73NQuickReference.

fm Page 1 Tuesday, August 12, 2003 1:26 PM

Agilent G1701DA
MSD ChemStation

5973 MSD / ChemStation

Quick Reference

Agilent Technologies
73NQuickReference.fm Page 2 Tuesday, August 12, 2003 1:26 PM

What’s New in Revision D.01.00

• A new toolbar has been added to the Top view • The method has been expanded to permit
and an expanded set of toolbars have been printers other than the default printer to be
added to Data Analysis. Moving the cursor of used for reports generated during Run
the mouse over a toolbar will display tool tips Method.
(quick descriptions) for each of the buttons.
• Headers in Data Analysis reports are now
• The sequence user interface or sample log configurable for the reports generated by Run
table has been transformed into a Method.
spreadsheet user interface.
• An improved BOOTP service has replaced the
• During sequencing the ABORT button in the previous BOOTP program. The new BOOTP
status panel has been changed to Pause. service will not interfere with shutting down or
When this is selected, the sequence will pause logging off the computer.
immediately. When the sequence is started, it
will restart the sequence from where it was • The SICL drivers have been updated to version
paused. L.02.01 . Version M.01.01 is on the software
CD and is for GPIB support.
• Long files names are supported. Data file and
method paths can be up to 100 characters
long. The names of individual data files and
methods can be up to 50 characters long.
Online Help
• User Interfaces for selecting or saving files
and directories have been enhanced with
browse buttons. Use the online help to learn about these
new features as well as to learn about
• Support for 5973A and 6890A instruments instrument control, data acquisition, data
analysis, methods, sequencing, tuning, and
using GPIB has been restored.
how to use system commands and
variables. Troubleshooting the MSD is
• It is now possible to disable Method included to help you diagnose problems.
Resolution for most changes in the 6890
configuration.

• The Manual Tune and Diagnostics / Vacuum

Control views have be merged into a single
view, Tune and Vacuum Control.

• A Tune Wizard has been provided to simplify

the modification of criteria (tune limits,
target ratios) used by the tuning algorithms.

• Loading data files in Data Analysis will now

preview the chromatogram.

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Using Online Help

To access the online help, select Help

Topics from the Help menu in any
window, or click the Help button on any
dialog box.

Item Description
Hide / Show Lets you turn on or off the
display of the list of help
topics.
Back Goes back to the previous help
topic.
Print Lets you print the current book
or help topic.
Contents Displays the list of help topics
(shown above).
Index Lets you use keywords to
search the help index for a
particular topic.
Search Lets you type a word or phrase
Help Icons
and then displays a list of all
the topics in the online help Indicates a book containing more help topics.
that contain those words. To open a book, select it then double-click.

Indicates an open book of help topics. To close

an open book, select it then double-click.

Indicates a help topic. To jump to a help topic,

select it then double-click.

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5973 MSD with a 6890 GC

ALS tower
ALS tray

Column oven

5973 MSD

Status display

6890 GC
On/off switch
Local control
panel

Status board

Keypad

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GC Keypad

The MSD ChemStation software provides instrument control for the 6890 GC. This allows you to use
the software, instead of the GC keypad, to program the instrument. However, there are times when you
may want to use the keypad to quickly perform one of the following tasks.

Prepare a run (manual injection)

Display column information

Stop a run
Start a run (manual injection)
Display the front injection
port temperature

Display the oven

temperature

Display the GC/MSD

interface temperature
(Thermal Aux 2)

Display the rear injection

port temperature

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Instrument Control View

The Instrument Control view is displayed when you start up

the MSD ChemStation. This is where you set and monitor See the online help for more details
instrument parameters. If you are in a different view, select on the menus, buttons, or windows
View / Instrument Control when you are ready to set up the used in the software.
system for data acquisition.

Acquisition Status Lets you tell at a glance the status of the current
instrument or run (if any).

Start Button Lets you start a run. When a run is not in progress, the
arrow is green. To start a run, click the green arrow, fill in the Sample
Information, and click Start Run. When a run is in progress, the arrow
is gray.
This button also shows the current data file name, sample information
(if any), and the vial number (1 if no ALS).

