (# Compounds)’ dialog box, do one of the following:
• To add a compound, click New.
• To edit a compound, double-click it (or select it and click Edit).
The Compound Editor dialog box opens (Figure 195). The dialog box is unpopulated for
a new compound. The minimum required information is the compound’s molecular
weight.
Figure 195. Compound Editor dialog box for editing mass list compounds

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Spectral Libraries view

3. To change the structure in or add a structure to the drawing area, use the structure tools,
load a structure file, or click ChemSpider to find a structure file.
For details, see these topics:
• Structure drawing tools and commands
• Load a structure from a structure file
• Find a structure in the ChemSpider database

Note If you are editing the structure for an existing entry in the mass list, the
Molecular Weight field is unavailable, and any formula or structure that you enter
must match the displayed molecular weight.

The chemical structure appears in the drawing pane and its molecular weight and formula
appear in their respective fields.
4. (Optional) In the Name box, type or edit the name of the compound.
5. (Optional) In the RT [min] box, enter a chromatographic retention time.
The application rounds the retention time to three decimal places.
6. Click Save.
The Edit ‘File Name (# Compounds)’ dialog box appears.
7. Review the new or edited compound. If necessary, use the filter row to display only the
new entry. See “Filter the tables on a study page or a list or library view.”
8. To save the changes to the mass list that you are editing, click Save.

Note If you attempt to close the dialog box without saving the changes, an Unsaved
Changes prompt appears.

Spectral Libraries view

The following spectral libraries are snapshots of the mzCloud database taken in July 2021:
• mzCloud Offline for mzVault_Endogenous_2021B
• mzCloud Offline for mzVault_Endogenous-Autoprocessed_2021B
• mzCloud Offline for mzVault_Autoprocessed_2021B
• mzCloud Offline for mzVault_Reference_2021B

You can create your own custom mzVault libraries by using the mzVault 2.3 SP1 application
or by exporting the spectral information from a Compound Discoverer result file from an LC
study. See “Export spectral data to a new or existing mzVault library.”

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Spectral Libraries view

Tip The Search mzVault node does not require the mzVault application, so installing the
mzVault 2.3 software is optional. However, Thermo Fisher Scientific recommends
installing the software to do any of the following:
• Edit existing spectral libraries.
• Create new spectral libraries with curated spectra.
• Convert existing legacy mzVault spectral libraries.

You can create new mzVault libraries with the Compound Discoverer 3.3 application, but
you are limited to exporting spectra from these result tables: Compounds and Expected
Compounds.

Note You cannot edit spectral libraries in the Compound Discoverer application. The
Edit button in the command bar is unavailable.

Table 198 provides instructions for managing the spectral libraries.

Table 198. Tasks for managing the spectral libraries
Task Procedure
Open the Spectral Libraries From the application menu bar, choose Lists & Libraries
view. > Spectral Libraries.
Add an mzVault library. Click Import, locate the library, and click Open.
Replace an mzVault library. In the Spectral Libraries view, select the library. Then,
click Replace, locate the library, and click Open.
Export an mzVault library. In the Spectral Libraries view, select the library. Then,
click Export, select a folder, and click Save.
Delete an mzVault library. In the Spectral Libraries view, select the library, and click
Delete.
Create a new but empty 1. In the Spectral Libraries view, click New.
mzVault library.
The Create New Spectral Library dialog box opens.

2. Name the file and click Create.

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Metabolika Pathways view

Metabolika Pathways view

Initially, the Metabolika Pathways view contains a list of the Metabolika pathways files
(.metabolika) that install with the Compound Discoverer application.

Use the Metabolika Pathways view to create new pathways, edit existing pathways, import and
export pathways, and replace pathways.

Tip To open the Metabolika Pathways view, from the application menu bar, choose Lists
& Libraries > Metabolika Pathways.

For details, see these topics:

• Metabolika Pathways view parameters
• Delete, import, export, and replace Metabolika pathways

For information about creating and editing Metabolika pathways, see “Edit new and existing
Metabolika pathways.”

Metabolika Pathways view parameters

Table 199 describes the buttons across the top of the view and the table columns from left to
right.
Table 199. Metabolika Pathways view parameter descriptions (Sheet 1 of 2)
Parameter Description
Filter row Use this row to filter the table as appropriate. See “Filter the tables
on a study page or a list or library view.”
Button
New Opens the Create New Metabolika Pathway dialog box for
naming the new Metabolika Pathway file.
Edit Opens Edit Metabolika Pathway ‘Pathway name’ dialog box.
Delete Deletes the selected Metabolika pathway files from the list.
Import Opens the file browser for selecting a Metabolika pathway file.
Export Opens the Save As dialog box for renaming the pathway, saving it
to a new directory, or both.
Replace Opens the file browser for selecting a Metabolika pathway file to
replace the currently selected file.
Column
Filename Displays the file name of the imported file.
Description User-editable field for adding descriptive information about the
pathway.

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Metabolika Pathways view

Table 199. Metabolika Pathways view parameter descriptions (Sheet 2 of 2)

Parameter Description
File Size Displays the file size of the imported file.
Uploaded Displays the date (month/day/year) and time (hour/minute) when
you added the file to the list in the following format:
MM/DD/yyyy HH:mm
Updated Displays the data and time when the file was updated.
Context Displays the source of the pathway.
State Specifies whether the pathway is available, corrupted, or missing.

If you remove a pathway file from the ServerFiles folder or edit a

pathway in the ServerFiles Folder, and then restart the application,
the state of the pathway changes to Missing or Corrupted,
respectively.

Delete, import, export, and replace Metabolika pathways

Table 200 describes how to delete, import, export, and replace Metabolika pathways.
Table 200. Deleting, importing, exporting, or replacing Metabolika pathways
Task Procedure
Delete Metabolika pathways 1. In the Metabolika Pathways view, select the pathways
from the list. and click Delete.
2. At the prompt, click Yes.
Import Metabolika pathway 1. In the Metabolika Pathways view, click Import.
files into the list.
2. Locate the files (.metabolika) and click Open.
Export Metabolika pathway 1. In the Metabolika Pathways view, select the
files to another folder. pathways, and then click Export.
2. In the Browse For Folder dialog box, select a folder
and click OK.

The application copies the files to the selected folder.

Replace a Metabolika pathway 1. In the Metabolika Pathways view, select the pathway
file with another Metabolika and click Replace.
pathway file.
2. Locate the replacement file and click Open.

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Edit new and existing Metabolika pathways

Edit new and existing Metabolika pathways

Use the Edit ‘File Name.metabolika’ dialog box to create a new Metabolika pathway or edit an
existing Metabolika pathway.

To create or edit a Metabolika pathway, see these topics:

• Create a new Metabolika Pathway file
• Edit an existing Metabolika pathway
• Modify the arrows in a Metabolika pathway
• Shortcut menu for the Metabolika pathway editor

Create a new Metabolika Pathway file

You can create new Metabolika Pathway files.

Y To create a new Metabolika pathway

1. From the application menu bar, choose Lists & Libraries > Metabolika Pathways.
1. In the Metabolika Pathways view, click New.
The Create New Metabolika Pathway dialog box opens.
2. Name the file and click Create.
The Edit Metabolika Pathway ‘File Name.metabolika’ dialog box opens.

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Edit new and existing Metabolika pathways

3. In the pathway editor, right-click and choose Add Structure.

Figure 196. Metabolika pathway editor with shortcut menu

The Compound Editor opens.

4. Use the Compound Editor to add new structures. See “Add and edit Metabolika pathway
structures.”
5. To add an arrow to indicate the direction between reactants and products, right-click a
structure and choose Add Arrow. To add more arrows, repeat this step.
By default, arrows are straight unidirectional lines with one arrowhead and four anchor
points (Figure 197). To change the arrow’s properties, see “Modify the arrows in a
Metabolika pathway.”
Figure 197. Selected arrow with four anchor points

6. To clean up the drawing, do any of the following:

• To delete a structure or an arrow, select it and press the Delete key.
• To delete all the drawing items, right-click and choose Select All. Then, press the
Delete key.
• To move a structure or an arrow, select it and hold down the left mouse button to
display the move pointer. Then, drag the items to another location.

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Edit new and existing Metabolika pathways

Edit an existing Metabolika pathway

Y To edit an existing Metabolika pathway

1. In the Metabolika Pathways view, select the pathway and click Edit.
The Metabolika pathway editor opens and displays the selected pathway or the beginning
section of the pathway in the left pane and the entire pathway at a lower zoom level in the
right pane. Use the tools in the upper right of the left pane to change the zoom level, and
the selection window in the right pane to display a different section of the pathway in the
left pane.
2. To modify the pathway, do any of the following:
• To edit a structure, right-click it and choose Edit Structure.
The Compound Editor opens.
• To add a structure, right-click it anywhere in the left pane and choose Add Structure.
The Compound Editor opens.
• To edit the arrows, see “Modify the arrows in a Metabolika pathway.”
3. To undo a change, use the CTRL+Z keys.
You can undo up to six changes.

Modify the arrows in a Metabolika pathway

To modify the arrows in a Metabolika pathway, see the following table.
Table 201. Modifying the arrows in a Metabolika pathway (Sheet 1 of 3)
Task Procedure
Move an arrow. 1. Select the arrow and hold down the left mouse
button to display the move pointer ( ).

2. Drag the arrow to another location.

Change the angle of an arrow. 1. Select the arrow to display its anchor points, and then
point to an end anchor point.
2. When this pointer ( ) appears, drag the end of the
arrow up or down as appropriate.

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Edit new and existing Metabolika pathways

Table 201. Modifying the arrows in a Metabolika pathway (Sheet 2 of 3)

Task Procedure
Change the curvature of an 1. Select the arrow to display its anchor points, and then
arrow. point to one of its two internal anchor points.
2. When this pointer ( ) appears, drag the pointer
arrow up or down as appropriate.

Straighten a curved arrow. Right-click the arrow and choose Reshape.

Make an arrow bidirectional to Right-click it and choose Is Reversible.
represent a reversible reaction.
Merge arrows. 1. Reshape the arrows into curves.
2. Overlay the curved arrows, and then select one of the
curves.

3. Point to any of the blue squares.

4. When this pointer ( ) appears, drag the selected
curve until the red square anchor points appear on
the second curve, and then release the mouse button.

5. To straighten one of the merged arrows, right-click it

and choose Reshape.

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Edit new and existing Metabolika pathways

Table 201. Modifying the arrows in a Metabolika pathway (Sheet 3 of 3)

Task Procedure
Add an arrow caption. 1. Right-click the arrow and choose Edit Arrow
Caption.
2. In the Plain HTML dialog box, type text or text with
standard HTML tags and click OK.

3. To lock the caption to the arrow, right-click the arrow

and choose Is Locked.

Shortcut menu for the Metabolika pathway editor

Table 202 describes the shortcut menu for the Metabolika pathway editor.
Table 202. Shortcut menu for the Metabolika pathway editor
Command Function
Add Arrow Adds a straight, unidirectional arrow.
Add Structure Opens the Compound Editor dialog box for adding a structure.
Add Standard Text Opens the Plain HTML dialog box for adding formatted text.
Merge Text and Arrow Merges a selected standard text string to a selected arrow.
Is Reversible Makes the selected arrow bidirectional.
Edit Structure Opens the Compound Editor dialog box for editing the selected
structure.

Available for a selected structure.

Edit Standard Text Use to edit standard text, which is text that is not associated with
a structure or an arrow.
Edit Arrow Caption Opens the Plain HTML dialog box for entering formatted text
as an arrow caption.
Reshape Straightens a curved arrow.
Is Locked Locks the arrow caption to the arrow.
Copy > Selection Copies the selected items. Press CTRL+V to paste the copied
items elsewhere in the dialog box.
Copy > Structure Copies the selected structure.
Copy > Pathway Copies the pathway.
Select All Selects all the drawing items in the dialog box.

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Edit new and existing Metabolika pathways

Add and edit Metabolika pathway structures

Use the Compound Editor to add structures to and edit the structures in a Metabolika
pathway.

Y To edit or add a structure to a Metabolika pathway

1. Open the Compound Editor for editing and adding Metabolika pathway structures by
doing one of the following:
• Right-click the workspace in the Edit Metabolika Pathway ‘pathway name’ dialog box
and choose Add Structure.
Figure 198. Edit Metabolika Pathway ‘pathway name’ dialog box with shortcut menu

• Double-click a structure in the pathway.

Figure 199 shows the Compound Editor dialog box for a new structure.

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Compound Classes view

Figure 199. Compound Editor dialog box for editing Metabolika pathway structures

Click to locate and

open a structure file.

Drawing area

Opens the ChemSpider application

2. Do one of the following:

• When adding a new structure, do any of the following:
– Use the drawing tools. See “Structure drawing tools and commands.”
– Load a structure file. See “Load a structure from a structure file.”
– Use the ChemSpider application. See “Find a structure in the ChemSpider
database.”
The application automatically populates the Molecular Weight and Formula boxes.
• When editing an existing structure, you are limited to structures that match the
current molecular weight and formula.

Compound Classes view

The Compound Classes view contains a library of compound class files. Each compound class
file contains a list of fragment ions.

When the processing workflow includes the Compound Class Scoring node with one or more
user-specified compound class lists of fragments, the application determines the probability
that an unknown compound belongs to the compound classes by comparing the ions detected
in the fragmentation scans to the fragments in the compound class lists.

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Compound Classes view

Tip To open the Compound Classes view, choose Lists & Libraries > Compound
Classes from the application menu bar.

The view opens as a tabbed page in the application window.

The application comes with four compound class lists:

• Omeprazole Compound Class.clib
This file contains the fragments for the target compound in the Compound Discoverer
Metabolism Tutorial.
• PFAS Fine Signature Fragment-lib.clib and PFAS General from FluoroMatch Suite.clib
These files contain fragments for the PFAS family of compounds. The following
processing workflow template uses these compound class files in the Compound Class
Scoring node:
PFAS Unknown ID w Database Searches and Molecular Networks.cdProcessingWF

Note For information about identifying compounds in the PFAS family, see “PFAS
identification.”

• Phosphatidycholine Compound Class.clib

Use the Compound Classes view, the Edit ‘Named Compound Class’ dialog box, and the
Fragmentation Editor to create your own compound class files.
Figure 200. Compound Classes view

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Compound Classes view

The process for editing the fragment structures in a compound class file is as follows:
1. From the application menu bar, choose Lists & Libraries > Compound Classes.
The Compound Classes view opens.
2. In the Compound Classes view, double-click the file that you want to edit.
The Edit Compound Class ‘File name’ dialog box opens.
3. In the Edit Compound Class dialog box, double-click the fragment that you want to edit.
The Fragment Editor opens.
4. Edit the fragment and click Save. Then, click Save to save the compound class file.

For more information about the Compound Classes view, see the following topics:
• Compound Classes view parameters
• Add new files to the Compound Classes library
• Delete, import, and export compound class files
• Edit compound class files
• Edit Compound Class dialog box parameters

Compound Classes view parameters

Table 203 describes the parameters in the Compound Classes view.
Table 203. Compound Classes view parameters (Sheet 1 of 2)
Parameter Description
Button
New Opens the Create New Compound Class dialog box for naming a
new and empty fragments file. After you name the file and click
Create, the Edit Compound Class dialog box opens for adding
fragments.
Edit Opens the fragments list for the selected compound class file.

Selecting a compound class file makes this button available.

Delete Deletes the selected file from the library.

Selecting a table row makes this button available.

Import Opens a dialog box for locating a compound class library file
(.clib).

The application adds the selected file to the library.

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Compound Classes view

Table 203. Compound Classes view parameters (Sheet 2 of 2)

Parameter Description
Export Opens the Save As dialog box for renaming and saving the selected
file to another folder.
Replace Replaces the selected file with the replacement file. Use this
command when the replacement file has the same name as the
current file.

Selecting a table row makes this button available.

Table columns
Filename Displays the file name of the library file.
Description User-editable field for adding descriptive information about the
file.
File Size Displays the file size of the file.
Uploaded Displays the date (month/day/year) and time (hour/minute) when
you added the file to the library in the following format:
MM/DD/YYYY HH:mm
Updated Displays the data and time when the file was updated.
Context Displays the description that you entered in the Context box of
the Create New Compound Class dialog box.
State Specifies whether the compound class file is available, corrupted,
or missing.

If you remove or edit a compound class file from its storage folder,
and then restart the application, the mass list’s state changes to
Missing or Corrupted, respectively.

Add new files to the Compound Classes library

A compound class file contains a list of fragment structures. To use a compound class file, you
must add it to the Compound Classes library.

Y To add new compound class files to the Compound Classes library

1. Open the Compound Classes view by choosing List & Libraries > Compound Classes
from the application menu bar.
2. In the Compound Classes view, click New.
The Create Compound Class dialog box opens.

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Compound Classes view

Figure 201. Create Compound Class dialog box

3. Name the compound class, optionally provide a brief description, and click Create.
The named compound class appears as a new row in the Compound Classes view and the
Edit Compound Class ‘Name’ dialog box opens. For information about this dialog box,
see “Edit Compound Class dialog box parameters.”
Figure 202. Edit Compound Class ‘Name’ dialog box

4. In the Edit Compound Class ‘Name’ dialog box, click New.

The Fragment Editor dialog box opens. Before you add any fragments to the new
compound class, the dialog’s title bar includes the following text: (No Fragments).
5. Define the fragments for the compound class. See Use the Fragment Editor to define
fragment ions.
6. After you add the fragments of interest, click Save.
The Edit Compound Class ‘File name’ dialog box dialog box closes.

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Compound Classes view

Delete, import, and export compound class files

In the Compound Class view of the Lists & Libraries page, you can directly delete, import, or
export compound class files (.clib) by using the appropriate command in the command bar at
the top of the view below the title bar.
Table 204. Deleting, importing, and exporting compound class files
Task Procedure
Delete a compound class file 1. In the Compound Classes view, select the compound
from the list. class of interest and click Delete.
2. At the prompt, click Yes.
Import a compound class file. 1. In the Compounds Class view, click Import.
2. Browse to and select a compound class library file
(.clib).
3. Click Open.
The application uploads the file to your local hard
drive in the ProgramData\Thermo\Compound
Discoverer X.X\ ServerFiles folder. A new entry
appears in the library. The entry displays the
following information about the compound class:
name, description, # fragments, date uploaded, date
updated, and file size.
Export a compound class file. 1. In the Compounds Class view, select the compound
class of interest and click Export.
2. In the Save As dialog box, browse to a storage
location for the file, change the file name when
applicable, and click Save.

Edit compound class files

Use the Edit Compound Class ‘File name’ dialog box to edit compound class files and the
Fragment Editor to edit the fragments in the files.

Y To edit a compound class file

1. In the Compound Classes view of the List & Libraries page, double-click the compound
class file that you want to edit. Or, select the file and click Edit.
The Edit Compound Class ‘File name’ dialog box opens with a list of fragments.

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Compound Classes view

Figure 203. Edit Compound Class dialog box for the Omeprazole Compound Class file

2. In the Edit Compound Class ‘File name’ dialog box, do the following as applicable:
• To add a new fragment by using the Fragment Editor, click New. Then, use the
Fragment Editor to define the fragment (see Use the Fragment Editor to define
fragment ions).
• To add new fragments by importing their structures from a CSV file or an SDF file,
click Import.
• To edit a fragment, select it and click Edit. Then, use the use the Fragment Editor to
edit the fragment (see Use the Fragment Editor to define fragment ions).
• To delete a fragment, select it and click Delete.
3. Click Save to save your edits and return to the library.

Edit Compound Class dialog box parameters

Table 205 describes the buttons and columns in the compound class editor.

For information about using the compound class editor, see these topics:
• Add new files to the Compound Classes library
• Edit compound class files

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Compound Classes view

Table 205. Edit ‘Name’ Compound Class dialog box parameters

Parameters Description
Buttons
New Opens the Fragment Editor for defining a fragment. See “Use
the Fragment Editor to define fragment ions.”
Edit Opens the Fragment Editor with the definition of the selected
fragment.
Delete Deletes the selected fragment.
Import Opens the Open dialog box for selecting a CSV file or an
SDF file.
Table columns
m/z Displays the m/z value of the fragment.
Structure Displays the structure of the fragment.
Formula Displays the formula of the fragment.
Charge Displays the charge of the fragment.
Comment Displays the description that you typed in the Create
Compound Class dialog box.

Use the Fragment Editor to define fragment ions

Use the Fragment Editor to define fragments for a compound class.

Note For information about using the drawing tools, see “Structure drawing tools and
commands.”

Y To open the Fragment Editor dialog box

1. Open the Compound Classes view from the application menu by choosing Lists &
Libraries > Compound Classes.
2. In the Compound Classes view, do one of the following:
• To edit the fragments list in a existing compound class file, select a compound class
file and click Edit. Then, in the Edit Compound Class ‘name’ (# fragments) dialog
box, select a fragment and click Edit.
• To create a new compound class file, click New. In the Create Compound Class
dialog box, name the library, type a description, and click OK. Then, in the Edit
‘Named Compound Class’ (No Fragments) dialog box, click New.
The Fragment Editor dialog box opens.

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Compound Classes view

Figure 204 shows the Fragment Editor dialog box.

Figure 204. Fragment Editor dialog box

Opens a structure.

Opens the Atom Properties dialog box

for adding a charge to the structure.

Drawing
area

The application
populates these
boxes as you draw
the structure.

3. Do either of the following:

• Use the drawing tools to add a structure to the drawing area. See “Structure drawing
tools and commands.”
• Open a structure file. See “Load a structure from a structure file.”
4. Add a charge to the structure as follows:
a. Select the atom where you want to add a charge.
b. Click the Atom Properties icon, .
The Atom Properties dialog box opens.

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Load a structure from a structure file

Figure 205. Atom Properties dialog box with an available Charge check box

c. In the Atom Properties dialog box, select the Charge check box.
d. Select the positive (+) or negative (–) option.
e. Click OK.

Load a structure from a structure file

You can load a structure from a structure file from any of the compound editors or the
fragment editor.

Y To load a structure from a structure file

1. In the editor’s toolbar, click the Load Structure from Disk button, .
The Open Structure dialog box opens.
2. In the Known Structure Formats list, select the format of the structure file: MOL Format
(.mol), Compressed Structure (.mcs), or Template (.tml).
3. Locate the structure file and click Open.
The chemical structure appears in the drawing pane, and the application automatically
populates the Elemental Composition and Molecular Weight boxes.

If the structure is not visible or it is only partially visible in the pane, right-click the pane and
choose Select All. Then, while pressing the SHIFT key, drag the structure into the pane.

Find a structure in the ChemSpider database

You can access the ChemSpider database from the Compound Editor dialog box or the
Compound Annotation Editor dialog box and search for a compound entry with a structure
file.

Note For an LC study, you can also access the ChemSpider database from the mzLogic
Analysis view.

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Find a structure in the ChemSpider database

Tip For information about the editors, see “Add and edit expected compounds with the
Compound Editor.” For information about the mzLogic Analysis view, see “mzLogic
Analysis view.”

Note The search accepts uncharged and charged structures.

Y To load a structure into the drawing area of the editor or mzLogic Analysis view

1. Click ChemSpider.
The ChemSpider Search dialog box opens.
2. In the Input box, enter a name, formula, molecular weight, or CSID.
3. Click Search.
4. Select a compound from the search results.

5. Click Select.
The chemical structure appears in the drawing pane and the molecular weight, name, and
formula of the compound appear in their respective fields.

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Structure drawing tools and commands

Structure drawing tools and commands

The Compound Editor, the Compound Annotation Editor, and the Fragment Editor include
a set of drawing tools.

Use the toolbar for these structure editors and the shortcut menu for the drawing area to draw,
manipulate, and save structures as described in the following topics:
• Toolbar for the structure editors
• Shortcut menu commands for the drawing area of the structure editors
• Use the structure icons in the toolbar
• Create template structures and adding them to a drawing
• Check the validity of a structure
• Manipulate structures
• Select atoms and bonds
• Move structures
• Save a structure to a structure file
• Edit atom properties

Note The application has three different Compound Editor dialog boxes and one
Fragment Editor dialog box that all have the same structure drawing tools. You can open
these dialog boxes from the following Lists & Libraries views: Expected Compounds,
Mass Lists, Metabolika Pathways, and Compound Classes.

Toolbar for the structure editors

The Compound Editor, Compound Annotation Editor, and Fragment Editor dialog boxes
have the same set of toolbar icons.

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Structure drawing tools and commands

Figure 206. Editor toolbar

Check
Redo Clean
Undo Atom Property
Templates
Copy to Clipboard

n-Membered
Ring
5-Membered Ring
6-Membered Ring
Save Structure to Disk Benzene Ring
Chain
Load Structure from Disk
Triple Bond
Selection Tool Double Bond
Single Bond

Shortcut menu commands for the drawing area of the structure editors
The structure editors include a drawing area for adding a two-dimensional structure.

Table 206 describes the drawing area’s shortcut menu commands.

Table 206. Shortcut menu commands for the drawing area
Menu command Description
Selection Tool Selects a portion of the structure.
Lasso Selection Selects an non-rectangular portion of the structure.
Rectangle Selection Selects a rectangular portion of the structure.
Cut Removes the selected portion of a structure.
Copy Copies the selected portion of a structure to the Clipboard.
Paste Copies a structure from the Clipboard to the drawing area.
Delete Deletes the selected portion of a structure.
Select All Selects everything in the drawing area.
Resize Resizes the selected portion of a structure.
Rotate Rotates the structure around the selected axis of rotation.
Mirror Reflects the structure along its vertical or horizontal axis.

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Structure drawing tools and commands

Use the structure icons in the toolbar

The structure editors include a set of structure icons.

Y To begin drawing a chemical structure

Tip Point to a drawing icon to display its description.

1. Click any of these structure icons, . Or, select a template

structure. See “Create template structures and adding them to a drawing.”
The cursor changes shape to represent the current drawing mode.
2. Click the drawing area where you want to place the selected structural feature.
Until you click another structure icon, you can continue to add the same structural
feature each time you click the drawing area.
3. Edit the atoms and bond properties. See these topics:
• Edit bond properties
• Edit atom properties

Create template structures and adding them to a drawing

Use the template tool on the structure editor toolbar to draw closely related chemical
structures.

Y To create, save, and open template structures

1. Open a structure file, paste a structure (InChi or MOL string), or draw a structure in the
drawing area of the structure editor.
2. In the toolbar, click the Save Structure to Disk button, .
3. In the Save Structure dialog box, do the following:
a. Browse to the folder where you want to store the file.
b. Name the file.
c. In the Save As Type list, select Template (*.tml).
d. Click Save.
4. To add a template structure to the drawing area, click the Templates icon, .
The Templates dialog box opens.

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Structure drawing tools and commands

5. In the Explorer view of the Templates dialog box, browse to and select the folder where
you store your structure files.
The title bar of the Templates dialog box changes from Templates to Templates – Folder
name, and the 2D structures appear above the Explorer view. The application displays all
of the structures in the folder. It does not differentiate between MOL files and Template
files.
Figure 207. Templates dialog box with a view of the stored structures

6. On the structure that you want to open, click any atom or bond.
The templates cursor, , appears in the drawing area of the Compound Editor dialog
box.
7. To place the selected structure in the drawing area, click the drawing area.

Check the validity of a structure

The structure editors do not prevent you from creating and saving invalid structures. To check
the validity of a structure as you create it or before you save it, use the check structure tool.

Note The check structure tool does not perform quantum mechanical or
thermodynamical calculations that address possible structural stability.

Y To check a structure

1. Click the Check icon, .

The check structure tool searches for formal errors and unusual structural features. If a
structure is formally incorrect or if the check structure tool finds its validity questionable,
the Check Structure message lists the errors and warnings.

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Structure drawing tools and commands

Figure 208. Check Structure message

2. Click OK.
The application automatically selects the atoms and bonds that it considers incorrect. The
application considers structures that are not connected as mixtures and reports them as
errors, but it does not select the mixtures.

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Structure drawing tools and commands

Manipulate structures
You can resize, rotate, mirror, clean, and verify structures in the drawing area of a structure
editor. After finishing a structure drawing, always check for errors before proceeding.

Table 207 describes how to manipulate structures.

Table 207. Manipulating structures (Sheet 1 of 2)
Task Procedure
Resize a structure 1. Select the structure or part of the structure that you want to
resize.
2. Right-click and choose Resize.
3. Drag one of the small rectangles on the edge of the structure
and release the mouse button.
Dragging one of the diagonal rectangles keeps the aspect ratio
constant during structure resizing.
Rotate a structure 1. Select the structure or part of the structure that you want to
rotate.
2. Right-click and choose Rotate.
A small circle with a cross in the middle, , appears. The
circle indicates the center of rotation.
3. Move the center of rotation by dragging the circle.

4. Rotate the selected structure around the center of rotation by

dragging any of the small rectangles on the edges of the
structure.

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Structure drawing tools and commands

Table 207. Manipulating structures (Sheet 2 of 2)

Task Procedure
Mirror a structure 1. Select the structure or part of the structure that you want to
mirror.
2. Right-click and choose Mirror.
3. Click one of the small rectangles on the edge of the structure.
• The top and bottom rectangles flip the selected structure
along a horizontal axis.
• The left and right rectangles flip the selected structure
along a vertical axis.
Clean a structure 1. Do one of the following:
• Select an entire structure.
• Select only the atoms that you want to clean.
The selected atoms must be connected.
2. Click the Clean icon, .
The cleaning tool helps you create a professional look for your
structures.

IMPORTANT In some complicated cases, the Clean function

can lead to structures that you might not find satisfactory. If this
occurs, click the Undo icon, .

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Structure drawing tools and commands

Select atoms and bonds

In the structure editors, you can select individual atoms and bonds, a contiguous portion of a
structure, an entire structure, or groups of atoms and bonds that are not adjacent to each
other.
Table 208. Selecting atoms and bonds
Task Procedure
Select an individual atom or Click the Selection Tool icon, and then click the
bond. individual atom or bond.
Choose a selection mode. Right-click anywhere in the drawing area of the
Compound Editor dialog box and choose Lasso
Selection or Rectangle Selection.

Lasso Selection Rectangle Selection

Select a group of adjacent Do one of the following:

atoms.
• Right-click and choose Rectangle Selection. Then
drag the cursor to form a rectangle around the atoms.
• Right-click and choose Lasso Selection. Then draw a
free-form shape around the atoms.
Select the entire structure. Do one of the following:
• Right-click the drawing area and choose Select All.
• Click the Selection Tool icon, and then double-click
anywhere in the drawing area, except on atoms or
bonds.

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 12 Manage the lists and libraries
Structure drawing tools and commands

Move structures
In the structure editors, you can move all or part of a structure or all the structures.
Table 209. Moving structures
Task Procedure
Move a structure. 1. Select the atoms or bonds that you want to move.
2. Drag the selected structures to a new location.
Move all the structures in the 1. Right-click the drawing area and choose Select All.
drawing area.
2. Click any atom or bond in the drawing area, and
then drag the structures to a new location.

Edit bond properties

In any of the structure editors, use the bond icons to change the bond multiplicity.

Y To change the multiplicity of a bond

Click , , or , and then click the bond that you want to change.

Edit atom properties

Use the Atom Properties dialog box to change the isotope of an atom or the entire element.
For more information about modifying compound structures, see “Structure drawing tools
and commands.”

IMPORTANT The application does not support compounds with a radical. It also does
support the R-Substituent feature.

Y To edit the element or nucleon number for a single atom in a structure

1. Open the structure that you want to edit.

Note For LC studies, the editor that opens depends on whether you are editing a
compound definition, a compound annotation, or a fragment definition:
• The Compound Editor dialog box opens when you add a new compound to or
edit a compound in the expected compounds list or a mass list.
• The Compound Annotation Editor dialog box opens when you edit the
annotations for a compound in the Compounds table, the Expected Compounds
table, or a Structure Proposals table.
• The Fragment Editor dialog box opens when you add a new fragment to or edit a
fragment in the Edit Compound Class dialog box.

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 12 Manage the lists and libraries
Structure drawing tools and commands

2. Click the Selection Tool icon, .

3. Do one of the following:
• Double-click the atom that you want to change.
–or–
• Select the atom that you want to change and click the Atom Properties icon, .
The Atom Properties dialog box opens with the properties of the selected atom displayed.

Tip In the Compound Editor dialog box, you can save compounds with charges. You
can also save compounds with radicals, but the application ignores radicals for data
processing.

Figure 209. Atom Properties dialog box, showing the properties for a charged nitrogen atom

4. To change the element, do the following:

• To change the atom to an element that is in the Element area, click the appropriate
Element button.
• To change the atom to an element not listed in the Element area, click Periodic
Table. Then, in the Periodic Table dialog box, select an element and click OK.
5. To add a charge, select the Charge check box, and then select the + (positive) or
– (negative) option.
6. To specify a less abundant isotope of the element, select the Isotope check box, and then
select the appropriate value in the Nucleon Number list.

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 12 Manage the lists and libraries
Copy and paste InChi strings and MOL strings

Tip For example, to create a compound that is labeled with one carbon-14 atom,
double-click the labeling site—the atom that you want to change. In the Atom
Properties dialog box, select the Isotope check box, and then select 14 in the Nucleon
Number list.

The application displays carbon-14 as [14]C—that is, the elemental composition of

carbon-14 labeled caffeine is displayed as C7 [14]C H10 N4 O2.

7. When you finish editing the selected atom, click OK.

Changes you make in the Atom Properties dialog box affect only the selected atom.

Save a structure to a structure file

After you draw or modify a structure, you can save the structure as a structure file (in MOL
format or as a compressed structure) or as a template file.

Y To save a structure as a structure file

1. Click the Save Structure to Disk button in the toolbar, .

2. In the Save Structure dialog box, do the following:
a. Browse to the directory where you want to store the file.
b. Name the structure file.
You can save structures under their actual names, regardless of length (for example,
1-Amino-2-hydroxyindane.mol).
c. In the Save As Type list, select a file type.
d. Click Save.

Copy and paste InChi strings and MOL strings

You can copy InChi or MOL strings to the Clipboard, and then paste them to the workspace
of the compound editor dialog boxes. You can also copy structures from the workspace of
compound editors to the Clipboard in these formats: InChi, MOL, or InChi Key string.

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 13

Use the License Manager

The following topics describe how to use the License Manager to activate or deactivate the
software license and to install new processing workflow nodes as they become available:
• Open the License Manager
• License Manager command bar
• Activate the software license
• Deactivate the software license for transfer to another computer
• Install or update a processing workflow node
• Obtain and install the KEGG license

Note After you install the Compound Discoverer application on your computer, you can
use the application without activating the license for up to 60 days.

After you activate the software license on one computer, you can deactivate the license and
transfer it to another computer.

Open the License Manager

Access the License Manager page from the Help menu.

Y To open the License Manager page

From the menu bar, choose Help > License Manager.

The License Manager opens as a tabbed document in the application window.

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 13 Use the License Manager
License Manager command bar

Figure 210. License Manager page

License Manager command bar

Table 210 describes the License Manager command bar.
Table 210. License Manager command bar
Command or feature Description
Activate Opens the License Activation dialog box where you can apply a
new activation code and activate the license on the current
computer.
Deactivate Opens the License Deactivation dialog box for deactivating the
software license.
Scan for Missing Features Activates a scan for newly installed processing workflow nodes.
Show Expired Licenses Selecting this check box displays any expired licenses.

Activate the software license

To activate your Compound Discoverer 3.3.x software license, see these topics as necessary:
1. Enter the product ID and the activation code
2. Follow one of these topics:
• Activate the license on an online computer
• Activate the license on an offline computer

Enter the product ID and the activation code

To activate your Compound Discoverer 3.3 license, you must know the product ID
(XCALI-XXXXX) and the activation code. Within one week of ordering the software, you
should receive an email from Thermo MS Licensing with the subject line “Your Order Is
Ready.” This email contains the product ID and activation code information.

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 13 Use the License Manager
Activate the software license

Y To enter the licensing information

1. On the License Manager page, click Activate.

The License Activation dialog box opens to the Activation Code view.
Figure 211. License Activation dialog box opened to the Activation Code view

2. If you have not already received your activation code, do the following:
a. Check your Junk Email folder.
b. If the email is not in your Junk Email folder, log in to your account at the following
URL. In the left navigation pane, under Software & Services, click Order History.
Then, in the list of ordered products, click the order number.
https://thermo.flexnetoperations.com
c. If you cannot find your account, send an email message to Licensing at
[email protected].
Provide the following information in the body of the message:
• Software application: Compound Discoverer
• Sales order number or purchase order number:____________________
• End user name:______________________
• End user email:______________________

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 13 Use the License Manager
Activate the software license

3. In the License Activation dialog box (Figure 211), enter the following:
• Your company name
• Your full name
• Your contact email address
• The product ID for the Compound Discoverer 3.3 application.
There are five possible product IDs. Four of the product IDs are for software
upgrades (see Table 211).
• The activation code. You can type or paste the activation code.
Table 211. Product IDs for the Compound Discoverer 3.3 software
Material Order No. Product ID Description
OPTON-31055 XCALI-65161 SW, Compound Discoverer 3.3 SP2
(single license)
OPTON-31056 XCALI-65161 SW, Compound Discoverer 3.3 SP2
(2 or more licenses)
OPTON-31060 XCALI-65162 SW, Compound Discoverer (CD) 3.3 SP2
upgrade from CD 1.0, CD 2.0, CD 2.1
OPTON-31061 XCALI-65163 SW, Compound Discoverer 3.3 SP2
upgrade from Compound Discoverer 3.0,
3.1, and 3.2
OPTON-31062 XCALI-65164 SW, Compound Discoverer 3.3 SP2 and
Mass Frontier 8.0 SR1 with Curator
OPTON-31063 XCALI-65165 SW, Compound Discoverer 3.3 SP2 and
Mass Frontier 8.0 SR1 with Curator
(2 or more licenses)

4. Depending on whether you are activating the license on an online or offline computer,
continue with the appropriate topics:
• Activate the license on an online computer
• Activate the license on an offline computer

Activate the license on an online computer

Follow these instructions if your processing computer has an Internet connection.

Y To activate the software license on an online computer

1. If you have not already entered the licensing information, enter it in the Activation Code
view of the License Activation dialog box.