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Run Time Clock Shows the elapsed time since the beginning of the
run if a run is in progress. The scheduled run time is shown below
the digital clock. When a run is not in progress, the Run Time clock
shows the elapsed time since the last run.
Stop Button Lets you stop the system when it is in Pre-Run,
Run, or Post-Run mode. The stop sign is red when a run is in
progress and gray when a run is not in progress.

Logbook Button Displays a menu where you can choose to view,

open, clear, save, or print a particular logbook.

Help Button Displays a menu where you can select an online help
topic for the Instrument Control view. Choose Help Topics to go to
the online help for the entire system.

Injector Button Lets you set parameters for the injector when
you have configured your system with an ALS.

Inlets Button Lets you set parameters for the GC inlet (injection
port) that is configured on your system.

Columns Button Lets you configure columns and set up ramped

flow and pressure programs.

Oven Button Displays a menu that lets you edit GC oven

parameters or GC monitor parameters. When the GC is ready, the
small square in the upper right corner is green. When the GC is not
ready, the square is red.

Aux Button Lets you set the temperature of the GC/MSD

interface (usually Thermal Aux 2).

MS Button Displays a menu that lets you edit MS acquisition

parameters, select another tune file, or edit MS monitors.

Monitor Each monitor displays one instrument parameter. See

the online help for a description of the instrument monitors.

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Top Menus

Method Sequence View Secured Control

Run... Run... Top Enable Security...
Instrument Control
Load... Load... Data Analysis (offline) Start Secured Control...
Save... Save...
Select Methods for Secured Control...
Edit Entire Method... Edit Sample Log Table... Set/Change Startup Method <...>
Print Set Change Standby Method <...>
Load and Run Sequence...
1 Print Sequence... Assign Sample Names to Method...
2 Use Sample-centric Secured Control...
3 1
4 2 Report Manager password...
3 Edit Accounts...
Set New Default Paths... 4

Exit Simulate Sequence

Position and Run...
Help
View Sequence Log...
View Sequence Quality Log
Help Topics
Print Sequence Log
Using Help
Import Sequence Information from CSV file...
View Revision Readme File
Batch Mode...
Review Revision History...
More...
About

Select View / Top to access

these menus.

The software menus shown on the following

pages are for an MSD ChemStation in
Enhanced Mode.

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Top Toolbar

Load Sequence Loads the selected sequence.

Save Sequence Saves the specified sequence.

Run Sequence Saves the specified sequence.

Edit Sequence Lets you set up or modify the sample log

table.

Print Sequence Prints the current sequence.

Simulate Sequence Simulates the current sequence.

Load Method Loads the selected method.

Save Method Saves the specified method.

Run Method Runs the current method. The Start Run

dialog box is displayed.

Edit Method Lets you modify the method parameters

for the current method.

Print Method Prints the current method.

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Instrument Control Menus

Method Instrument View Abort

Run... Inlet/Injection Types Top Abort

Instrument Control
Load... GC Edit Parameters... Data Analysis (offline)
Save... GC Plot...
GC Monitors... Tune and Vacuum Control...
Edit Entire Method...
Additional Method Information... Acquire RTLock Calibration Data...
Print Unlock Method...

1 Disable Method Resolution

2
3 Select MS Tune File...
4 MS SIM/Scan Parameters...
Change MSD Temperatures...
Exit MS Monitors...

Edit MS Tune Parameters...

Perform MS Autotune...

EMF Utilities...

Window Qualify Help

Cascade Checkout Tune Help Topics
Tile Horizontal Tune Evaluation Using Help
Tile Vertical View Tunes...
Arrange Icons Sensitivity Check Review Revision History...
Arrange Plots and Monitors Software Validation View Revision Readme File
Installation Checklist About
1 Familiarization Checklist
2
3
4

Select View / Instrument Control to

access these menus.