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 13 Use the License Manager
Activate the software license

2. Click Online Activation to process the activation code.

3. At the confirmation prompt, click OK.
4. At the “new features” prompt, click OK.

This completes the online license activation process.

Activate the license on an offline computer

Follow these instructions if your processing computer is not connected to the Internet.

Note Activating the license on an offline computer is a three-step process that requires
access to an online computer.
1. Create an activation request file (Activation-Activation Code.req) on the offline
computer.
2. Transfer the activation request file to an online computer where you upload it to the
licensing portal to obtain a response file (activation.xml).
3. Transfer the response file (activation.xml) to the offline computer, and then process it
by clicking Process Response File in the License Activation dialog box.

Y To activate the software license on an offline computer

1. If you have not already entered the licensing information in the Activation Code view of
the License Activation dialog box, enter it now.
2. In the License Activation dialog box, click Offline Activation.
The Save Request File dialog box opens.
3. Save the activation request file (Activation-Activation Code.req).
Figure 212. Save Request File dialog box with activation code

The Offline Activation instructions appear.

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 13 Use the License Manager
Activate the software license

Figure 213. Offline activation instructions

4. Click OK.
The Activation Code view of the License Activation dialog box reappears.

Tip When you close the Offline Activation dialog box, the application automatically
saves the URL to the Clipboard, so that you can save the URL to a file for use on an
online computer.

5. (Optional) Save the URL to a file.

6. Keep the License Activation dialog box open on this offline computer.

IMPORTANT If you accidentally close the License Activation dialog box, start over at
step 1.

7. To download the response file (activation.xml) from the licensing server, do the following
on an online computer:
a. Transfer the activation request file ((Activation-Activation Code.req) to the online
computer.
b. Go to the following URL (case sensitive):
https://thermo.flexnetoperations.com/control/thmo/offlineActivation
The Life Sciences Mass Spectrometry Software Download and Licensing Portal
opens.
c. Click Choose File or Browse, browse to and select the request file
(Activation Activation Code.req), click Open, and then click Process.

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 13 Use the License Manager
Activate the software license

Note Whether the page includes a Choose File button or a Browse button
depends on the web browser.

The server downloads the activation file.

Figure 214. Software licensing portal with a view of a downloaded response file

Transfer this file to your offline computer.

d. Save the response file (activation.xml).
8. To activate the license on the offline computer, do the following:
a. Transfer the response file (activation.xml) to this computer.
b. In the License Activation dialog box that you left open, click Process Response File.
The Open Response File dialog box opens.
c. Browse to and select the response file (activation.xml), and then click Open.
d. At the “license response processed” prompt, click OK.
e. At the “new features” prompt, click OK.

This completes the offline license activation process. The License Manager indicates that the
license for the specified product (XCALI-XXXXX) is permanent.

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 13 Use the License Manager
Deactivate the software license for transfer to another computer

Deactivate the software license for transfer to another computer

To transfer the software license to another computer, you must first deactivate the license on
the current computer.

Follow the appropriate topic:

• Deactivate the software license on an online computer
• Deactivate the software license on an offline computer

Deactivate the software license on an online computer

Follow this procedure if your computer has Internet access.

Y To deactivate the software license on an online computer

1. On the License Manager page, select the software product that you want to deactivate,
and then click Deactivate.
The License Deactivation dialog box opens. The Product ID box is populated with the
selected product’s ID, and Activation Code box is populated with the activation code for
your license.
Figure 215. License Deactivation dialog box populated with the product ID and activation code

2. If the computer is connected to the Internet, click Online Deactivation.

3. At the confirmation prompt, click Yes.
The license deactivation process is complete, and the product ID disappears from the
License Manager page.

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 13 Use the License Manager
Deactivate the software license for transfer to another computer

Deactivate the software license on an offline computer

If your processing computer is not connected to the Internet, follow these instructions to
deactivate the software license.

Note Deactivating the license on an offline computer is a three-step process that requires
access to an online computer.
1. Create a deactivation request file (Deactivation-Activation Code.req) on the offline
computer. This step only starts the license deactivation process.
2. Transfer the deactivation request file (Deactivation-Activation Code.req) to an online
computer where you upload it to the licensing portal to obtain a response file
(activation.xml).
3. Transfer the response file to the offline computer, and then process it to complete the
deactivation process.

Y To deactivate the software license on an offline computer

1. On the offline computer, create the deactivation request file as follows:

a. On the License Manager page, select the software license that you want to deactivate,
and then click Deactivate.
The License Deactivation dialog box opens. The Product ID box is populated with
the selected product’s ID, and Activation Code box is populated with the activation
code for your license.
b. Click Offline Deactivation.
c. At the confirm deactivation prompt, click Yes.
The Save Request File dialog box opens. The File Name box displays the following
text: Deactivation Activation Code.req.
d. Save the deactivation request file.
e. At the prompt, which displays the location of the saved request file, click OK.
The license state changes to Deactivation in Progress, and the URL is copied to the
Clipboard.
f. (Optional) Copy the URL to a file.
2. From the online computer, retrieve the response file (activation.xml) as follows:
a. Transfer the deactivation request file and the file with the URL to this computer.
b. Go to the following URL (case sensitive):
https://thermo.flexnetoperations.com/control/thmo/offlineActivation
The Life Sciences Mass Spectrometry Software Download and Licensing Portal
opens.

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 13 Use the License Manager
Install or update a processing workflow node

c. Click Choose File, browse to and select the Deactivation Activation Code.req file,
click Open, and then click Process.
The server downloads the response file.
d. Save the response file (activation.xml).
3. Complete the deactivation process on the offline computer as follows:
a. Transfer the response file (activation.xml) to this computer.
b. On the License Manager page, select the license that you are in the process of
deactivating, and click Deactivate.
The License Deactivation dialog box opens.
c. Click Process Response File.
The Open Response File dialog box opens.
d. Select the response file (activation.xml) and click Open.
The license disappears from the License Manager page.

Install or update a processing workflow node

The application uses a node-based workflow to process raw data files. Following set
guidelines, you can create your own custom workflow nodes. In addition, Thermo Fisher
Scientific might occasionally provide custom workflow nodes on its customer website.

Y To install a new processing workflow node

1. Download the executable files and store them in the appropriate folder on the computer
where you are running the application.
2. Open the License Manager page.
3. Click Scan for Missing Features.
4. Close and reopen the application.
5. Choose Help > About.
The About Compound Discoverer dialog box opens with the Patent and Legal Notices
page displayed.
6. Expand the Nodes list and verify that it lists the new node.

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 13 Use the License Manager
Obtain and install the KEGG license

Obtain and install the KEGG license

To use the Map to KEGG Pathways workflow node in the Compound Discoverer application,
you must install a valid KEGG license on your processing computer. To license the KEGG
Pathways module, you must contact Pathway Solutions for the activation key. After you
obtain the activation key from Pathway Solutions, you must install it on your processing
computer by using the Compound Discoverer License Manager.

Note You must contact Pathway Solutions for a KEGG license. Kanehisa Laboratories
does not provide KEGG licenses for the Compound Discoverer application.

For details, see these topics:

• Contact Pathway Solutions to obtain a KEGG Pathways activation key
• Install the KEGG license

Contact Pathway Solutions to obtain a KEGG Pathways activation key

To obtain the activation key for the KEGG Pathways module, contact Pathway Solutions at
the following email address: [email protected]

Include the following information in your email:

• Your full name: First and last name
• Institution: Institution name
• Software: Compound Discoverer
• Version number: 3.3
• License type: Commercial or academic*

*If you are applying for an academic license, you must include the following statement in your
email:
I certify that I work for an academic institution, and that I will not use KEGG for any
commercial purposes (including collaborative research with a commercial entity).

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 13 Use the License Manager
Obtain and install the KEGG license

Install the KEGG license

After you receive the KEGG activation key from Pathway Solutions, follow this procedure to
install it.

Y To install the KEGG license

1. From the menu bar of the Compound Discoverer application, choose Help > License
Manager.
2. Click Activate.
3. In the License Activation dialog box, enter the name of your company, your full name,
your email address, the product ID number (XCALI-23456), and the activation code that
you received from Pathway Solutions.
4. Follow the instructions for online or offline activation as appropriate.
After you install the license, it might appear under Compound Discoverer_KEGG. If the
License Manager displays an expiration date, the license is valid.

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 14

Compound Discoverer configuration options

To set up the configuration options for the Compound Discoverer application, do the
following as needed:
• Open the Configuration page
• Select the maximum number of parallel processing jobs
• Select where to store temporary data
• Turn off the auto-save feature for studies
• Hide the workflow node numbers
• Set up the global color palette
• Specify the default mzCloud mass tolerance settings
• Set up a BioCyc account and optionally purchase a subscription
• Specify the fragmentation databases

Open the Configuration page

Use the Configuration page to set up the global configuration options for the application.

Y To open the Configuration page

From the menu bar, choose Help > Configuration.

Select the maximum number of parallel processing jobs

Use the Parallel Option view of the Configuration page to specify the maximum number of
analyses (jobs) that the application can process in parallel.

Y To change the maximum number of parallel jobs

1. In the application menu bar, choose Help > Configuration.

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 14 Compound Discoverer configuration options
Select where to store temporary data

2. In the left pane of the Configuration page, select Parallel Options under Server Settings.
The Parallel Options view opens.
3. In the Maximum Number of Processing Workflows in Parallel Execution box, type or
select an integer from 1 to 4.
The default value is equal to half the number of CPU cores in the processing computer.
4. Click Save Current Settings.

Select where to store temporary data

Use the Scratch Directory Options view of the Configuration page to change the folder where
the application stores temporary data during data processing.

Y To change the scratch directory

1. In the application menu bar, choose Help > Configuration.

2. In the left pane of the Configuration page, choose Scratch Directory Options under
Server Settings.
The Current Scratch Directory box lists the current location of the scratch folder.
Figure 216. Scratch Directory Options view

3. Click the browse button next to New Scratch Directory and locate the new directory.
4. Click Save Current Settings.
5. Restart the application.
6. Reopen the Scratch Directory Options view and make sure that the Current Scratch
Directory box lists the new scratch directory.

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 14 Compound Discoverer configuration options
Turn off the auto-save feature for studies

Turn off the auto-save feature for studies

If you want the application to automatically save changes that you make to studies, including
the list of result files on the Analysis Results page, do not turn off the auto-save feature.

Y To turn off the auto-save feature

1. In the application menu bar, choose Help > Configuration.

2. In the left pane of the Configuration page, under Client Settings, choose Study
Management Settings.
Figure 217. Study Management Settings view with the default setting

3. Clear the Save Study Automatically On Close and After Analysis Submit check box.
4. Click Save Current Settings.
5. Restart the application.

Hide the workflow node numbers

When you create a processing workflow by dragging the workflow nodes into the Workflow
Tree pane, the application automatically adds an integer to each workflow node. Use the
Workflow Editor Settings view to hide these numbers.

Y To hide the workflow node numbers

1. In the application menu, choose Help > Configuration.

2. In the left pane of the Configuration page, under Client Settings, choose Workflow
Editor Settings.
3. Under Workflow Settings, select the Hide Node Numbers check box.

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 14 Compound Discoverer configuration options
Set up the global color palette

Figure 218. Workflow Editor Settings view

4. Click Save Current Settings.

Set up the global color palette

Use the Color Schema view of the Configuration page to select one of the standard global
color palettes or create a custom color palette. The colormap selection affects the sample
group colors in the following views: Chromatograms, Trend Charts, Principal Component
Analysis, and Descriptive Statistics. The selection does not affect the color-coding in the result
tables.
Figure 219. Color Schema view

Clicking New opens the

Color Palette Configuration
dialog box.

For details about setting up the global color palette, see the following topics:
• Open the color schema view of the configuration page
• Select a standard color palette
• Create new custom color palettes

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 14 Compound Discoverer configuration options
Set up the global color palette

• Delete custom color palettes

• Import custom color palettes
• Export custom color palettes
• Edit custom color palettes
• Add colors to a custom palette
• Insert colors in a custom palette
• Replace a color in a custom palette
• Remove a color from a custom palette
• Select a color in the gradient color chart

Open the color schema view of the configuration page

Y To open the Color Schema view

1. From the menu bar, choose Help > Configuration.

2. In the left pane of the Configuration page, under Client Settings, choose Color Schema.

Select a standard color palette

For visualizing chart data, you can select from four standard color palettes on the Color
Schema view of the Configuration page.

Y To select a standard color palette

1. Open the color schema view of the configuration page.

2. In the Selected Palette list, select from four palettes.
• Compound Discoverer

• Proteome Discoverer

• 60 Distinct Colors

• Deuteranopia, Protanopia, and Tritanopia

3. Click Save Current Settings.

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 14 Compound Discoverer configuration options
Set up the global color palette

Create new custom color palettes

When you create a custom color palette, you can select any of the colors in the color chart.

Y To create a custom color palette

1. Open the color schema view of the configuration page.

2. Click New.
The Color Palette Configuration dialog box opens.
Figure 220. Color Palette Configuration dialog box

3. Name the custom color palette.

4. Add selected colors to the custom color palette. See “Edit custom color palettes.”
5. Click Save.
The custom color palette appears as the selected palette in the Selected Palette list of the
Color Schema view.
6. To apply the new color palette, click Save Current Settings.

Delete custom color palettes

A custom color palette is any palette other than one of the four standard palettes.

Y To delete a custom color palette

1. Open the color schema view of the configuration page.

2. Select the custom color palette in the Selected Palette list.
3. Click Delete.

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 14 Compound Discoverer configuration options
Set up the global color palette

Import custom color palettes

Y To import a custom color palette

1. Open the color schema view of the configuration page.

2. Click Import.
3. Locate the color palette file (XML) and click Open.
The import color palette appears in the Selected Palette list.

Export custom color palettes

After you create a custom color palette, you can export it as an XML file.

Y To export a custom color palette

1. Open the color schema view of the configuration page.

2. Select the custom color palette that you want to export in the Selected Palette list.
3. Click Export.
4. Name the palette and click Save.

Edit custom color palettes

Y To edit a custom color palette

1. Open the color schema view of the configuration page.

2. Select the custom color palette that you want to edit in the Selected Palette list.
3. Click Edit.
The Color Palette Configuration dialog box opens.
4. Do any of the following:
• Add a color to the custom color palette. See “Add colors to a custom palette.”
• Insert a color into the custom color palette. See “Insert colors in a custom palette.”
• Replace a color in the custom color palette. See “Replace a color in a custom palette.”
• Remove a color from the custom color palette. See “Remove a color from a custom
palette.”
5. Click Save.
The name of the custom palette appears in the Selected Palette list.

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 14 Compound Discoverer configuration options
Set up the global color palette

Add colors to a custom palette

After you open a custom color palette for editing, you can add colors to it.

Y To add a color to a custom color palette

1. Open the color schema view of the configuration page.

2. Select the custom color palette that you want to edit from the Selected Palette list.
The Color Palette Configuration dialog box opens.
3. To add a color to a custom color palette, select the color in the gradient color chart.
4. Click Add.
In the Palette Colors area, the new color appears to the right of the current colors.
5. When you finish editing the color palette, click Save.

Insert colors in a custom palette

After you open a custom color palette for editing, you can insert colors.

Y To insert a color in a custom color palette

1. Open the color schema view of the configuration page.

2. Select the custom color palette that you want to edit from the Selected Palette list.
The Color Palette Configuration dialog box opens.
3. To insert a color in a custom color palette, select its insertion point—the color to the right
of the intended position—in the Palette Colors area.
4. Select the new color in the gradient color chart.

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 14 Compound Discoverer configuration options
Set up the global color palette

Figure 221. Color Palette Configuration dialog box with the basic options view
Selected color
Selected position for insertion

5. Click Insert.
In the Palette Colors area, the new color appears to the left of the currently selected color.
Figure 222. Custom color palette with the color red inserted to the left of the color green

6. When you finish editing the color palette, click Save.

Replace a color in a custom palette

After you open a custom color palette for editing, you can replace the colors.

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 14 Compound Discoverer configuration options
Set up the global color palette

Y To replace a color with another color

1. Open the color schema view of the configuration page.

2. Select the custom color palette that you want to edit from the Selected Palette list.
The Color Palette Configuration dialog box opens.
3. To replace a color with another color, select the color to replace in the Palette Colors area.
4. Select a color in the gradient color chart.
5. Click Replace.
6. When you finish editing the color palette, click Save.

Remove a color from a custom palette

After you open a custom color palette for editing, you can remove one or more colors.

Y To remove a color from a custom color palette

1. Open the color schema view of the configuration page.

2. Select the custom color palette that you want to edit from the Selected Palette list, and
then click Edit.
The Color Palette Configuration dialog box opens.
3. Select the color in the Palette Colors area.
4. Click Remove.
5. When you finish editing the color palette, click Save.

Select a color in the gradient color chart

The Color Palette Configuration dialog box that opens when you click either New or Edit in
the Color Schema view of the Configuration page includes a gradient color chart.

Y To select a color for a custom color palette in the gradient color chart

1. Open the color schema view of the configuration page.

2. Do one of the following:
• To add a color to a new custom color palette, click New.
The Color Palette Configuration dialog box opens. The Palette Name box is empty.

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 14 Compound Discoverer configuration options
Specify the default mzCloud mass tolerance settings

• To edit an existing custom color palette, select it in the Selected Palette list, and then
click Edit.
The Color Palette Configuration dialog box opens. The Palette Name box displays
the name of the custom color palette that you selected.
3. Do any of the following:
• Click a color in the hexadecimal color gradient chart.
• Enter an RGB formula or an HSB formula by typing numeric values or using the
slider.
• Select the Advanced Options check box and use the separate sliders for red, green,
blue, hue, saturation, and brightness.
Figure 223. Advanced Options view of the Color Palette Configuration dialog box

Advanced Options check box

• Enter the hexadecimal code.

Specify the default mzCloud mass tolerance settings

Use the Submit Single Spectrum to mzCloud Options view to set up the mass tolerance
settings for a manual mzCloud search. See “Search the mzCloud database for a matching
fragmentation spectrum.”

Y To set up the mass tolerance settings for a manual mzCloud search

1. In the application menu bar, choose Help > Configuration.

1. In the left pane of the Configuration page, under Miscellaneous settings, choose Submit
Single Spectrum to mzCloud Options.

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 14 Compound Discoverer configuration options
Set up a BioCyc account and optionally purchase a subscription

2. Do any of the following:

• For the mass tolerance of scans acquired in the Orbitrap mass analyzer, select the
units, and then type an appropriate value in the FT Mass Tolerance box.
• For the mass tolerance of scans acquired in the ion trap mass analyzer, select the units,
and then type an appropriate value in the IT Mass Tolerance box.
• If your processing workflows (for LC studies) include the Search mzCloud node,
select the Use mzCloud Node Settings check box to use the node settings. See
“Search mzCloud node.”
3. Click Save the Current Settings.

Table 212 describes the options for submitting single scans to the mzCloud database.
Table 212. Submit Single Spectrum to mzCloud Options view
Parameter Description
FT Mass Tolerance Specifies the mass tolerance for scans acquired with an FT mass
analyzer.

Default: 12 ppm
IT Mass Tolerance Specifies the mass tolerance for scans acquired with an ion trap
mass analyzer.

Default 0.4 Da
Use mzCloud Node When this check box is selected, the application uses the settings
Settings in the Search mzCloud processing workflow node if the analysis
included this node.

Default: Selected

Set up a BioCyc account and optionally purchase a subscription

Follow the instructions in the BioCyc User Login view on the Configuration page to set up
your BioCyc user account, subscription, or both.

To obtain access to all the BioCyc databases, you must do one of the following:
• If you do not have a BioCyc user account, you must create a new BioCyc account on the
Sign Up page of the BioCyc website, and then enter, test, and save your account
information in the BioCyc User Login view. When you create a new account, you
automatically have 30 days of trial access to all the BioCyc databases.
• If you already have an existing account, you can request a 30-day trial access period to all
the BioCyc databases. Or, you can purchase an individual subscription or an institutional
subscription. If you do not request a 30-day trial access period or purchase a subscription,
you will have access to only the EcoCyc and MetaCyc databases.

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 14 Compound Discoverer configuration options
Set up a BioCyc account and optionally purchase a subscription

To obtain access to all the BioCyc databases, do the following:

1. Open the BioCyc User Login view.
2. Do the following as needed:
• Create a BioCyc user account
• Purchase a subscription or request a free 30-day trial period
• Enter, test, and save your BioCyc user account information

Note To access the BioCyc website where you set up a user account, purchase a
subscription, or request 30 days of free trial access to all the BioCyc database, you must
have Internet access.

Open the BioCyc User Login view

Use the BioCyc User Login view of the Compound Discoverer application to test and save
your BioCyc credentials.

Y To open the BioCyc User Login view

1. From the application window, choose Help > Configuration.

The Configuration page opens.
2. In the left pane, under Miscellaneous settings, select BioCyc User Login.
The BioCyc User Login view appears at the right.
• If you have an organization subscription, the Organization Subscription area displays
the organization name in green. Otherwise, the area displays the following text in red:
No Valid Subscription Found.
• If you have already set up a BioCyc user account—that is, you have entered and
tested your credentials and saved the settings—the Username box displays your email
address. Otherwise, the following text appears in red under User Subscription:
No Valid Subscription Found.
Figure 224 shows the default BioCyc User Login page for a user without an organization
subscription and who has not entered and tested their BioCyc user account information.

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 14 Compound Discoverer configuration options
Set up a BioCyc account and optionally purchase a subscription

Figure 224. BioCyc User Login page for a user without a subscription

Instructions

3. Do one of the following:

• If you do not have a BioCyc user account, go to “Create a BioCyc user account.”
If the Username box is empty, you do not have a BioCyc user account or you have not
entered, tested, and saved your user account information.
• If you have a BioCyc user account, but you do not have access to all the BioCyc
databases that you want access to, go to “Purchase a subscription or request a free
30-day trial period.”

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 14 Compound Discoverer configuration options
Set up a BioCyc account and optionally purchase a subscription

Create a BioCyc user account

You must have Internet access to set up a BioCyc user account. You can access the Sign Up
page of the BioCyc website from the BioCyc User Login view of the Compound Discoverer
application.

Y To create a new BioCyc account

1. Open the BioCyc User Login view, if you closed it.

2. Go to https://biocy.org/new-account.shtml.
The Sign Up page of the BioCyc website opens.
3. Follow the instructions on the Sign Up page of the BioCyc website to create your new
user account.
4. Go to “Enter, test, and save your BioCyc user account information.”

Purchase a subscription or request a free 30-day trial period

To access all the BioCyc databases, you must have a user account and one of the following: a
paid subscription or an unexpired free trial period that provides access to all the BioCyc
databases.

Y To purchase a subscription or request a free 30-day trial period

1. Open the BioCyc User Login view, if you closed it.

2. Go to https://biocyc.org/thermofisher.shtml.
3. Follow the instructions on this page to purchase an individual subscription or an
institutional subscription or to request a 30-day free trial period.
You must be logged in to the BioCyc website to purchase a subscription. If the following
message appears when you click Checkout, log in as requested.

You can log in to the BioCyc website by clicking LOGIN at the top of most of the Web
site pages. See Figure 225.

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 14 Compound Discoverer configuration options
Set up a BioCyc account and optionally purchase a subscription

Figure 225. BioCyc Login page (top portion)

Enter, test, and save your BioCyc user account information

After you create your BioCyc user account on the Sign Up page of the BioCyc website, you
must enter, test, and save your account information in the BioCyc User Login view of the
Compound Discoverer application.

Y To enter, test, and save your account information

1. Open the BioCyc User Login view, if you closed it.

2. In the User Subscription area of the BioCyc User Login view, enter your user name (email
address) and password.
3. Below the Password box, click Test Credentials.
4. At the bottom right of the BioCyc User Login view, click Save Current Settings.
Figure 226 shows the subscription information for a new user account with unexpired
access to all the BioCyc databases.
Figure 226. Settings for a new user account with unexpired access to all the BioCyc databases

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 14 Compound Discoverer configuration options
Specify the fragmentation databases

Specify the fragmentation databases

Use the HighChem Fragmentation Options view to select the fragmentation databases.

Currently, there is only one available fragmentation database. This view is reserved for future
use.

Y To open the HighChem Fragmentation Options view

In the left pane of the Configuration page, under Miscellaneous Settings, select
HighChem Fragmentation Options.

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 15

Common operations for manipulating data tables

The following topics describe the common operations that you can perform on the tables in
the Lists and Libraries view, on the pages of a study, and in result files:
• Move table rows up or down
• Sort data tables
• Freeze table rows
• Group table rows
• Change the position of table columns
• Freeze table columns
• Show or hide table columns
• Copy table entries to the clipboard
• Filter the tables on a study page or a list or library view
• Set up a custom filter with multiple conditions

Move table rows up or down

Use the following procedure to move through the rows in a data table.

Y To move up or down through the rows of a result or library table

To move down, press the Tab key.

To move up, hold down the SHIFT key and press the Tab key.

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 15 Common operations for manipulating data tables
Sort data tables

Sort data tables

To sort the data tables, see these topics:
• Sort table entries by one or more columns
• Sort table entries by a column with a distribution map

Sort table entries by one or more columns

Y To sort the rows based on the contents of one or more columns

1. Click a column header to sort the rows between ascending order (A, B, C …) and
descending order (Z, Y, X …), based on the contents of the column.

Note The application treats formulas the same as text strings and sorts them by the
order of the characters in the formula string, not by the actual number of elements in
the formula.

2. To sort the data by a second column, hold down the CTRL key and click the second
column heading.

Sort table entries by a column with a distribution map

Y To sort a table by a column that contains a distribution map

1. Click the expand icon to display the vertical headings of the subordinate columns.
Column
heading
Expand
icon
Subordinate
column headings

2. Select the heading of the subordinate column that you want to sort by.
The selected subordinate column heading appears in bold text.
3. Click the column heading to sort the table rows.

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 15 Common operations for manipulating data tables
Freeze table rows

Freeze table rows

Use the following procedure to freeze table rows.

Y To affix rows at the top of the table

Click the pin icon, , next to the row number of the row that you want to freeze.
The row moves to the top of the table, its pin icon changes to the pinned position, , and
a blue bar that defines the bottom of the freeze pane appears below the fixed row.
As you fix additional rows, they move up to the freeze pane in the order selected and their
icons change to pinned, . The row just above the blue bar is the last fixed row.
When you scroll the table, the freeze pane remains at the top. Figure 227 shows a
compound library with caffeine in the freeze pane.
Figure 227. Compound library with a freeze pane

Blue bar that defines the

Pin icon to the right of the row number bottom of the freeze pane

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 15 Common operations for manipulating data tables
Group table rows

Group table rows

For a table on a study page, use the Enable Row Grouping shortcut menu command to group
items by a column heading.

Y To group and ungroup the table rows on a study page

1. Right-click the page and choose Enable Row Grouping.

The Group by Area bar appears above the table heading row.
2. Drag the column heading that you want to group by into the Group by Area bar.
Figure 228 shows the column heading for a study factor being dragged to the Group by
Area bar.
Figure 228. Group by Area bar above the table heading row

Column heading

3. To ungroup the table rows, drag the column heading out of the Group by Area bar.
Figure 229 shows the study factor (Phenotype) column heading inside the Group by Area
bar, and the table rows grouped by the study factor value (Lean, Fatty, or n/a).

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 15 Common operations for manipulating data tables
Change the position of table columns

Figure 229. Samples table grouped by phenotype

Column heading in the Group by Area bar

4. To turn off the group by row feature, right-click the page and choose Disable Row
Grouping.

Change the position of table columns

You can save the layout changes to a result table. Changes to the table layout in any of the
Lists & Libraries views are temporary.

To change the position of table columns, see the following topics:

• Change the column order
• Stack two table columns into one column

Change the column order

Y To change the order of the columns in a table

1. To move a column to the left of its current position, drag the column header to the left.
Release the mouse button when the cursor ( ) appears over the column delineator.

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 15 Common operations for manipulating data tables
Change the position of table columns

Note If you release the mouse button when the column-stacking cursor ( )
appears instead of when the column-reordering cursor ( ) appears, the application
stacks the two columns. See Stack two table columns into one column.

Figure 230. Moving a column to the left

Original Column 1 Heading Column 2 Heading Column 3 Heading
arrangement

Dragging
Column 1 Heading Column 2 Heading Column 3 Heading
column 3
Column 3 Heading
to the left

New Column 1 Heading Column 3 Heading Column 2 Heading

arrangement

2. To save the current layout for a result file, choose File > Save from the menu bar.

Note To save the current layout to a layout file that you can apply to other result files,
choose Window > Save Layout. Then, in the Save Result Layout dialog box, name
the layout and click OK.

Stack two table columns into one column

Stacking table columns can make it easier to compare the results in two table columns.

Figure 231 shows an example where the Area and Norm. Area columns of a compounds table
are stacked.
Figure 231. Stacked columns

Y To stack two table columns into one column

1. Drag the column header of the column that you want to stack below the column header
of the column that you want on top. Release the mouse button when the cursor ( )
appears over the column heading.

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 15 Common operations for manipulating data tables
Freeze table columns

Figure 232. Stacking two columns into one column

Original Column 1 Heading Column 2 Heading Column 3 Heading
arrangement 1 Column 1 Entry Column 2 Entry Column 3 Entry
2 Column 1 Entry Column 2 Entry Column 3 Entry

Dragging Column 1 Heading Column 2 Heading Column 3 Heading

Column 3 Heading
column 3 1 Column 1 Entry Column 2 Entry Column 3 Entry
into column 2 2 Column 1 Entry Column 2 Entry Column 3 Entry

New Column 1 Heading Column 2 Heading

arrangement Column 3 Heading
Column 1 Entry Column 2 Entry
1
Column 3 Entry
Column 1 Entry Column 2 Entry
2
Column 3 Entry

2. To save the current layout for a result file, choose File > Save from the menu bar.

Freeze table columns

In a result table, to more easily compare values in columns that are not next to each other, you
can lock columns in place so that they are always visible as you scroll through the unlocked
columns.

Note Except for the Input Files table, the Checked column is, by default, the first column
in every result table—that is, Checked is the text in first column’s heading row.

Y To lock table columns to the left of the first column

1. Right-click the table and choose Enable Column Fixing.

A pin icon, , appears to the right of each column heading.
2. Click the pin icons for the columns that you want to move to the left of the first column.
The columns move to the left of the Checked column and their pins face down, .

Show or hide table columns

Use the Field Chooser dialog box to show or hide columns in any of the result tables or tables
in the Lists & Libraries views. The changes to tables in any of the Lists & Libraries views are
temporary. You can save the layout changes to a result table by choosing Window > Save
Layout.

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 15 Common operations for manipulating data tables
Show or hide table columns

Note You can hide or show columns in these tables that are available from the Lists &
Libraries menu—Expected Compounds, Transformations, Neutral Losses, Adducts, and
Ion Definitions.

Y To show or hide columns in a list view or result table

1. Click the Field Chooser icon, , in the upper-left corner of the table.
Figure 233. Field chooser icon in the upper-left corner of the main Study Information table
Field Chooser icon

The Field Chooser dialog box opens with a list of all of the column headers for the
current table in alphabetical order.
Figure 234. Field Chooser dialog box for the Study Information table

2. In the Field Chooser dialog box, clear the check box for each column that you want to
hide. To show those columns again, select their corresponding check boxes.
The table updates and shows or hides your chosen columns immediately.

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 15 Common operations for manipulating data tables
Copy table entries to the clipboard

Copy table entries to the clipboard

You can copy a single table cell, a single table row, or multiple table rows to the Clipboard,
and then paste the Clipboard contents into other documents, such as a Notepad text
document or Microsoft Office documents.

Note The application does not copy the compound structure in the Structure column of
the Expected Compounds library to the Clipboard.

For details, see these topics:

• Copy the contents of a single table cell to the Clipboard
• Copy the contents of a single table row to the Clipboard
• Copy the contents of multiple rows to the Clipboard

Copy the contents of a single table cell to the Clipboard

Y To copy table cells to the Clipboard

1. Right-click anywhere in the table and choose Cell Selection Mode.

2. To select multiple table cells, use the CTRL key or the SHIFT key.
The selected cells turn a lighter blue than the other cells in the row, as shown in the
following figure.

Selected table cell

3. Right-click and choose Copy from the shortcut menu.

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 15 Common operations for manipulating data tables
Filter the tables on a study page or a list or library view

Copy the contents of a single table row to the Clipboard

Y To copy a single table row to the Clipboard

Do one of the following:

• To copy a single row to the Clipboard, right-click the row and choose Copy.
• To copy a single row and the table header, right-click the row and choose Copy with
Headers.

Copy the contents of multiple rows to the Clipboard

Y To copy multiple rows to the Clipboard

Do one of the following:

• To copy a range of contiguous rows to the Clipboard, while holding down the
SHIFT key, click the first and last row in the range. Then, right-click the last row to
open the shortcut menu and choose Copy to copy the row contents or choose Copy
with Headers to copy the row contents and the table header.
• To copy noncontiguous rows to the Clipboard, while holding down the CTRL key,
click each row that you want to copy. Then, right-click the last row to open the
shortcut menu and choose Copy to copy the row contents or choose Copy with
Headers to copy the row contents and the table header.

Filter the tables on a study page or a list or library view

For the tables on the study pages or in the Lists & Libraries views, use the filters in the filter
row below the column headers to reduce the number of entries in the current display. The
filtering effect is not permanent; closing a filtered list or study removes the filters.

Note For information about filtering the tables in the result files, see “Filter the data for
data reduction.”

To set up single-condition filters for the table columns, see these topics:
• Set up single-condition filters for the table columns
• Set up a single-condition wild card filter
• Set up a single-condition filter for numeric data

For information about setting up custom filters with the Custom Filter Selection dialog box,
see “Set up a custom filter with multiple conditions.”

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 15 Common operations for manipulating data tables
Filter the tables on a study page or a list or library view

Set up single-condition filters for the table columns

Y To set up filters for one or more table columns

1. In the table’s filter row, do the following for each column that you want to filter by:
a. Click the operator symbol (Aa or =) and select an operator from the list.
b. Set up the operand by selecting or typing a value in the operand box.
After you set up a filter, the applied filter icon, , appears to the right of the operand
box, and the table displays only those rows with entries that fulfill the filter condition.
2. To remove a single filter, click the filter icon, , to the right of the operand box.

Set up a single-condition wild card filter

Y To set up a wild card filter for a table column

1. In the operator list in the filter row, select Like (Wildcards) or Not Like (Wildcards).
2. In the operand box, select or type text and use an asterisk “*” to replace more than one
character or use a question mark “?” to replace only one character.

Tip For example, to filter the entries in the transformations library by the presence of
nitrogen in the arriving group, do the following in the Arriving Group column:
• Select * Like (Wildcards) in the operator list.
• Type *N* in the operand box.

Set up a single-condition filter for numeric data

Y To set up a filter for a table column with numeric data

Do any of the following:

• To set up a filter that uses a specific table entry in the operand list, select any of these
operators: Equals, Not Equals, Less Than, Less Than or Equal To, Greater Than, or
Greater Than or Equal To.
• To set up a filter that uses any of these operands: (Blanks), (NonBlanks), Above
Average, Below Average, Top 10, Top 10 percentile, Bottom 10, or Bottom 10
percentile, select either Equals or Not Equals in the operator list.
• To display the top n number of entries, select Top in the operator list and type an
integer value in the operand box.
• To display the bottom n number of entries, select Bottom in the operator list and
type an integer value in the operand box.

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 15 Common operations for manipulating data tables
Filter the tables on a study page or a list or library view

• To display the top n percentile of entries, select Top Percentile in the operator list
and type a numeric value in the operand box.
• To display the bottom n percentile of entries, select Bottom Percentile in the
operator list and type a numeric value in the operand box.

Operators and operands for a single-condition table filter

The filter for each table column consists of an operator and an operand. In an unfiltered table,
the filter row displays the default operator, which is represented by its symbol, and an empty
operand box for each column. To set up a table filter, you select the operator from a fixed list,
and you select the operand from a list or type a value in the operand box.

The selections in the operator list depend on whether the column contains text or numeric
entries. After you select an operator, the operator symbol appears in the filter row to the left of
the operand box. For more information about the operator lists, see Table 214 on page 748
and Table 215 on page 749.

For all columns, the operand list includes the following: Custom, Blanks, NonBlanks, and the
column entries. For numerical-entry columns, the operand list also includes the following:
Above Average, Below Average, Top 10, Top 10 Percentile, Bottom 10, and Bottom 10
Percentile. For more information, see Table 213.

After you set up a column filter, the applied filter icon, , appears to the right of the operand
box. Figure 235 shows a filtered Ion Definitions list that reduces the number of displayed
entries to 10 by using the total adduct mass. The filter row of the Adducts Total Mass column
displays the equals symbol ( )for the mathematical operator, the selection of Top 10 for the
operand, and the applied filter icon, .

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 15 Common operations for manipulating data tables
Filter the tables on a study page or a list or library view

Figure 235. Ion Definitions list that is filtered by the adduct mass
Operator
Operand
Applied filter icon

Filter
row

Table 213 describes the available operand selections and the valid typed operand entries for
both text and numeric columns.
Table 213. Operands for the table columns on a study page or Lists & Libraries view (Sheet 1 of 3)
Operand Description
All table columns
(Custom) Applies the custom filter that you set up by using the Custom
Filter Selection dialog box.

A custom filter contains more than one condition. If you set up a

single-condition filter, the operand box lists the single condition
rather than the (Custom) setting.
(Blanks) Compatible operators: Equals and Not Equals

(Blanks)—Displays the table rows that have blank entries in the

filtered column.

(Blanks)—Displays the table rows that have entries in the

filtered column.

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 15 Common operations for manipulating data tables
Filter the tables on a study page or a list or library view

Table 213. Operands for the table columns on a study page or Lists & Libraries view (Sheet 2 of 3)
Operand Description
(NonBlanks) Compatible operators: Equals and Not Equals

(NonBlanks)—Displays the table rows that have entries in the

filtered column.

(NonBlanks)—Displays the table rows that have blank entries

in the filtered column.
Selected entry Table 214 on page 748 describes the compatible operators for text
entries. Table 215 on page 749 describes the compatible operators
for numeric entries.

Filters the table rows by using the selected entry and operator.
Typed alphanumeric Table 214 describes the compatible operators for text entries.
text or numeric value Table 215 describes the compatible operators for numeric entries.