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Tune and Vacuum Control Menus

File Tune Vacuum Execute

Reset to Defaults Tune MSD Vacuum Status... MS ON
Load Tune Values... QuickTune MS OFF
Save Tune Values... Pump Down...
Autotune (Atune.U) Vent... Profile scan
Trace on Low Mass Autotune (Lomass.U) Repeat profile
View Trace... Purge Calibrant Valve Detailed profile
Instrument Trace... Standard Spectra Tune (Stune.U) Power-on Temperatures
DFTPP Tune (DFTPP.U) Initialize MS Interface Ramp Lenses
Print BFB Tune (BFB.U)
Printer Orientation... Tune Wizard... Spectrum scan
Generate Report... Find mass...
Air and Water Check
View Tunes... Tune Evaluation Determine Mass Axis Correction Factors
Set View Tunes Report Options... Optimize Quadrupole Frequency

Restore Previous Tune(s)...

Exit

Calibrate Parameters Status View

Mass axis Manual Tune... MS Status Top
MS I/O Test Instrument Control
Mass #2 widths Edit Tune and Display Parameters... MS Temperature Controller Status Data Analysis (offline)
Mass #3 widths Edit MS Temperatures...
Peakwidth Linearity Edit Ramp Parameters... View Instrument Macro Log...
Edit Dynamically Ramped Parameters... View Tune Log...
Adjust Abundances
Ramp Repeller Clear Instrument Macro Log...
Ramp Ion Focus Clear Tune Log...
Ramp Entrance Lens
Ramp Entrance Lens Offset MS Error Codes...
Logbook/Sequence Log Error Codes...
Maximize Sensitivity

Abort Help
Abort Help Topics
Troubleshooting
Using Help

About

Select View / Tune and Vacuum

Control from Instrument Control to
access these menus.

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Data Analysis Menus

File Method Chromatogram Spectrum

Load Data File... Run Method... Chromatogram Scaling... Add

Next Data File Run CustomAnalysis Draw Chromatogram - No Labels Subtract
List Header... Draw Chromatogram With Labels Tabulate
Edit File Info... Load Method... Select Chromatogram Labels... Select Library...
Take Snapshot Save Method... Edit Strategy...
Subtract Background (BSB) Extract Ion Chromatograms Edit Library...
Edit Method... Display Ion Chromatograms in Merged Format
Select Signals... Edit CustomAnalysis... Library Search Report
Select Integrator
Select Printer... Generate AutoSIM Method... MS Signal Integration Parameters... Change Spectral Display...
Printer Setup... GC Signal Integration Parameters... Find Mass Spectrum
Print 1 AutoIntegrate
Abort 2 Integrate
3 Integration Results...
Export Data to CSV File... Percent Report
Export Data to AIA format... Batch Mode...
Import AIA Raw Data Files...

1
2
3

Exit

Calibrate Quantitate Tools View

Set Up Quantitation... Calculate DOLIST... EasyID

AutoQuant Setup Generate Report DOSCAN... QEdit Quant Result
Edit Compounds... Process Scan List Edit Non Target Peaks
Update... Use Classic Reports Parametric Retrieval
List... Report Options... Export 3-D Data... Align GC
Clear... Review Peak Purity
Report Non Target Peaks... Locate A Compound...
Use Method Aligned GC trace Locate All Compounds... Results Screener
Trace Mode Quant... RTLock Setup
Set Overlay Parameters...
Custom Reports... Overlay Chromatograms...
Print Report
Update Database Signal to Noise check...

Select Template/Database Change Data State... Help

Options...
Configure Report Headers... Help Topics
Using Help
Generate Screen Results for Current File Review Revision History...
Generate Screen Report for Current File View Revision Readme file
Generate/Print Screen Report for Current File About
Generate/Print Screen Report for Multiple Files...
Specify Method Screen Database...
Change Screen Database Parameters...
List Screen Database...
Select View / Data Analysis (offline) to Exclude Zero Qualifiers
access these menus. Copy Window...
Reset Windows...
The View menu in Data Analysis lets you
access other Data Analysis modes
(shown on the following pages).

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EasyID Menus

EasyID Spectrum Integrate

Co Next Compound Draw Next Integration Parameters

Goto Compound # Draw Previous Save compound specific integration parameters
Xpand Chromatographic Window +/- 2 minutes Tabulate Remove compound specific integration parameters
Original Chromatographic Window
Graphics Report to the Printer Add Integrate
Subtract
Restart Quick QEdit
Select Library...
Set Extract Window Start Edit Strategy... ChromEval View
Set Extract Window Stop Edit Library...
Evaluate Resolution Data Analysis
Abort Changes and Exit Display Reference Spectra Evaluate Tailing
Exit and Save Changes Evaluate Degradation
Update Reference Spectrum

Select View / EasyID in Data

Analysis to access these menus.