Filters the table rows by using the typed text entry and the selected
operator.
Additional selections for numeric value columns
Above Average Compatible operators: Equals and Not Equals

(Above Average)—Displays the table rows with numeric values

in the filtered column that are greater than the calculated column
average.

(Above Average)—Displays the table rows with numeric values

in the filtered column that are equal to or less than the calculated
column average.
Below Average Compatible operators: Equals and Not Equals

(Below Average)—Displays the table rows with numeric values

in the filtered column that are less than the calculated column
average.

(Below Average)—Displays the table rows with numeric values

in the filtered column that are equal to or greater than the
calculated column average.
Top 10 Compatible operators: Equals and Not Equals

(Top 10)—Displays the top 10 table rows for the filter

condition.

(Top 10)—Displays the table rows with numeric values in the

filtered column that are less than those of the top 10 table rows.

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 15 Common operations for manipulating data tables
Filter the tables on a study page or a list or library view

Table 213. Operands for the table columns on a study page or Lists & Libraries view (Sheet 3 of 3)
Operand Description
Top 10 Percentile Compatible operators: Equals and Not Equals

(Top 10 Percentile)—Displays the top 10th percentile of table

rows for the filter condition.

(Top 10 Percentile)—Displays the table rows with numeric

values in the filtered column that are less than those of the top
10th percentile.
Bottom 10 Compatible operators: Equals and Not Equals

(Bottom 10)—Displays the bottom 10 table rows for the filter

condition.

(Bottom 10)—Displays the table rows with numeric values in

the filtered column that are greater than those of the bottom 10
table rows.
Bottom 10 Percentile Compatible operators: Equals and Not Equals

(Bottom 10 Percentile)—Displays the bottom 10th percentile

of table rows for the filter condition.

(Bottom 10 Percentile)—Displays the table rows with numeric

values in the filtered column that are greater than those of the
bottom 10th percentile.

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 15 Common operations for manipulating data tables
Filter the tables on a study page or a list or library view

Table 214 describes the operators for columns with text entries.
Table 214. Operators for text columns
Symbol Text selection Effect
Equals Displays the text entries that exactly match the selected or
typed operand.
Not equals Displays the text entries that do not exactly match the
selected or typed operand.
Less than For alphabetic text entries, displays the text entries that
begin with a letter in the alphabet that comes before the
selected or typed operand.
Less than or equal –
to
Greater than –
Greater than or –
equal to
Contains Displays the text entries that contain the text in the selected
or typed operand.
Does not contain Displays the text entries that do not contain the text in the
selected or typed operand.
Like (wildcards) Displays the text entries that contain the selected or typed
text and any additional text represented by an asterisk.
Not like Hides the text entries that contain the selected or typed text
(wildcards) and any additional text represented by an asterisk.
Match (regular Displays the text entries that contain the same text as the
expression) selected or typed operand.
Does not match Displays the text entries that do not contain the same text as
(regular the selected or typed operand.
expression)
Starts with Displays the text entries that start with the selected or typed
operand.
Does not start Displays the text entries that do not start with the selected
with or typed operand.
Ends with Displays the text entries that end with the selected or typed
operand.
Does not end Displays the text entries that do not end with the selected or
with typed operand.

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 15 Common operations for manipulating data tables
Set up a custom filter with multiple conditions

Table 215 describes the operators for columns with numeric entries.
Table 215. Operators for numeric columns
Symbol Text selection Effect
Equals Displays the numerical entries that equal the selected operand.
Not equals Displays the numerical entries that are not equal to the selected
operand.
Less than Displays the numerical entries that are less than the selected
operand.
Less than or Displays the numerical entries that are less than or equal to the
equal to selected operand.
Greater than Displays the numerical entries that are greater than the selected
operand.
Greater than Displays the numerical entries that are greater than or equal to
or equal to the selected operand.
Top Displays the n highest entries in the table, where n equals the
integer typed in the operand box.
Bottom Displays the n lowest entries in the table, where n equals the
integer typed in the operand box.
Top Displays the entries in the top nth percentile, where n equals the
percentile percentage typed in the operand box.
Bottom Displays the entries in the bottom nth percentile, where n equals
percentile the percentage typed in the operand box.

Set up a custom filter with multiple conditions

Use the Custom Filter Selection dialog box to set up a custom filter with multiple conditions
for a library or list table or a table on a study page.

Y To set up a custom filter

1. Select (Custom) from the operand list for a table column.

The Custom Filter Selection dialog box opens.

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Set up a custom filter with multiple conditions

Figure 236. Custom Filter Selection dialog box with no conditions

2. Do the following for each condition that you want to add to a group:
a. Click Add Condition.
A new table row appears.
b. Select an operator from the Operator list and an operand from the Operand list.
As you add conditions to the group, the application updates the group filter in the
gray area below the table.
3. To add the last condition to the group, click its row number.
Figure 237. Clicking the row number in the last row to add the row to the group

Click the row

number.

The last condition appears in the group filter area. By default, the application applies the
AND operator to all of the conditions in the group (Figure 238). A vertical blue bar to
the left of the condition rows indicates an AND group.

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 15 Common operations for manipulating data tables
Set up a custom filter with multiple conditions

Figure 238. Group filter with three conditions and the AND group operator

Third condition

4. To change the group operator from AND to OR or from OR to AND, click Toggle.
An orange bar to the left of the condition rows indicates an OR group.
Figure 239. Group filter with three conditions and the OR group operator

5. To add an overlapping group to the filter, do the following:

a. Select the rows that you want to group, using the SHIFT key for contiguous rows or
the CTRL key for noncontiguous rows.
The selected rows are highlighted in blue and the ‘And’ Group and ‘Or’ Group
buttons become available.

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 15 Common operations for manipulating data tables
Set up a custom filter with multiple conditions

Figure 240. Selection of two noncontiguous rows

b. Specify the group type by clicking ‘And’ Group or ‘Or’ Group.

The application applies the second group definition and the Ungroup button
becomes available.
Figure 241. A set of filter conditions with two groups

6. To remove conditions from a group, select the conditions and click Ungroup.
7. To apply the filter, click OK.
The Custom Filter Selection dialog box closes, the text (Custom) appears in the operand
box, and the application applies the custom filter to the entries in the selected filter
column.

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 15 Common operations for manipulating data tables
Set up a custom filter with multiple conditions

Custom Filter Selection dialog box

Table 216 describes the features of the Custom Filter Selection dialog box.
Table 216. Custom Filter Selection dialog box features
Feature Description
Buttons or icons
+ Add Condition Adds a blank condition row to the condition table.
– Remove Condition(s) Removes the selected conditions. Selected conditions are
highlighted in blue.
‘And’ Group When the filter contains more than one group, applies the
AND group type to a set of selected conditions.
‘Or’ Group When the filter contains more than one group, applies the
OR group type to a set of selected conditions.
Toggle Changes the selected AND group to an OR group or the
reverse.
Ungroup As you create groups, group label columns appear to the left
of the Operator column.

When conditions belong to more than one group, removes

the second group condition for the selected conditions.
OK Closes the dialog box and applies the filter conditions.
Cancel Closes the dialog box without applying the filter conditions.
Table
Operator column Use to select an operator for the filter condition.

See Table 214 on page 748 for a list of the operators for the
text entry columns. See Table 215 on page 749 for a list of the
operators for the numerical entry columns.
Operand column Use to select or type an operand for the filter condition.

See Table 213 on page 745 for a list of the operands for the
library columns.
Third column Displays comments about the filter condition. For example,
this box displays “Condition is empty” until you define the
operator and the operand for a condition.
Filter description area
This area, which is highlighted in gray, displays the group filter conditions.

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 16

Explore compound relations with the molecular

networks viewer
To use the molecular networks feature to investigate possible relations between compounds in
the Compounds table, see the following topics:
• Overview of using the molecular networks feature
• How the Generate Molecular Networks node works
• Information displayed in the Similar Compounds table
• Send compounds to the molecular networks viewer
• Mark selected compounds in the main compounds table
• Modify the simulation in the molecular networks viewer
• Molecular networks viewer toolbar
• Panes at the left of the molecular networks viewer
• Pane at the right of the molecular networks viewer

Overview of using the molecular networks feature

To use the molecular networks feature, follow this process:
1. Process your raw data files with a processing workflow that includes the Generate
Molecular Networks node, which is a node under Compound Scoring.
2. To review the processed results, open the result file. See “Open, close, and update result
files.”
3. (Optional) Using the Result Filters view, apply a filter to display only the compounds of
interest.

Note For an LC study, the compounds must have MS2 scans.

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 16 Explore compound relations with the molecular networks viewer
How the Generate Molecular Networks node works

4. Do one or both of the following:

• To view a table of similar compounds, select a compound of interest in the
Compounds table. Then, open the related Similar Compounds Related table for the
selected compound.
• To view the molecular networks, follow the instructions in “Send compounds to the
molecular networks viewer.”
The viewer opens in a local browser window—that is, the viewer retrieves the data
from the current result file. The viewer does not connect to the Internet.

How the Generate Molecular Networks node works

To express the similarity between pairs of compounds, the Generate Molecular Networks
node uses the assigned elemental compositions and fragmentation data.

For an LC study, a minimum processing workflow that includes the Generate Molecular
Networks node consists of untargeted compound detection, grouping, and annotation
assignment. To validate the elemental composition differences, the workflow must contain at
least one search node or the Predict Compositions node.

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 16 Explore compound relations with the molecular networks viewer
How the Generate Molecular Networks node works

Figure 242. Example processing workflow with the Generate Molecular Networks node

The input to the Generate Molecular Networks node is a list of annotated compounds, and
the output from the node is a table of similar compounds for each detected compound.

Note If you do not select any transformations for the Generate Molecular Networks node,
the node does not consider the elemental compositions of the detected compounds for
scoring.

The node processes the data as follows:

1. Generates possible transformation pathways according to the user-specified settings.
• If there are multiple pathways to the same elemental composition, the node selects
the shorter pathway.

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 16 Explore compound relations with the molecular networks viewer
Information displayed in the Similar Compounds table

• If there are compounds with the same elemental composition (isomers with different
retention times), the node adds a pathway of length 0.
2. For each pair of compounds that have assigned elemental compositions, the node finds a
matching pathway that explains the elemental composition difference between the two
compounds.
3. For each pair of compounds that have fragmentation data, the node calculates the spectral
similarity by FISh Scoring as follows:
a. Matches the fragments for both compounds by directly comparing their masses.
b. For the remaining unmatched fragments, the node does the following to match the
fragments:
• Uses the mass shift of the assigned pathway to match “shifted” fragments (if
enabled). In addition, it uses all possible permutations of the individual pathway
steps (if enabled).
• Uses the mass shift between the two compounds to match “shifted” fragments (if
enabled).
c. Calculates the similarity scores.
4. Applies specified rules and thresholds to the connections (matched pairs).
5. Stores valid connections to the results file.
6. Applies specified view filters on the results table.

Information displayed in the Similar Compounds table

The Generate Molecular Networks node stores all the valid connections between each pair of
compounds and creates a related table of Similar Compounds. The table shows all the
connections between the selected compound and its related compounds, with additional
information about the similarity between them.

You can consider each stored connection as a reaction, where one compound is a substrate
that is converted into a product through a specific transformation pathway. The Direction
column indicates the direction of the reaction between the selected compound in the main
compounds table and the similar compound in the related Similar Compounds table.

A Forward connection indicates that the selected compound is a substrate, to which the
transformation has been applied to generate the similar compound. A Reverse connection
indicates that the selected compound is a product of applying the transformation to the
similar compound.

In Figure 243, paraxanthine is listed as a demethylation product of caffeine (substrate).

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 16 Explore compound relations with the molecular networks viewer
Send compounds to the molecular networks viewer

Figure 243. Caffeine and one of its demethylation products (the Tags column is hidden)

Send compounds to the molecular networks viewer

After you process a set of input files with a processing workflow that includes the Generate
Molecular Networks node, you can export the molecular networks for a specified number of
compounds to the molecular networks viewer. The viewer takes on the appearance of your
default browser, but it is not connected to the Internet.

Note For an LC study, you can export compounds to the molecular networks viewer from
the Compounds table.

Y To send the molecular networks to the viewer

1. (Optional) To display only the compounds of interest, filter the compounds table.
2. (Optional) Sort the compounds table by the columns of interest.

Note The application only exports compounds that appear in the table in the order
that they appear in the table, beginning with row 1. It does not export compounds
that are hidden by applied result filters or compounds in row numbers greater than
the Compounds Limit value.

3. Right-click the compounds table and choose Molecular Networks > Send to Viewer.
The Export Molecular Networks dialog box opens with the following default settings:
• Destination: Study folder where the current result file resides
• Name: Name of the current result file
• Compounds Limit: 3000
• Open Viewer After Export: Selected

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 16 Explore compound relations with the molecular networks viewer
Send compounds to the molecular networks viewer

Figure 244. Export Molecular Networks dialog box

4. Do any of the following:

• To change the destination folder, click the browse icon and select another folder.
• To change the name of the final folder where the application stores the web page
components, type a different name in the Name box.
• To change the maximum number of compounds to export, type a number from 1 to
3000 in the Compounds Limit box.

Note Increasing the number of compounds increases the processing time.

• To set the viewer to NOT automatically open in the default browser after you click
Export, clear the Open Viewer After Export check box.
5. Click Export.
If you selected the Open Viewer After Export check box and Internet Explorer is not the
default browser, the viewer opens in the Move mode ( ) in the default browser.
6. If you did not select the Open Viewer After Export check box, browse to the destination
folder. Then, right-click the index.html file and choose a browser.

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Mark selected compounds in the main compounds table

Figure 245. Choosing a browser for the molecular networks viewer

Note For the Internet Explorer browser, click Allow Blocked Content.

The viewer opens in the Move mode ( ) in the browser that you selected.
The browser does not connect to the Internet. The application derives the information
that it plots in the browser from the current result file.

Mark selected compounds in the main compounds table

You can copy the information for selected nodes in the molecular networks viewer to the
Clipboard, and then use this information to mark compounds in the Compounds table of a
result file for an LC study.

Y To mark selected compounds in a compounds table

1. Send compounds to the molecular networks viewer as described in “Send compounds to

the molecular networks viewer.”
2. Keep the compounds table open.
3. In the molecular networks viewer, do the following:
a. Turn on the selection mode by clicking the Selection Tool icon, . Then, click the
nodes that you want to select, one-by-one. Or, hold down the SHIFT key and drag
mouse cursor across the nodes that you want to select.

Note To deselect a single node, click it. To deselect multiple nodes, hold down
the CTRL+SHIFT keys and drag the mouse cursor across all the selected nodes.

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Mark selected compounds in the main compounds table

When you select a node it turns pink, and its molecular weight and retention time
appear in the Selected Items pane.
Figure 246. Molecular networks viewer with information about selected nodes in the
Selected Items pane

b. Click Copy.
The viewer copies the list of selected compounds to the Clipboard and displays
instructions about how to mark the selected compounds.
Figure 247. Instructions in the right pane about marking the compounds

4. Right-click the Compounds table for LC studies and choose Molecular Networks >
Mark Selected > one of the tags.

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Modify the simulation in the molecular networks viewer

Figure 248. Molecular Networks shortcut menu commands

The Compound Discoverer application marks the compounds in the result table that
match the selected items list from the Clipboard with the selected tag.
Figure 249. Marked compounds in the Compounds table

Modify the simulation in the molecular networks viewer

Use the molecular networks viewer to visualize the similarity between compounds of interest
and to tag compounds of interest in the compounds table.

Note For an LC study, you can visualize the similarity between the compounds in the
Compounds table for an untargeted workflow.

When you send compounds from a Compounds table to the molecular networks viewer, the
following occur:
1. The Compound Discoverer application sends the user-specified number of compounds to
the viewer. The application sends only compounds that are visible in the table, it does not
send compounds that are currently filtered out (with any of the result filters). In addition,
it sends the compounds in order of their row numbers, which can vary depending on how
you sort the table.
2. The viewer opens in a local browser window and displays the data in the current result
file; it does not connect to the Internet. The viewer processes the data and displays an
initial molecular network simulation using filter and threshold settings that you specified
in the Generate Molecular Networks workflow node.

In the left pane of the viewer, you can change the settings for the filters and the thresholds, the
node style, and the link style. In addition, you can search for a named compound or
transformation and isolate the display to a specific cluster.

In the right pane of the viewer, you can view information for each node or link that you point
to in the graph area.

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Modify the simulation in the molecular networks viewer

The viewer has three independent modes—Move, Seek, or Selection. When the viewer is in
one of the basic modes, you can turn the fourth mode—Isolation—on or off by
double-clicking a node. By default, the viewer opens in the Move mode ( ) where you can
move and rearrange the nodes.

For details, see these topics:

• Move, Seek, and Selection modes
• Use the Isolation mode to display specific clusters
• Use the Toggle Backbone tool to display the backbone of a cluster
• Color-coded nodes
• Change the node style to display a pie chart or a structure
• Size the nodes by peak area or MW of a compound
• Colorize a link by its score, coverage, or number of fragments
• Add directional arrows to the links
• Interactive functions performed by using the mouse pointer

Move, Seek, and Selection modes

The molecular networks viewer has three independent modes—Move, Seek, and Selection.
• Use the Move mode to move and rearrange the nodes.
• Use the Seek mode to reveal information about filtered links.
• Use the Selection mode to select individual nodes and add them to the export list where
you can them to the Clipboard.

The functions in the left pane are available in all three modes.

Move mode
The molecular networks viewer opens to the Move mode ( ) for moving and
rearranging the nodes.

Seek mode
When you turn on the Seek mode ( ), you can mark nodes as parent compounds.
Then, view connection details in the right pane. A parent compound is the starting
compound that undergoes chemical transformations.

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Modify the simulation in the molecular networks viewer

Y To view the connections for a parent node

1. Click the Seek icon, , in the toolbar at the top left of the graph pane to turn on the
Seek mode.
The right pane changes to the Seek Links pane.
2. Click a node of interest in the graph pane.
A red outline indicates the selected node. Information about the selected node appears in
the Seek Links pane.
3. Point to another node in the graph pane.
In the graph pane, a link appears between the parent node and the query node. If the two
nodes are linked, the link is black. If the nodes are not linked, the link is red.
A description of the query link appears in the Seek Links pane at the right.
• If the compounds are related through a transformation reaction, the Seek Links pane
describes the transformation with a black arrow showing the direction of the
transformation.
• If the compounds are not related through a transformation reaction, the Seek Links
pane describes the nonexistent link between the two compounds with a red X over
the black arrow.

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Modify the simulation in the molecular networks viewer

Figure 250. Seek mode showing a nonexistent link

Parent node
(2, 6-dimethyl-nonane)

The red X
indicates that
the link does
not exist.

Mouse cursor pointing to query node

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Modify the simulation in the molecular networks viewer

Selection mode
When you turn on the Selection mode ( ), you can select individual nodes
(compounds) and add them to the export list in the right pane of the view.
Table 217. Selection mode tasks
Task Procedure
Turn on the Selection mode. Click the Selection icon, , in the upper-left
corner of the plot area.
Select nodes. Turn on the Selection mode. Then, click the
nodes, one by one. Or, hold down the SHIFT
key and drag the mouse cursor across the nodes
that you want to select.

When you click a node, it turns pink, and its

molecular weight and retention time appear in
the Selected Items list.

Copy selected nodes to the Clipboard. In the Selected Items pane, click Copy.
Clear the export list. In the Select Items pane, click Clear.
Deselect nodes. Click each selected node one-by-one. Or, hold
down the CTRL+SHIFT keys and drag the
mouse cursor across the selected nodes.

When you click a selected node, its color turns

from pink to its original color and its molecular
weight and retention time disappear from the
selected items pane.

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Modify the simulation in the molecular networks viewer

Use the Isolation mode to display specific clusters

Use the Isolation mode to display only the cluster of interest. The graph displays the
connections to the selected node up to the maximum reaction depth that you specify under
Isolation. See “Isolation pane.”

Y To turn on the isolation mode to isolate a specific cluster

1. Double-click the node of interest.

2. To exit the Isolation mode, double-click the orange node—that is, double-click the node
that you clicked to enter the isolation mode.

Use the Toggle Backbone tool to display the backbone of a cluster

The backbone of a node cluster includes only the links with the highest confidence.

Y To view the backbones of the clusters in the molecular networks graph area

Click the Toggle Backbone icon, , in the molecular networks toolbar.

Figure 251. Graph area with five clusters with more than two nodes

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Modify the simulation in the molecular networks viewer

Figure 252. Backbone view

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Modify the simulation in the molecular networks viewer

Color-coded nodes
In the molecular networks viewer, the identification status for a compound is indicated by the
color of its node.
Table 218. Node colors for compounds in the Compounds table
Color Meaning
Light green The processing workflow identified the compound by its fragmentation
spectra during an mzCloud or mzVault library search.
Dark green The processing workflow identified the compound by its formula and a
database match (but not an mzCloud match).

The database match is from a mass list search or a ChemSpider search.

Blue For LC/MS/MS data, the processing workflow determined only the formula
of the compound.
Gray The processing workflow determined only the mass of the compound or the
mass of the compound does not match the formula annotation—that is, the
difference between the formula annotation and the observed mass is greater
than 5 ppm. This difference is highlighted by an orange background in the
Annot. ΔMass column.

Figure 253 shows the molecular networks display for the 13 compounds in the Compounds
table shown in Figure 254. Pointing to one of the gray nodes displays the information for the
unknown compound.
Figure 253. Pointing to one of the gray nodes shows the information for the unknown compound
without a formula

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Modify the simulation in the molecular networks viewer

Figure 254 shows the Compounds table for the 13 compounds that were sent to the
molecular networks viewer.

No. Description
1 Light green nodes represent the eight compounds that are identified by name and
formula and have mzCloud matches.
2 A dark green node represents the compound that is identified by formula and a
ChemSpider database match but does not have any mzCloud matches.
3 A blue node represents the unknown compound that has a formula annotation but
no database matches.
4 Gray nodes represent one compound that is identified only by its molecular weight
and two compounds that are identified by formula and molecular weight, but the
mass annotation for each of these compounds does not match the formula
annotation (Annot. ΔMass > 5 ppm).

Figure 254. Compounds table with identified and unidentified compounds

1 2 3 4

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Modify the simulation in the molecular networks viewer

Change the node style to display a pie chart or a structure

By default, the nodes appear as circles of different sizes depending on the confidence of the
match. You can also select to display the nodes as pie charts or to show the structure of the
compound they represent.

Y To display each node as a pie chart

1. In the left pane of the molecular networks viewer, click Node Style.
2. Do one of the following:
• Select the Show Confidence option.
Each node appears as a solid circle. The color of the node reflects the confidence of
the match.
• Select the Show Pie Charts option.
Each node appears as a pie chart of the relative areas of the compound in the study
groups. The color of the node’s border reflects the confidence of the match.
• Select the Show Structures option.
Each node appears as a circle with a molecular weight, formula, or structure. The
color of the node’s border reflects the confidence of the match.

Regardless of the node style, pointing to a node displays the following information about the
compound at the top of the right pane: name, formula, RT, maximum area (across the input
files), and number of fragments in the fragmentation spectrum.

The bottom of the right pane displays a pie chart for the relative areas of the compound in the
study groups or the separate input files when the analysis does not include study groups.

Figure 255 shows a pie chart for the relative areas for caffeine in samples collected from a
human subject in the morning versus the evening.

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Modify the simulation in the molecular networks viewer

Figure 255. Information displayed when you point to a node

Pie chart of the

relative areas for the
two study groups

Size the nodes by peak area or MW of a compound

In the molecular networks viewer, the node size is proportional to the Max. Area or MW of a
compound, depending on the option that you select.

Y To select whether the node size is proportional to the compound’s peak area or MW

1. In the left pane of the molecular networks viewer, click Node Style.
2. Select one of these options: By Area or By Mass.

Colorize a link by its score, coverage, or number of fragments

The molecular networks viewer displays links in the following colors: gray > orange >
dark-red. The link color is proportional to the MSn Score, the Forward or Reverse Coverage
(max), or the number of Forward or Reverse Matches (max), depending on the option that
you select. If a connection has no fragmentation data, the link appears as a dashed gray line.

Y To select a different option to colorize a link by

1. In the left pane of the molecular networks viewer, click Link Style.
2. Select one of these options: By Score, By Coverage, or By Fragments.

Tip By default, the link color is a function of the MSn score. The length of each link has
no meaning. To investigate the clusters, try colorizing the links by the other options.

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Add directional arrows to the links

By default, the connections between the nodes do not show the transformation direction.

Y To add directional arrows to the links

1. In the left pane of the molecular networks viewer, click Link Style.
2. Click the Show Arrows check box.
3. To display the transformation in the right pane, point to the arrow.
Figure 256. Pointing to a directional arrow for a link

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Molecular networks viewer toolbar

Interactive functions performed by using the mouse pointer

Table 219 describes the interactive tasks that you can perform with the mouse pointer in the
molecular networks viewer.
Table 219. Interactive functions in the molecular networks viewer
Task Procedure
Show information about a compound. Point to the compound.
(graph node)
Information about the compound appears in the
right pane, and all the compound’s relations are
highlighted in the graph area.
Show information about a graph link Point to the link (connecting line).
(relation).
Information about the connection between the
two compounds appears.

Molecular networks viewer toolbar

The toolbar at the top left of the graph pane includes eight tools.
Table 220. Molecular network viewer toolbar icons
Toolbar icon Tooltip Use
Move Tool Move and rearrange nodes.

Seek Tool Reveal missing connections between nodes.

Selection Tool Add nodes to the export list.

Toggle Isolation Isolate a node.

Toggle Backbone Display the backbone node connections in a

cluster. The backbone node connections in a
cluster are the connections with the highest
confidence.
Restart Simulation Restart the simulation in the graph area of the
molecular network viewer.
Stop Simulation Stop the simulation while it is processing.

Reset Pan and Zoom Reset, pan, and zoom in the graph area.

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Panes at the left of the molecular networks viewer

Panes at the left of the molecular networks viewer

The molecular networks viewer has the following panes to the left of the graphical display:
• Search pane
• Graph Info pane
• Isolation pane
• Filters pane
• Thresholds pane
• Clusters pane
• Node Style pane
• Link Style pane

Tip To open or close a pane, point to the upper-right corner of the pane to display the
Hide text or the Show text. When text appears, click it.

Figure 257. Dropdown panes to the left of the graphical display

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Panes at the left of the molecular networks viewer

Search pane
Use the Search pane of the molecular networks viewer to highlight nodes or links in the graph
area by searching for the name of a compound or the name of a transformation, respectively.

Task Procedure
Highlight nodes, in red, for In the Search pane, type the compound’s name in the
compounds with a specified text Compound box.
string in their names.
The viewer highlights all compounds with the
specified text string in the graph area.
Highlight links, in red, for the In the Search pane, type the transformation’s name in
same named transformation. the Transformation box.

Graph Info pane

The Graph Info pane of the molecular networks viewer provides a visual summary about the
compounds that you exported from the compounds table of a result file.

The two bar colors and the background color behind the bars represent the following:
• Blue bar—represents the relative portion of the currently visible items.
• Dark gray bar—represents the relative portion of all items of a particular type.
• Light-gray background—represents the total number of items.
Figure 258. Graph Info pane of the molecular networks viewer

Table 221. Graph Info pane of the molecular networks viewer (Sheet 1 of 2)
Parameter Description
Nodes Indicates the number of nodes in the graph area.
Orphans Indicates the number of nodes without any connection (according to
the current filters and thresholds).
Identified Indicates the number of compounds with an assigned name.

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Panes at the left of the molecular networks viewer

Table 221. Graph Info pane of the molecular networks viewer (Sheet 2 of 2)
Parameter Description
Unknown Indicates the number of compounds without an assigned name.
Links Indicates the number of all connections.
Transform. Indicates the number of connections with assigned transformations.
MSn Indicates the number of connections with fragmentation data.
Both Indicates the number of connections with assigned transformations
and fragmentation data.

Isolation pane
If the main graph is in the Isolation mode, the Isolation pane of the molecular networks
viewer provides dynamic control over the maximum depth of the graph.
Figure 259. Isolation pane of the molecular networks viewer

For information about turning on the Isolation mode, see “Use the Isolation mode to display
specific clusters.”

Filters pane
Use the filters in the Filters pane of the molecular networks viewer to limit the amount of
visible data.
Figure 260. Filters pane of the molecular networks viewer (default settings)

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Panes at the left of the molecular networks viewer

Table 222. Filters pane of the molecular networks viewer

Filter Description
Unknown Orphans Select to display compounds without a name or connection.

Default: Not enabled

Identified Orphans Select to display named compounds without a connection.

Default: Not enabled

Require Transformation Clear to display links without assigned transformations.

Default: Enabled
Require MSn Clear to display links without fragmentation data.

Default: Enabled

Thresholds pane
To show or hide low confidence relationships between compounds in the molecular networks
viewer, adjust the settings in the Thresholds pane. By default, the thresholds are set to those
specified in the processing workflow.
Figure 261. Thresholds pane of the molecular networks viewer

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 16 Explore compound relations with the molecular networks viewer
Panes at the left of the molecular networks viewer

Table 223. Thresholds pane in the molecular networks viewer

Threshold Description
Score Specifies the minimum MSn Score for a connection to be
visible.

Range: 0 to 100
Coverage Specifies the minimum Forward or Reverse Coverage for a
connection to be visible.

Range: 0 to 100
Matched Fragments Specifies the minimum number of matched fragments for a
Forward or Reverse search for a connection to be visible.

Minimum: 0

Clusters pane
Use the Clusters pane to limit the number of nodes per cluster. The viewer applies the Node
Links limit first and then applies the Cluster size limit. By default, the thresholds are set to
those specified in the processing workflow.
Figure 262. Clusters pane of the molecular networks viewer

Table 224. Clusters pane in the molecular networks viewer

Threshold Description
Node Links Specifies the maximum number of connections for a single
node, which limits the number of direct neighbors for each
node.

Range: 1 to 50
Cluster Size Specifies the maximum number of nodes within a single
cluster. As you reduce the cluster size, the algorithm
excludes nodes connected by links with lower scores.
Reducing the cluster size to 2 reduces the number of nodes
per cluster to two nodes with one shared link.

Range: 2 to 100

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 16 Explore compound relations with the molecular networks viewer
Panes at the left of the molecular networks viewer

Node Style pane

Use the Node Style pane to specify what determines the size of the node and whether to
display each node as a pie chart or a single color.

You can select either Show Confidence or Show Pie Charts and either Size by Area or Size by
Mass.
Figure 263. Node Style pane of the molecular networks viewer

Table 225. Node Style pane in the molecular networks viewer

Option Description
Show Confidence Displays each node as a solid color according to the confidence of
the identification. A matching spectrum in the mzCloud mass
spectral database provides the most confidence.
Show Pie Charts Displays each node as a pie chart of the relative areas of the
compound in each input file or each study group.
Show Structures Displays a structure when available on the node.
Size by Area Sizes each node according to the maximum area of the compound
relative to the other compounds.
Size by Mass Sizes each node according to the molecular weight of the
compound relative to the other compounds.
Uniform Size Displays all the nodes at a uniform size.

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 16 Explore compound relations with the molecular networks viewer
Pane at the right of the molecular networks viewer

Link Style pane

Use the Link Style pane to specify whether the connectors between the nodes display the
transformation direction and what determines the color of each connector.
Figure 264. Link Style pane of the molecular networks viewer

Table 226. Node Style pane in the molecular networks viewer

Option Description
Show Arrows Selecting this option turns on directional arrows for the
connectors.
Select the option that determines the color of each link.

The molecular networks viewer displays links in the following colors: gray > orange >
dark-red. If a connection has no fragmentation data, the link appears as a gray-dashed line.
Color by Score The link color is proportional to the MSn Score.
Color by Coverage The link color is proportional to the Forward or Reverse Coverage
(max).
Color by Fragments The link color is proportional to the number of Forward or
Reverse Matches (max).

Pane at the right of the molecular networks viewer

When you point to a link or node in the molecular networks viewer, information appears on
the right side of the viewer. For a link, the information pane displays the assigned pathway
name, elemental composition, mass difference, and fragmentation scores, followed by the
reaction from one compound to the other. For each compound, it shows the assigned name,
elemental composition, retention time, molecular weight, maximum area, and number of
used fragments.

The information automatically disappears from the right pane when you move the pointer
away from the node or link.

Tip To prevent the information about the selected node or link from disappearing or
changing when you move the mouse pointer, hold the SHIFT key while you move the
pointer.

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 16 Explore compound relations with the molecular networks viewer
Pane at the right of the molecular networks viewer

When the molecular networks view is in the Selection mode and you are not pointing to a
node or connector, the Selected Items pane appears to the right of the graphical display. For
details about creating a list of compounds to mark, see “Mark selected compounds in the
main compounds table.”

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 17

Test communication to the online databases

A typical Compound Discoverer analysis that identifies unknown compounds searches mass
spectrum databases on the Internet. To run these searches, the application must have
unblocked access to the mass spectral databases on the Internet.

The following topics describe how to test and troubleshoot the application’s access to the
online mass spectrum databases:
• Troubleshoot access to the online databases
• Run the communication tests
• Check the URLs for the online databases in your browser
• Specify the IP address of the proxy server
• Set the correct time and time zone on the processing computer

Troubleshoot access to the online databases

Y To test and troubleshoot the application’s access to the online databases

1. Run the communication tests. See “Run the communication tests.”

If the communication tests succeed, the application has access to the online databases.
2. If a communication test fails, do the following:
• If only the mzCloud communication test fails, check the Date and Time settings on
the processing computer. See “Set the correct time and time zone on the processing
computer.”
• If the Check BioCyc user credentials test for the BioCyc database fails, check the
subscription information in the BioCyc User Login view of the Configuration page.

IMPORTANT If you do not have an organization subscription for the BioCyc

database, you must create a BioCyc user account or obtain an individual
subscription, and then enter, test, and save your account credentials in the BioCyc
User Login view. See “Set up a BioCyc account and optionally purchase a
subscription.”

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 17 Test communication to the online databases
Run the communication tests

• If any of the other communication tests also fail, check the access to the URLs for the
online databases. See “Check the URLs for the online databases in your browser.”
If you can access the URLs for the online databases through your browser, but the
communication tests still fail, the firewall or proxy setting for your company network
is blocking the application’s access to the online databases.
3. If the communication tests fail, but you can access the URLs for the online databases, do
the following as applicable:
• If a firewall is blocking the application’s access to the online databases, ask your IT
department to make sure that the company firewall is not blocking “Thermo
Compound Discoverer” or “Thermo Compound Discoverer Server” from accessing
the URLs. The application uses the following protocol: http port 80.
• If a proxy setting is blocking access, see “Specify the IP address of the proxy server.”

Run the communication tests

Use the Communication Tests dialog box to test your processing computer’s access to the
online databases.

Y To verify that your computer has access to the external databases

1. From the menu bar, choose Help > Communication Tests.

The Communication Tests dialog box opens.
2. To open the page for the database that you want to access, click its tab.
3. Click Run Tests.
Figure 265 shows the communication tests in progress.

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 17 Test communication to the online databases
Run the communication tests

Figure 265. BioCyc communication tests

4. Depending on whether the communication tests are successful, do the following:

• If the tests are successful, your computer has access to the required databases on the
Internet and you can run analyses that require access to these databases.
• If only the mzCloud test fails, check the Date and Time settings for the processing
computer. See “Set the correct time and time zone on the processing computer.”
• If any of the other tests also fail, check the access to the URLs in your browser. See
“Check the URLs for the online databases in your browser.”

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 17 Test communication to the online databases
Check the URLs for the online databases in your browser

Check the URLs for the online databases in your browser

Table 227 lists the URLs for the online mass spectrum databases. If a communication test
fails, test the URL for the affected database.
Table 227. URLs of online mass spectrum databases
Database URL
mzCloud Identity https://www.mzcloud.org/
https://identity.mzcloud.org/
https://www.mzcloud.org/Services/MzCloudApiV1.svc
https://www.mzcloud.org/Services/MzCloudApiLightService.svc
ChemSpider http://www.chemspider.com
http://api.rsc.org/
KEGG: Kyoto http://www.kegg.jp/
Encyclopedia of Genes
http://rest.kegg.jp
and Genomes
https://proxy.online-licensing.net
BioCyc https://biocyc.org/
https://biocyc.org/web-services.shtml
https://tf.biocy.org

Specify the IP address of the proxy server

If the communication tests fail but you can access the online databases through your browser,
follow this procedure to specify the IP address of the proxy server.

Y To configure the IP address of the proxy server

1. Go to drive:\Program Files\Thermo\Compound Discoverer 3.3\bin\Config.

2. Open the Proxy.config file in Notepad.
3. Remove the text that is highlighted in yellow in Figure 266—that is, remove the XML
comment delimiters: <!-- and -->.
Figure 266. Proxy configuration setting with XML comment delimiters

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 17 Test communication to the online databases
Set the correct time and time zone on the processing computer

4. Replace the text that is highlighted in yellow in Figure 267 with your company proxy
address.
Figure 267. Default proxy address highlighted in yellow

Set the correct time and time zone on the processing computer
The mzCloud communication test includes a validation of the date and time settings on the
processing computer. If the mzCloud communication test fails, but the other communication
tests succeed, check the date and time settings for the processing computer.

Y To check the time and time zone settings

1. Open the Date and Time dialog box or view by typing Date in the Windows search box.

2. Make sure that both the date and time and time zone settings are correct.

Tip If your computer is not part of a network domain that synchronizes the
computer’s clock to the network server, you can use an Internet server to synchronize
the computer’s clock.

3. If the Internet Time tab is available, click it and synchronize the computer’s clock with an
Internet server.

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 A

Experiment design for comparison statistics

To understand how and when to use the biological replicate study factor, see these topics:
• Biological versus technical replicates
• Non-Nested versus nested experiment designs

Biological versus technical replicates

Biological replicates are samples from biological individuals (or non-biological entities) of the
same type under the same conditions and provide a measure of the variability associated with
these conditions.

Technical replicates are replicate samples from the same entity under the same conditions.
Technical replicates from the same entity under the same conditions provide a measure of the
sampling error, and replicate injections from the same sample solution provide a measure of
the instrument error.