QEdit Menus

QEdit Spectrum ChromEval Display View

CO Next Compound Draw Next Evaluate Resolution Normal Data Analysis

Goto Compound Draw Previous Evaluate Tailing Qualifiers
Xpand Chromatographic Window Tabulate Evaluate Degradation
Original Chromatographic Window
Graphics Report to the Printer Add
Subtract
QDEL Compound
Select Library...
Next File Edit Strategy...
Load Data File... Edit Library...
Restart Quick QEdit
Display Reference Spectra
Abort Changes and Exit
Exit and Save Changes

Select View / QEdit Quant Result in

Data Analysis to access these menus.

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Parametric Retrieval Menus

File Spectrum Library Retrieve

Load... Draw Next Select Library... Set Parameters...

List Header Draw Previous Edit Strategy... Select Library...
Take Snapshot Edit Library...
Subtract Background (BSB) Tabulate Continue Results
Library Search Report...
Print Current View Add
Normalized Subtract Read JCAMP File...
Save Parameters Write JCAMP File...
Abort
Exit Subset Library...
Add Current Entry

Structures Options View Help

Select Structure Database... Select Normalization Ion Standard Menu Help Topics
Set Structure Parameters... Extend Database Headers...
Command Line Library Entry Only About
Stack TIC and Library Entry
Manual Integration Unknown and Library Entry
Unknown, Library Entry, and Difference
Copy Window...
Reset Windows

Select View / Parametric Retrieval in

Data Analysis to access these menus.

Align GC Menus

Alignment View

Show Current Method Alignment Points Data Analysis

Perform Alignment
Restore Alignment Chromatograms

Abort
Exit/Save

Select View / Align GC in Data

Analysis to access these menus.

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Review Peak Purity Menus

PkPurity Spectrum Help

Next Peak Add Help Topics

Previous Peak Subtract Peak Purity
Select Peak... Tabulate Using Help
Print Selected Window...
Return to DA

Select View / Review Peak Purity in

Data Analysis to access these menus.

Quick Screener Menus

Screener Spectrum ChromEval Display View

CO Next Compound Draw Next Evaluate Resolution Normal Data Analysis

Goto Compound Draw Previous Evaluate Tailing Qualifiers
Xpand Chromatographic Window Tabulate Evaluate Degradation
Original Chromatographic Window
Graphics Report to the Printer Add
Subtract
QDEL Compound
Select Library...
Next File Edit Strategy...
Load Data File... Edit Library...
Restart Quick Screener
ReRun Screen Display Reference Spectra

Abort Changes and Exit

Exit and Save Changes
Select View / Results Screener in
Data Analysis to access these menus.

RTLock Menus

RTLock View Help

Data Analysis Help...

View Current Method Setpoints
Calculate New Curve from Selected Peaks
Restore Nominal Chromatogram
.
Report RTLock Calibration...
Print...

Relock Method...
Use AutoRelock

Unlock Method...
Select View / RTLock Setup in
Data Analysis to access these menus.

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Data Analysis Toolbar Buttons

Load Data File Loads the selected data Close Screen Reports Closes the currently
(.D) file and displays the total ion displayed screen reports.
chromatogram (TIC) for that file.

Load Method Loads the selected method EasyID Lets you update expected
(.M) file. retention times and ion ratios for MS data
in an existing quantitation database on a
compound-by-compound basis.
Save Method Saves any changes made to
the current method. QEdit Quant Result Lets you review and
edit quantitation results once a data file
has been quantitated.
Take Snapshot Displays the data that
has been acquired up to the time the Generate Signal-to-Noise Report Lets
snapshot is activated. GC/MS data only. you perform a signal-to-noise check and
then display or print the report.
Print Lets you print the selected window,
the TIC and spectrum, or the current Review Peak Purity Helps you detect
method. overlapping peaks (multiple-component
peaks) in your chromatogram.
Copy Window Lets you copy the selected
window to the clipboard. Retention Time Locking Accesses the
RTLock Setup view which is used for
retention time locking tasks.
Reset Windows Rearranges the graphics
windows to their default positions. CUSTOMTOOL1 Lets you run a
user-created macro. This macro must first
be created and then named CUSTOMTOOL1.
Execute Command Executes the command See the online help for Using and Writing
that is typed into the command line. Macros, and Data Analysis Commands.