You can add only one biological replicate factor to a study. The application treats study factors
nested under a biological replicate factor as technical replicates.

Non-Nested versus nested experiment designs

When you add a biological replicate factor to study, you can set up two different experiment
designs—nested and non-nested. In non-nested experiments, the biological replicates are
independent of each other—that is, you do not reuse individual entities to study multiple
condition states (study factor items).

In non-nested experiments, different sets of biological replicates are used for each condition.
Figure 268 shows a non-nested experiment where replicate samples are taken from two sets of
rats under two conditions. Tom, Jerry, and Hector are fed a normal diet; and Tai, Fernando,
and Pierre are fed a low-calorie diet.

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 A Experiment design for comparison statistics
Non-Nested versus nested experiment designs

Figure 268. Non-nested design with independent sets of rats for the two dietary conditions

Normal Diet Low-Calorie Diet

Different set of rats for each condition

Tom Jerry Hector Tai Fernando Pierre

1 2 3 1 2 3 1 2 3 1 2 3 1 2 3 1 2 3
Three technical replicates for each rat

In nested experiments, the same set of biological replicates are used for each condition.
Figure 269 shows a nested experiment where replicate samples are taken from the same three
rats under two conditions—a normal diet and a low-calorie diet. Tom, Jerry, and Pierre are
the biological replicates.
Figure 269. Nested design with the same three rats under two dietary conditions

Normal Diet Low-Calorie Diet

Same three biological replicates per condition

Tom
Rat1 Jerry2
Rat Hector
Rat 3 Tom1
Rat Jerry2
Rat Hector
Rat 3

1 2 3 1 2 3 1 2 3 1 2 3 1 2 3 1 2 3
Three technical replicates for each rat

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 A Experiment design for comparison statistics
Non-Nested versus nested experiment designs

To set up the comparison ratios for a nested design with technical replicates, add the following
study factors:
• A factor for the variable being studied with an itemized list of the variable states
• A biological replicate factor with an itemized list of the entities being studied
• (Optional) A factor for the technical replicates

Figure 270 shows the study factors for the experiment shown in Figure 269.
Figure 270. Study factors for the nested design experiment

Numerical factor

Categorical factor

Biological Replicate factor

Figure 271 shows the generated sample groups and ratios for the nested design. The sample
groups—Low-cal Diet and Normal Diet—are highlighted in green. The two sample groups
contain the same values for the Rat Biological Replicate factor—Tom, Jerry, and Pierre. The
technical replicates for each biological replicate are grouped together and the biological
replicates are highlighted in yellow. As shown in the Generated Ratios area, for each selected
denominator, the Differential Analysis node calculates one group ratio and individual ratios
for each biological replicate. In the result file, the Compounds table includes a Ratio column
for the group ratio and Bio. Rep. Ratio columns for the biological replicate ratios.

Note The application calculates p-values as follows:

• Uses the t-test when comparing two sample groups.
• Uses ANOVA when comparing more than two sample groups.

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 A Experiment design for comparison statistics
Non-Nested versus nested experiment designs

Figure 271. Nested design example

Thermo Scientific Compound Discoverer User Guide for LC Studies 791

 I

Index

A alignment features 63
Alignment Model parameter 228
Abort command, Job Queue 150
Alignment property, reporting 614
Activate button, License Manager 705
activation code, licensing 705 alignment, chromatographic 196, 205, 237, 470
activation request (.req) file 708 Allow Aromatic Cleavage parameter 362
ammonium adduct 272, 279
activation response file (activation.xml) 708
analyses
Activation Type parameter 234, 241
reprocessing 154, 156
Actual Size icon, reporting 608
reviewing 153
Add Column command 669 sample groups and ratios for 127, 142
Add Files command, study 173 submitting to the job queue 144
Add Items icon, reporting 607 troubleshooting 143
Add Plot command 402 Analysis pane 158
Add Structure Proposal command 377 Analysis Results page of a study 152
Add Tag command 376 analysis results, opening 334
adding Analysis Sequence Details window 153
adducts to the library 644 analysis summary 371
biological replicate factors to a study 39, 114 Analysis Validation Issues prompt 145
categorical factors to a study 112
Analyze Labeled Compounds node 270
charges to a structure 690
AnchorBottom property, reporting 614
compounds to the library 638
custom explanations to a result file 356 AND logical conjunction, filtering with 367–368, 370
fragments lists to the Compound Classes list 210 Angle property, reporting 617
input files to a new study 107 Annotate Full Spectrum Tree check box 362
input files to the Analysis pane 140 annotations
ion definitions to the library 649 copying 414
manual peaks to a specialized trace 400 editing 355
numeric factors to a study 113 fragmentation scan 408
page break after the page footer of a report 600 Appearance properties, reporting 614
transformations to the library 654 Appendix section, reporting 606
Adduct Editor 644 application
adducts menu bar 43
library 642 toolbar 48
Align Columns icon, reporting 607 applications, installing
Align Retention Times (ChromAlign) node Compound Discoverer 26
limitations 237 mzVault 28
Align Retention Times node Apply Dealkylation parameter 264
limitations 237 Apply Dearylation parameter 264
using 228 Apply Filters button, Result Filters view 371

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 Index: B

Apply FISh Scoring check box 357 biological replicate factor 114
Apply FISh Scoring command 377 blanks
Apply Missing Value Imputation node 285 Blank sample type 98, 119, 184
Apply mzLogic node 319 Exclude Blanks parameter 293–294
Apply QC Corrections node Mark Background Compounds node 199, 206, 290
parameter descriptions 286 Normalize Areas node 293–294
Apply SERRF QC Correction node 288 blocked IP addresses 783
arranging windows, tool for 58 blue circles, KEGG database 465
Arriving Group blue coverage bars in spectrum tree pane 537
data entry box 655 bond multiplicity, changing 701
parameter 656 borders, adding to a report template item 602
result table column 513 borders, adding to design items 602
Transformations library column 653 bracket, using in elemental composition formula 161
arrows Bulk Ratio Generation area 133
layout guide tool 58 By File check box, Analysis pane 144, 158
Metabolika pathway 678
molecular networks viewer 773
Assign command, Input File Characterization page 119
C
Assign Compound Annotations node 295 Calculate Score button 485
Atom Properties dialog box CanGrow property, reporting 617
using for charged fragments 691 CaptionPosition property, reporting 614
using for neutral compounds 702 carbon-14 labeled compounds 703
Auto Layout command, Workflows page 190 categorical study factors 39
AutoReplaceFields property, reporting 617 Caution symbol 191
auto-save option for studies 718 Caution symbol, Analysis pane 141
Autosize property, reporting 617 Caution symbol, Analysis view 143
Average Peak Width parameter 198, 257, 261 Ceiling selection, mass defect 231, 320
Avg. Exchange column 517 Cell Selection Mode command 375
axis labels Cell Selection Mode shortcut menu command 741
Hierarchical Cluster Analysis view 482 Character spacing property, reporting 614
Histogram Chart 421 Charge parameter 163–164, 167, 646
Scatter Chart 432–433 charge state parameter 239, 243
charge, adding to a structure 702
B charged structures 690
BackColor property, reporting 614 Chart Type parameter 427
Bar Chart page, displaying 423 Check All Down-Regulated Points command 463
Barcode design item 611 Check All Up-Regulated Points command 463
BarHeight property, reporting 614 Check icon, structure checking tool 696
base ions 208, 272, 279 Check Point command 434
batch effects, time dependent 84 Check Structure message box 696
Behavior properties, reporting 617 CheckAlignment property, reporting 617
best fit MS scan 505 CheckBox design item, reporting 610
best MS1 scan for a compound 71 Checked property filter, Result Filters view 365
best MS2 scan for a compound 72 Checked property, reporting 617
BioCyc credentials, saving 731 CheckSumEnabled property 617
BioCyc Pathways table 545 ChemSpider Results table 533
BioCyc Pathways view 467 Chromatogram Peaks table 489
BioCyc Results table 546, 550 Chromatograms view
shortcut menu commands 403
BioCyc User Login view 727
working with 405
Biological Replicate Factor 39, 114, 175, 788
chromatographic peak apex, red line indicating 505

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 Index: D

Clear All button, Result Filters view 371 Copy Image command 402
Clear Compound Annotation command 377 Copy Points command 402
Clear Frozen Content command 403 Copy with Headers command 375
Clipboard copying
pasting result table rows 375 Chromatograms view as a table of data points 402
pasting structures 375 Chromatograms view as an image 402
Close Sub-Report icon, reporting 607 Copy to Clipboard dialog box 163
Collapse All Column Headers command 376 elemental composition of a compound 161
collapsible left pane result tables 375
Chromatograms view 340 structures to the Clipboard 375
Mass Spectrum view 411 study factors 115, 175
Options pane, Result Charts view 416 cover page, report template 580, 605
Collect Small Segments parameter, Pie Chart 428 coverage bars in spectrum tree pane 537
Color legend, Scatter Chart view 433 CoverPage section, reporting 605
color map, selecting 719 Create Analog Trace node
color palettes, standard 720 connections 220
color schemes, selecting for a report template 573 parameter descriptions 246
color-coded named tags 345 Create FISh Trace node, parameter descriptions 248
ColumnCount property, reporting 619 Create Mass Trace node, parameter descriptions 250
ColumnDirection property, reporting 618 Create Pattern Trace node, parameter descriptions 252
columns, application table Create Report icon 568
changing the order 737 creation date, result file 372
stacking 738 CrossSectionBox design item 612
columns, report CrossSectionLine design item 612
aligning 602, 607 CSV files 61, 163, 375, 662
transposing 572 CTRL key, using 399
ColumnSpacing property, reporting 619 CTRL+SHIFT keys, deselect nodes by using 760
communication tests 783 Culture property, reporting 619
compatibility, software 25 Current Workflow Issues pane 143
Compound Annotation Editor dialog box 355 Custom Filter Selection dialog box, features 753
Compound Area Corrections view 472 Custom Isotope Ratio Pattern option 164
compound class editor 688 custom layout 354
compound class files, managing 687 custom tags
Compound Class Matches table 551 defining 345
Compound Class Scoring node 321 exporting 352
Compound Classes library 684 filtering by 351
Compound Classes library, modifying 682 importing 352
Compound Discoverer application window 43 saving to a TAGS file 352
Custom Tags Editor 345, 352
Compound Editor dialog box
for editing mass list compounds 671 Customize Report dialog box 570
shortcut menu 694 CV switching, FAIMS experiment 63, 242–243
using 638
compounds labeled with carbon-14 703 D
Compounds table 514 data points, minimum number for peak detection 257, 261
compounds, library of expected 635 Data properties, reporting 619
Configuration page 716 Data Source parameter 429
contacting us 30 Data Source, Scatter Chart 433
context menus for the result tables 374 DataField property, reporting 620
Continuous View icon, reporting 632 date and time information, reporting 570
Control sample type 98, 184 deactivating the software license 711
Copy command 434

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 Index: E

deactivation request file 712 Edit Sub-Report icon 596

dealkylation step, description 262 editors
decimal precision for Is Equal To filter 365 Adduct Editor 644
default layout, result file 355 biological replicate factor editor 114
Define from Elemental Composition Formula option 163 categorical factor editor 112
Degradants folder 210 Compound Annotation Editor 355
compound class editor 688
deleting
compounds, library 637, 643 Compound Editor 638
Fragment Editor 689
fragments, compound class 689
Isotope Ratio Editor 159
ion definitions, library 648
numeric factor editor 113
mass lists 665
Transformation Editor 654
raw data files, effect of 171
study factors 115 elemental composition
transformations, library 653 Expected Compounds view column 637
workflow nodes in the Workflow Tree pane 193 selecting a structure for 639
workspace sections, report template 600 Elemental Composition parameter 164
dendrograms 476 elemental composition, labeled compounds 703
Description box, working with 208 elements, changing 702
Descriptive Statistics view 453 EMF files 390
Deselect All Visible Points command 435 Enable Column Fixing command 375
Deselect Point command 434 Enable Column Fixing shortcut menu command 739
design items, report template Enable Row Grouping command 736
adding to a report template 601 Enabled property, reporting 618
Section Report pane 610 End property, reporting 622
Design properties, reporting 622 enhancements
DetailSection, reporting 605 for LC studies in the 3.3.0 release 36
Detect Compounds (Legacy) node 271 service pack release 33
deuteranopia, colormap for 720 Environmental folder 210
diamond pattern tool 58 error bars 440
Differential Analysis view 457 error messages, data processing 372
Dimension Lines icon, reporting 608 exclamation mark 192
direct match annotations 408 exclamation symbol 178
directional arrows exclusion list 382
layout guide tool 58 executing runs in parallel 716
Metabolika pathways 678 Execution State column
Discriminate By check boxes 341 Analysis Results page 152
Distance Function parameter 482 Job Queue page 151
Distribute Selection to All command 403 Expand All Column Headers command 376
double bonds 298 Expected Compounds library
Down Arrow, using 399 features 636
initial 635
downloading documents 22
dragging input files to the Analysis pane 140 Expected Compounds per File table 506
Expected Compounds view 636
drawing
Metabolika pathways 676 Expected Features per File table 508
structure annotations 355 Expected Finder node
connections 221
using 194, 196–197
E Expected Formulas table 510
E and L folder 210 experimental variables 39
Edit button, Analysis pane 158 Export > As Mass List command 388–389
Edit Compound Annotation command 376

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 Index: F

Export > Compounds to a New mzVault Library automatic peak width detection algorithm 237
command 378 Find icon, reporting 629
Export > Single Compound to an Existing mzVault Library Find Missing Files command 181
command 378 firewalls 784
Export As Xcalibur Inclusion/Exclusion List command 378 FISh coverage score 79
Export Image As command 402 FISh scoring
Export Points As command 402 applying to targeted compounds 408
Export Spectra node applying to untargeted compounds 409
connections 220 FISh Scoring node
parameter descriptions 226 connections 220
Export to Existing Mass List dialog box 389 using 253
Export to New Mass List dialog box 388 FISh Scoring Queue view 486
Export to Text File command 375 FISh Trace Fragments table 492
exporting Fit Page icon, reporting 632
compounds to a new mzVault library 387 Fit Width icon, reporting 632
custom tags 352 Floor selection, mass defect 231, 320
data to a CSV file 381 flowchart, reporting 564
mass list for the TraceFinder application 385 fold change 457
reports 630
folder structure 99
single compound to an existing mzVault library 386
Font property, reporting 615
study information 100
Xcalibur inclusion/exclusion lists 382 Food Research folder 210
ForeColor property, reporting 615
Extract Sample Information From Sample Names
dialog box 120 Forensics folder 211
Format Border dialog box, report template 602
FormatString property, reporting 615
F Forward connection, molecular networking 757
Factor Unit box, numeric factor 113 Fractional Mass selection, mass defect 231
factory default result file layout 353 Fragment Editor 689
Factory Defaults command 418, 423, 427, 432 Fragment Mode parameter 249
FAIMS-MS experiment 63 FreeStyle data-visualization application 163
Features table 525 Freeze Content command, Chromatograms view 403
Field Chooser icon, using to show or hide columns 740 freeze pane 735
file path, input files 177 full gap
Files for Analysis area 140 Missing Value Imputation node 285
Fill Gaps node
connections 218
parameter descriptions 280
G
Filter By check boxes 341 GdiCharSet property, reporting 615
Filter By check boxes, Chromatograms view 340 GdiVerticalFont property, reporting 615
Filter By Mass Defect node 230 gear icon, workflow nodes with 155
Filter By Scan Event node 233 Generate Expected Compounds node
Filter Centroids node 236 connections 221
using 261
filter set file
saving 366 Generate Molecular Networks node 322
summary 373 Get from Clipboard button, Isotope Ratio Editor 162
Filter Summary page 373 Get from Composition Formula button, Isotope Ratio
filters summary 373 Editor 162
Find dialog box, reporting 630 global settings 716
Find Expected Compounds (Legacy) node Go to Same Item in Main Table command 378
automatic peak width detection algorithm 237 gray status rectangle 495–496
Find Expected Compounds node 255, 258 green background, table cell with 559

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 Index: H

green circles, KEGG database 465 Impurities folder 211

green status rectangle 495–496 imputation methods 94
grid ruler, horizontal size 627 In ChemSpider column, Predicted Compositions table 302
Group By check boxes 341 InChi string, pasting from the Clipboard 639
Group By check boxes, Chromatograms view 340 inclusion list 382
Group By Sample check box 342 inclusion/exclusion lists, exporting 382
Group Compounds node 282 indenting a related table in report templates 572
Group Expected Compounds node indenting columns in report templates 576
connections 221 indicator icon, Result Filters window 367
parameter descriptions 266 Individual Traces parameter 248
grouping table rows 736 Input File Characterization page 109
groups, sample 129 Input File Selection page 107
guide tool 58 input files
adding to a new study 107
H dragging to the Analysis pane 140
modifying the location of 178
heat map 478
Input Files page of a study 176
Height property, reporting 622
Input Files table 493
Help menu 47
installation instructions 25
hidden
Internet Explorer, set as default browser 410
result tables 344
Ion Definition Editor dialog box 650–651
table columns 739
Ion Definitions library
Hide Grid icon, reporting 608
adding ion definitions 649
Hierarchical Cluster Analysis view 476
deleting entries 648
hierarchy of the study variables, changing 130 description 645
HighChem Fragmentation Options view 732 exporting 649
Highest Charge State parameter 239 features 646
high-mass compounds, predicted composition for 299 IP addresses, blocked 783
Histogram Chart Isolation tool 774
displaying histograms 418 Isotope check box 702–703
parameters 418
isotope pattern
hydrogen-to-carbon ratio 298 brackets, using to identify isotopic atoms 161
Hyperlink property, reporting 620 custom 164
intensity tolerance 272, 299
I Pattern List Editor 166
reevaluating precursors 245
Identification Only sample type 98
Isotope Ratio Editor, using 159
Ignore text pattern button, using 126
Isotope Ratios parameter 252
image files
adding pictures to a report template 611 isotopologues 87, 520
changing the logo image in a report template 582 Isotopologues Distribution Chart 442
saving data points to 390
selecting the logo image for a report template 573, 577 J
Image property, reporting 620 Job Queue page 146
images of graphs 390 jobs
importing processing in parallel 727
compound class files 687 promoting 148
compound library 61
custom tags 352
ion definition libraries 649 K
mzVault libraries 673 KeepTogether property, reporting 618
transformation libraries 654 KEGG Pathways table 547