CUSTOMTOOL2 Lets you run a

Abort Stops a command or macro. user-created macro. This macro must first
be created and then named CUSTOMTOOL2.
See the online help for Using and Writing
Macros, and Data Analysis Commands.
Toggle Command Line Turns the display of
the command line on or off. CUSTOMTOOL3 Lets you run a
user-created macro. This macro must first
be created and then named CUSTOMTOOL3.
Edit Colors Lets you adjust the colors of See the online help for Using and Writing
various display items in Data Analysis. Macros, and Data Analysis Commands.

Toggle Graphics Lets you minimize or

maximize the displayed graphics.

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Draw Chromatogram Redraws the original Set Up Quantitation Lets you set up a
chromatogram of the current data file quantitation database by specifying
without labels or integration marks. quantitation database globals and entering
compounds into the database.
Scale Chromatogram Scales the selected
chromatogram by the specified scale AutoQuant Setup Provides a semi-
factors. automated way to create a quantitation
database.
Extract Ion Chromatogram Extracts and
displays extracted ion chromatograms Edit Compounds Lets you review and edit
(EICs) from the total ion chromatogram information in the quantitation database
(TIC) of the current data file. compound-by-compound.

Merged Format Causes extracted ion Update Calibration Lets you add, delete,
chromatograms to be displayed overlaid on or update a calibration level in the current
each other. quantitation database.

Overlay Chromatograms Lets you select Calculate Quant Report Quantitates the
multiple chromatograms to be displayed current file and generates a quantitation
superimposed on each other. report.

AutoIntegrate Tries to find the best Generate Quant Report Generates a

integration parameters for the current quantitation report for a file that has
chromatogram and then integrates the already been quantitated.
chromatogram.
Print Quant Report Prints the
Integrate Integrates the current quantitation report.
chromatogram using parameters set for
the current integrator.
Custom Reports Starts the Custom
Subtract Spectrum Subtracts one Reports software. If the method does not
spectrum from another and displays the have a quantitation database, or no data
difference. file is loaded, you can use default values.

Select Library Lets you select the libraries Print Custom Report Prints the custom
that will be used for PBM searches of the report template specified by the method
currently selected spectrum. using the current data file.

Library Search Report Integrates the Online Help Displays the MSD
current TIC, searches the current library, ChemStation online help.
and generates a report.

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To vent (shut down) the MSD

1 If your system is equipped with a gauge

controller, switch off the triode gauge
controller.
2 Before venting a CI MSD, press the Gas Off
button (turns off the reagent gas flow and
closes the isolation valve.)

WA R N I N G
On a CI MSD, the Gas Off light must be on when the
MSD is venting.

3 From the Tune and Vacuum Control view,

select Vent from the Vacuum menu in the
software. Follow the instructions presented.
4 Set the GC/MSD interface heater and the GC
oven temperatures to ambient (25°C).

WA R N I N G
CAUT IO N
If you are using hydrogen as a carrier gas, the carrier
gas flow must be off before turning off the MSD Do not turn the knob too far, or the O-ring may fall
power. If the foreline pump is off, hydrogen will out of its groove. Be sure to retighten the knob
accumulate in the MSD and an explosion may occur. before pumping down.
Read the Hydrogen Carrier Gas Safety Guide
(5955-5398) before operating the MSD with
hydrogen carrier gas. WA R N IN G
Allow the analyzer to cool to near room temperature
before touching it.
CAUT IO N
Be sure the GC oven and GC/MSD interface are cool
before turning off carrier gas flow. CAUT IO N
Always wear clean gloves while handling any parts
that go inside the analyzer chamber.
5 When prompted, turn off the MSD power
switch.
6 Unplug the MSD power cord. WA R N IN G
When the MSD is vented, do not put the ChemStation
7 Remove the analyzer cover. into the Top view. Doing so will turn on the interface
heater.
8 Turn the vent valve knob counterclockwise only
3/4 turns or until you hear the hissing sound
of air flowing into the analyzer chamber.

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To pump down (start up) the MSD

1 Make sure your system meets all of the 5 Press lightly on the side board to ensure a
following conditions before you pump down: correct seal.
o The vent valve is closed (the knob is turned The rough pump will make a gurgling noise.
all the way clockwise.) This noise should stop within a minute. If the
o All other vacuum seals and fittings are in noise continues, there is a large air leak in
place and fastened correctly. (The front your system, probably at the side plate seal,
side plate screw should not be tightened the interface column nut, or the vent valve.
unless hazardous carrier or reagent
gases are being used.) 6 Once communication with the PC is
established, click OK. Within 10 to 15 minutes
o The MSD is connected to a grounded power the diffusion pump should be hot, or the turbo
source. pump speed up to 80%. The turbo pump
o The GC/MSD interface extends into the should eventually reach 95%.
GC oven.
CAUT IO N
o A conditioned capillary column is installed in
the GC inlet and in the GC/MSD interface. If these conditions are not met, the foreline pump
will be shut off. You must then power cycle the MSD.
o The GC is on, but the heated zones for the If the MSD does not pump down correctly, see the
GC/MSD interface, the injection port, and online help for information on troubleshooting air
the oven are off. leaks and other vacuum problems.
o Carrier gas of at least 99.999% purity is
plumbed to the GC with the recommended 7 When prompted, turn on the GC/MSD
traps. interface heater and GC oven. Click OK when
o If hydrogen is used as carrier gas, carrier you have done so. The software will turn on
gas flow is off and the front sideplate the ion source and mass filter (quad) heaters.
thumbscrew is loosely fastened. The temperature setpoints are stored in the
current autotune (*.u) file.
o The foreline pump exhaust is properly
vented. CAUT IO N
WA R N I N G Do not turn on any GC heated zones until carrier
gas flow is on. Heating a column with no carrier gas
Make sure your MSD meets ALL the conditions listed flow will damage the column.
above. Failure to do so can result in personal injury.
8 After the message Ok to run appears, wait
2 Select Tune and Vacuum Control from the two hours for the MSD to reach thermal
View menu. equilibrium.

3 Select Pump Down from the Vacuum menu. CAUT IO N

4 When prompted, switch on the MSD. Data acquired before the MSD has reached thermal
equilibrium might not be reproducible.

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To tune your MSD

You should tune the MSD periodically to maintain To use Manual Tune
its optimum performance. Tuning is the process Manual tuning lets you interactively set the MSD
of adjusting MSD parameters so the instrument parameters, such as lens voltages and tuning
meets certain performance criteria. How often masses, to values that meet the needs of your
you should tune is determined by the number and particular analysis. You can often obtain greater
type of samples you are running, as well as the sensitivity than you can with autotune.
overall condition of your system.
Manual tuning allows you to ramp individual
Note Always tune the MSD with the same GC parameters and to specify the range and step
oven temperature and column flow, and the same size for the ramp. The results of the ramp are
analyzer temperature that will be used for data displayed visually with the optimum value for the
acquisition. parameter clearly marked on the plot.
Keep the Tune reports in a notebook so that You can acquire two types of data in manual
successive reports can be easily compared. tune: profile scans (plots the abundance and
peak shape of the tune masses) and spectrum
To use Autotune scans (scans plot response across the entire
1 From the Instrument Control view, select mass range).
Perform MS Autotune from the Instrument
menu. See the online help for more details about manual
tuning.
2 Select one of the following options, depending
on the instrument performance required by
your application, then click OK.
o Autotune
Results in maximum sensitivity over the full
scan range.
o Low Mass Autotune
Tunes for the low-mass range.
o Standard Spectra Tune
Results in a standard response over the
full scan range. This option may reduce
sensitivity.
o QuickTune
Adjusts the peak width, mass assignment,
and abundance without changing ion ratios.
3 Review the Tune report.
4 To view the history of tune results, select View
Tunes from the Qualify menu.