Thermo Scientific Compound Discoverer User Guide for LC Studies 797

 Index: L

Kendrick Formula 231, 320 logo image

Known Structure Formats list 691 changing 582
report templates 570
selecting 573
L Lowest Charge State parameter 239
Label design item, reporting 591, 610
Label Style parameter 428
labeled compounds 161, 252
M
Labeled Compounds per File table 530 Manual Peak Integration command 405
Labeled Features table 529 Manual Peaks table 494
Labeling Status column 520 manual peaks, comparing to an XIC trace 200
Labels Font parameter 428 Map to BioCyc Pathways node 313
landscape orientation 627 Map to KEGG Pathways node 314
landscape paper orientation, report template 577 Map to Metabolika Pathways node 315
Last Changed parameter 175 Mark Background Compounds node
layout files, result 353 connections 218
parameter descriptions 290
Layout properties, reporting 622
Mass Analyzer parameter 240
layout, result table
moving the columns to the left or right 737 Mass Defect Plot view 445
stacking two table columns into one column 738 Mass Defect Type parameter 231
Leaving Group Mass List Search Results table 535
parameter, Transformation Editor 656 mass lists
result table column 513 exporting compounds to a new mass list 388–389
Legend Size command 404 Mass Lists library 661, 667
libraries mass range switching 63, 242
adducts 642 mass spectrometers, HRAM 275
compound classes 683 Max. Collision Energy parameter 234, 241
expected compounds 635 Max. Concurrent Entries, Xcalibur exclusion list 384
ion definitions 646 Max. Depth parameter 362
mass lists 661 Max. Occurrence parameter 656
license activation methods, online 708 Max. Precursor Mass parameter 239
License Deactivation dialog box 711 Max. Wavelength parameter 247
License Manager page 704 Maximum Shift parameter 229
license, software MaxLength property, reporting 620
activation 708 menu bar, application 43
deactivation 711
Merge Features node 200, 269
Life Sciences Mass Spectrometry Software Download and
Merged Features table 494
Licensing Portal 709
Metabolika Pathways table 549
Line design item 611
Metabolika Pathways view 470
Line Weight property, reporting 615
Metabolika pathways, deleting, importing, exporting, or
LineColor property, reporting 615
replacing 675
lines, adding to report templates 572
Metabolism folder 211
LineSpacing property, reporting 615 Metabolomics folder 211
LineStyle property, reporting 615
Min. Collision Energy parameter 234, 241
Linkage Method parameter 482
Min. Precursor Mass parameter 239
Lipidomics folder, workflow templates 211 Min. Wavelength parameter 247
Load button, Scatter Chart view 432
Minimum Peak Count parameter 240
Load Custom Tags Editor Settings dialog box 352 minimum peak intensity setting, recommended 275
Load Filter Set dialog box 371
mirror plots
Location property, reporting 622 add to a report template 587
creating 410

Thermo Scientific Compound Discoverer User Guide for LC Studies 798

 Index: N

graph type 590 Node Style pane 780

mirror structures 699 nodes, workflow
Miscellaneous properties, reporting 623 connections 220
missing chromatographic peak areas 94 parameters 225
missing files, resolving 179 Nominal Mass Rounding parameter 231, 320
mobile phase, background compounds in 290 Normalize Areas node
MOL string, pasting from the Clipboard 639 connections 218, 222
molecular network viewer parameter descriptions 292
adding directional arrows 773 normalized areas, viewing 456
color-coding the links 772, 781 Nucleon Number list 703
Move tool 774 number of spectra forwarded, data processing 372
moving table columns in a result table 737 Numerical Factors 39
MS Order parameter 233, 240, 250, 253 NWRatio property, reporting 615
MS2 column 503, 521
MultiLine property, reporting 618 O
Multipage view icon, reporting 632 obsolete workflow nodes 155
multiple chromatograms, overlaying 399 Open Analysis Template command, study 173
mzCloud offline libraries 71 Open Common command, Workflows page 190
mzCloud Results table 537 Open Response File dialog box 710
mzCloud search node 304 opening
mzCloud Similarity button 485 Atom Properties dialog box 702
mzCloud, submitting a single sample to 726 existing studies 171
mzLogic Analysis view 484 report templates 568
mzLogic score 484 structure files 691
mzVault libraries Options pane, Scatter Chart view 433
adding compounds 386 OR logical conjunction, filtering with 368, 370
creating new 387 orange background, table cell with 559
mzVault Results table 540 orange status rectangle 495
Order, result table column 513
N Orientation parameter, Custom Report dialog box 577
n/a assignment, study factor 127 orientation, report template page 570
n/a label on a workflow node 155 OutputFormat property, reporting 616
NarrowBarWidth property, reporting 615 Overlay Cell Size box, Metabolika Pathways view 470
negative charge option 691 overlaying multiple chromatograms in one plot 399
nested experiments 39
nested statistical models 114 P
neutral losses Padding property, reporting 622
detection and visualization 81 page break, adding to a report 600
Neutral Losses node 327 page numbers, adding to report templates 570
Neutral Losses result table 554 page orientation, selecting for a report 573
New Analysis command, study 173 Page Thumbnails pane, reporting 633
New Study and Analysis Wizard PageBreak design item, reporting 611
Extract Sample Information From Sample Names
PageFooter section, reporting 605
dialog box 120
PageHeader bar, reporting 586
Input File Characterization page 109
PageHeader section, reporting 605
Input File Selection page 107
Sample Groups and Ratios page 127 Pan Mode icon, reporting 609, 633
Study Name and Processing Workflow page 102 paper size
NewColumn property, reporting 620 PaperKind parameter, Custom Report
dialog box 570, 577
NewPage property, reporting 621
selecting for a report 573

Thermo Scientific Compound Discoverer User Guide for LC Studies 799

 Index: Q

Parallel Options view 716 protanopia, colormap for 720

parallel processing 727 proxy server 786
parameter settings, processing workflow 372 publications, images for 390
partial gap p-values
Missing Value Imputation node 285 Differential Analysis node 206
Partial Least Squares - Discriminant Analysis view 463 result table column 559
Pattern List Editor 166 volcano plot 457
Pattern Scoring node
connections 223 Q
parameter descriptions 326
QRCode property, reporting 624
PDA detector, chromatograms 246
Quality Control sample type 98
PDF file type, exporting reports 630
QuietZone property, reporting 616
peak area imputation 94
peak rating filter
description 65 R
parameter settings for 283 Radius property, reporting 622
per- and polyfluoroalkyl substances 89 ratios, generating 133
PFAS 88 RDBE calculation 298
Phase red background, table cell with 559
parameter 656 red bar, heat map 477
result table column 513 red circle with exclamation symbol 178
Picture design item, reporting 611 red circles, KEGG database 465
PictureAlignment property, reporting 616 red line, vertical 505
pie charts, parameter descriptions 427 red status rectangle 495–496
pinning reference file for retention time alignment 63
Options panel, Scatter Chart view 417 Refresh button, Scatter Chart view 433
result table columns 375
Refresh command 417
study or result files on the Start Page 53
Regular Expression Builder area, Extract Sample Information
table rows 735
from Sample Names dialog box 126
plot grid, Scatter Chart view 433
regular expression operators 123
Polarity Mode parameter 235, 242
Related Structures table 512
Polarity parameter 250, 253
related tables
polarity switching data 196 basic targeted workflow 201
polarity, ionization 142, 249–250, 253 indenting in a report template 572
pooled quality control samples 84 untargeted workflow 207
portrait orientation 627 Relative Intensity command 405
portrait paper orientation, report template 577 Relative Mass Defect parameter selection 231
positive charge option 691 Remove All Plots command 402
Predict Compositions node 297 Remove All Tags in All Tables command 376
Predicted Compositions table 542 Remove Analysis Result Files message box 178
presentations, images for 390 Remove Files command, study 173
Principal Component Analysis view 446 Remove Input File message box 178
PrintAtBottom property, reporting 618 Remove Plot command 402
printing reports 631 Remove Tag command 376
Process Response File button 710 removing
Processing Message Summary page 372 chromatogram plots 398, 402
processing messages summary 372 color schemes 574, 577
product ID for software license 705 completed runs from the job queue 148
Progress column, Job Queue 151 input files from the Input Files page 178
Promote button 148 result or study files from the Start Page 53
reordering table columns in a result file 737

Thermo Scientific Compound Discoverer User Guide for LC Studies 800

 Index: S

RepeatToFill property, reporting 618 Compounds 514

report designer page Expected Compounds per File 506
description 578 Expected Features per File 508
opening 580 Expected Formulas 510
shortcut menu 609 Features 525
Report Preview dialog box, reporting 628 FISh Trace Fragments 492
Report Print dialog box, reporting 628 Input Files 493
report resolution page 629 KEGG Pathways 547
Labeled Compounds per File 530
report resolution page, reporting 628
Labeled Features 529
ReportInfo design item, reporting 612
Manual Peaks 494
reporting
Mass List Search Results 535
Customize Report dialog box, using 570
Merged Features 494
exporting reports 630
Metabolika Pathways 549
previewing reports 628
Metabolika Results 550
printing reports 631
mzCloud Results 537
properties
mzVault Results 540
Appearance 614
Neutral Losses table 554
Behavior 617 Predicted Compositions 542
Data 619 Related Structures 512
Design 622 Specialized Traces 497
Layout 622 Statistical Methods 556
Miscellaneous 623 Structure Proposals 499
report templates Transformations 513
creating 570
retention time alignment 63
data-and-time stamp, adding to reports 582
Retention Time Correction view 470
editing 578
for LC studies 567 Reverse connection, molecular networking 757
page numbers 570 reviewing
Reprocess command, Analysis Results page 152 analyses 152
reprocessing an analysis 154 result files 333
RichTextBox design item, reporting 611
request file, activation process 708
right-click menus for the result tables 374
requirements
minimum number of data points for peak RightToLeft property, reporting 618
detection 257, 261 ring equivalents 298
requirements, software and hardware 23 rotating structures 698
Reset button, Customize Report dialog box 577 Rotation property, reporting 616
resetting factory default layout, result file 353 Round selection, mass defect 231, 320
resizing structures 698 Row Selection Mode, shortcut menu selection 161
Resolution parameter 164 rows, table
restoring, factory default layout 353 copying 741
pinning 735
Result Charts view 416
sorting 734
Result Exporter node 331
RT Offset parameter 246
result files
rulers, report template 622, 627
naming 158
opening 334 Run command, Analysis pane 145, 158
Result Filters view 362 runs
parallel processing 716
result tables
BioCyc Pathways 313 promoting 148
BioCyc Results 546, 550
ChemSpider Results 533 S
Chromatogram Peaks 489 S/N Threshold parameter 243
Compound Class Matches 551

Thermo Scientific Compound Discoverer User Guide for LC Studies 801

 Index: S

Sample Groups and Ratios page 127 Shape design item, reporting 611
sample groups and ratios, analysis summary 371 SHIFT key, using 733
sample types 184 Shift key, using 399, 760
Samples page of a study 182 shifted match annotations 408
Save As icon, report designer page 606 shortcut menu commands
Save Common command, Workflows page 190 Chromatogram View 401
Save Custom Tags Editor Settings dialog box 348 Compound Editor dialog box 694
Save Filter dialog box 371 for result tables with a Structure column 375
saving for result tables with a Tags column 376
all changes to open pages 44 Mass Spectrum View 414
analysis templates 158 molecular network viewer 377
auto-save option for studies 718 report designer page 609
BioCyc credentials 731 result tables 374
current page 44 tabbed documents 57
custom tags to a TAGS file 352 Show All Tables check box, Result Filters view 364, 371
data points to a text file 61 Show Details icon, Input Files page 177, 180
data points to image files 61 Show Detected Peaks command 404
filter sets 366 Show Dots icon, reporting 608
processing workflow templates 190, 224 Show Gridlines command 404
report templates 606 Show Legend command 404
result file layout 353 Show Lines icon, reporting 608
study factors 113, 115, 175 Show Standard Errors command 440
Scale Areas node 293 Show Tooltips command 403
scaling factor, chromatographic peak area 294 ShrinkToFit property, reporting 619
Scan for Missing Features button, License Manager 713 side-by-side view arrangement 59
Scan Polarity parameter 249 Single Page View icon, reporting 632
Scan Type parameter 235, 241 Size property, reporting 622
Scripting Node 331 SizeMode, reporting 622
Search ChemSpider node 301 sizing bar, report designer page 600, 604
Search Mass Lists node 302 Small Slice Collection parameter, Pie Chart 429
Search mzCloud node 304 Small Slice Threshold (%) parameter 429
Search mzVault node 309 Snap Lines icon, reporting 608
Search Neutral Losses node 327 Snap to Grid icon, reporting 608
Search Results icon, reporting 633 Snapshot Mode icon, reporting 630, 633
sections, report designer page 604 software requirements 23
Seek tool 774 sorting
Select All Visible Points command 435 analyses on the Job Queue page 149
Select Mode icon, reporting 608 distribution maps, result table 734
Select Spectra node result table rows 734
connections 220 study variables 131
parameter descriptions 237 Sorting icon, study variable 131
using 236 Specialized Traces table 497
Select/Deselect Item in All Groups icon 133 Specify FISh Scoring Settings dialog box 360
Selection mode 766 Spectrum Maximum parameter 247
Selection Mode icon, reporting 630, 633 spreadsheet
selection mode, choosing 700 exporting data to 375, 379
Selection tool 774 exporting the contents of a report 630
Selection Tool, using 700 stable isotope labeling experiments 87, 270, 442, 520
Set As Input File To shortcut menu command 184 Stable Isotope Labeling folder 212
Set Sample Type To command 119, 183 stacking table columns in a result file 738
Set Tags command 376 stacking the views 59

Thermo Scientific Compound Discoverer User Guide for LC Studies 802

 Index: T

Standard Mass Defect parameter selection 231 changing the sort order 131
Standard sample type 98, 184 hierarchy 131
Start Page Style property, reporting 616
hiding 53 SubReport design item, editing 607
icon 49 Summaries view 371
pin icon 53 summaries, processing 371
recent file lists 53 Summed Trace parameter 248
shortcut menu 57 SupplementOptions property, reporting 616
Start property, reporting 623 symbol, Caution 191
Statistical Methods table 556 symbols
status columns exclamation mark 192
Expected Finder, Consolidated Peaks table 496 synchronizing the computer’s clock 787
Unknown Detector, Consolidated Peaks table 496
systematic error removal with random forests (SERRF) 85
structure
cleaning 699
copying to the Clipboard 391 T
creating a mirror image 699 table rows
moving 701 copying 741
resizing 698 grouping 736
rotating 698 pinning 735
saving 703 sorting 734
structure drawing tools, using 693 tables
Structure Editor module filtering 742
Atom Properties dialog box 701 freezing columns 739
bond multiplicity 701 sorting 734
bond properties 701 Tag property, reporting 621
clean structure 699 Tags column 376
structure files, opening 691 TAGS file 352
Structure Proposals table 499 tags, named and color-coded 345
structures tags, result table 345
checking validity 696 template tool, using 695
mirror 699 text file 61
resizing 698
Text property, reporting 621
rotating 698
TextJustify property, reporting 616
Structures column 392
Thermo MS Licensing, email from 705
structures, charged 690
Thermo Scientific website, user documents 22
structures, checking the validity 696
Thumbnails Pane icon, reporting 633
studies
time zone settings 787
Analysis Results page 152
TML files 695
Input Files page 180
Samples page 182 Toggle Sidebar icon, reporting 631
Study Definition page 175 tool, guide or position 58
Studies Folder parameter 99 toolbar, application 48
study factors, three type of 39 tooltips 439
Study Name and Processing Workflow page 102 Total Intensity Threshold parameter 239
study name for a result file, finding 373 Total Scan parameter 246
Study Summary page 373 Trace Type parameter 246, 250
study template files TraceFinder application, mass list for 385
creating 100 Transformation Editor 654
selecting 102 transformations
study variables adding 654
assigning 109 editing 656

Thermo Scientific Compound Discoverer User Guide for LC Studies 803

 Index: U

exporting 654 Mass Defect Plot view 445

importing 654 Metabolika Pathways view 470
Transformations library mzLogic Analysis view 484
description 651 Partial Least Squares - Discriminant Analysis 463
features 652 Pie Chart page, Result Charts view 426
Transformations table 513 Principal Component Analysis 446
Transformations view 651 Result Charts 416
Transpose Data Fields shortcut menu command 609 Result Filters 362
Retention Time Correction 470
transposing columns in a report template 602
Scatter Chart page, Result Charts view 430
transposing the columns in a report template 572
Summaries (result) 371
Trend Chart view 435
Trend Chart 435
tritanopia, colormap for 720
Visible property, reporting 619
troubleshooting
access to the Online databases 783
Analysis pane Caution symbol 143 W
Current Workflow Issues pane 143 warning symbols 171
warnings
U peak rating filter 65
Wavelength Range parameter 247
Undo All Zoom/Pan command 401, 434
whisker 436
Undo Last Zoom/Pan command 401
width
unrecognized scan event filters 243
logo image container 577
Use Fragmentation Libraries check box 362
object, report template 622
Use Isotope Pattern in Precursor Reevaluation parameter 245 Overlay Cell Size box, Metabolika Pathways view 470
Use Libraries parameter 249 page width, report template 627
Use Normalized Areas check box 456 window position tool 58
UV-Vis detectors, chromatograms 246 workflow nodes
installing 713
V list of 225
numbers, hiding 718
validation issues
parameters for
missing Assign Compound Annotations node 146
Align Retention Times node 228
missing Differential Analysis node 145
Analyze Labeled Compounds 270
vector images 390
Apply Missing Value Imputation node 285
verbose messages, displaying in Job Queue 149 Apply mzLogic node 319
VerticalAlignment property, reporting 616 Apply QC Corrections 286
VerticalText property, reporting 616 Apply SERRF QC Correction node 288
View menu 45 Assign Compound Annotations node 295
viewer, molecular networking 762 Compound Class Scoring node 321
views Create Analog Trace node 246
Bar Chart page, Result Charts view 423 Create FISh Trace node 248
BioCyc Pathways 467 Create Mass Trace node 250
Chromatograms 394 Create Pattern Trace node 252
Compound Area Corrections 472 Detect Compounds (legacy) node 271
copying data to the Clipboard 390 Export Spectra node 226
Descriptive Statistics 453 Export Xcalibur Inclusion/Exclusion List node 330
FISh Scoring Queue 486 Fill Gaps node 280
Hierarchical Cluster Analysis view 476 Filter By Mass Defect node 230
Histogram Chart page, Result Charts view 418 Filter By Scan Event node 233
Isotopologues Distribution Chart 442 Filter Centroids node 236
Job Queue page 146 Find Expected Compounds node 255, 258
KEGG Pathways 465 FISh Scoring node 253

Thermo Scientific Compound Discoverer User Guide for LC Studies 804

 Index: X

Generate Expected Compounds node 261

Generate Molecular Networks node 322
Group Compounds node 282
Group Expected Compounds node 266
Map to BioCyc Pathways node 313
Map to KEGG Pathways node 314
Map to Metabolika Pathways node 315
Mark Background Compounds node 290
Merge Features node 269
Normalize Areas node 292
Pattern Scoring node 326
Predict Compositions node 297
Result Exporter node 331
Scale Areas node 293
Scripting Node 331
Search ChemSpider node 301
Search Mass Lists node 302
Search mzCloud node 304
Search mzVault node 309
Search Neutral Losses node 327
Select Spectra node 236
workflow summary 372
workspace sections, report designer page 604
Wrapmode property, reporting 616

X
X Axis Type parameter, Scatter Chart 432
X marks 403
Xcalibur Inclusion/Exclusion list, exporting 381

Y
Y Axis Type parameter, Scatter Chart 432
yellow background, table cell with 559
yellow-green background, table cell with 559

Z
Z Axis Type parameter, Scatter Chart 432
Zoom In icon, reporting 608
Zoom Out command 434
Zoom Out icon, reporting 608, 632
z-score transformation 481

Thermo Scientific Compound Discoverer User Guide for LC Studies 805