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To acquire data

To set up the GC for use with the MSD To inject a sample manually
1 Select Instrument / Inlet/Injection Types. 1 Select Manual as the injection source on the
Select the appropriate injection source and Inlet and Injection Parameters box.
select the Use MS checkbox. Click OK.
2 Press the Prep Run key on the GC keypad. This
2 Click the Aux button. Verify that you are using cancels the gas saver flow, brings the inlet
auxiliary channel 2, the heater is on and set flow to its setpoint value, and closes the
to the desired temperature, and that MSD is purge valve (for splitless injection only).
selected as the Type. Click OK.
3 Select Run from the Method menu from the
3 Click the Columns button. Verify that the Top or Instrument Control view.
detector is MSD and that Vacuum is selected
for Outlet psi. Click OK. 4 When the Start Run box appears, specify the
sample information as described below:
To inject a sample with the autosampler o Specify a unique data file name for the
1 Place the autosampler vial containing the sample.
sample into the autosampler tray. o (optional) Fill in the Operator Name,
2 Select Run from the Method menu in the Sample Name, and Misc Info fields to
document the injection.
Top or Instrument Control view.
o Make sure that the Data Acquisition option
3 When the Start Run box appears, specify the is selected.
sample information:
o (optional) Select the Data Analysis option
o Specify a unique data file name for the if you want to generate any Data Analysis
sample. reports specified in the method.
o Enter the position number of the sample vial 5 Click Run Method to initiate the run. If the
in the Vial field (1 – 100). temperatures are stable, the Prepare To Inject
o (optional) Fill in the Operator Name, box appears. Otherwise, the message Waiting
Sample Name, and Misc Info fields to for GC ready is displayed.
document the injection. 6 When the GC temperatures have stabilized
o Make sure that the Data Acquisition (the Pre Run light on the GC is steady), inject
option is selected. Select the Data Analysis the sample and press Start on the GC.
option if you want to generate any of the
reports specified in the method.
CAUT IO N
4 Click Run Method to initiate the run.
Do not inject before the GC is ready. This will cause
inconsistent results.
CAUT IO N
Do not use the Start button on the GC to start a
run when using the autosampler.

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To analyze MS data

To load a data file To average spectra

1 In Data Analysis, select Load from the File menu. 1 Position the pointer in the chromatogram at the
2 Select a data file (double-click on a file name or starting time for the range you want to average.
type a name and click OK). The chromatogram for 2 Press the right mouse button while dragging the
the data file is loaded and displayed in window [2]. mouse to the end of the range you want to average.
3 Release the mouse button. The spectra in the
selected range are averaged and the averaged
A data file must be loaded to perform any
spectrum is displayed in window [1].
of the following tasks.
To add two spectra
To integrate a chromatogram 1 Select a spectrum (double-click the right mouse
button in the chromatogram).
1 If the integrator you wish to use is not currently
selected, open the Chromatogram menu and click 2 Select a second spectrum (double-click the right
Select Integrator. Choose an integrator and mouse button in the chromatogram).
click OK. 3 Select Add from the Spectrum menu. The two
2 Select Integrate from the Chromatogram menu. spectra are added together and the resulting
spectrum is displayed in window [1].
3 (optional) Select List Results from the
Chromatogram menu. A report of tabulated results To subtract two spectra
is displayed on the screen. When you are finished
viewing the results, click Done. 1 Select a spectrum (double-click the right mouse
button in the chromatogram).
To select a spectrum 2 Select the spectrum to be subtracted (double-click
• Double-click the right mouse button on the time the right mouse button in the chromatogram).
point of interest in the chromatogram. The spectrum 3 Select Subtract from the Spectrum menu.
appears in window [1]. The spectrum selected in Step 2 is subtracted from
the spectrum selected in Step 1 and the resulting
To zoom in spectrum is displayed in window [1].
1 Position the pointer at one corner of the area you
wish to expand in a chromatogram or spectrum. To subtract background spectra
2 Press and hold the left mouse button while dragging 1 Select a spectrum or average a range of spectra to
the mouse to select the area you wish to expand. subtract from the data file.
3 Release the mouse button. The selected area 2 Select Subtract Background (BSB) from the File
expands to fill the existing window. menu. The system performs the following tasks:

• The selected spectrum is subtracted from every

To zoom out
scan in the current data file.
1 Position the pointer anywhere in the zoomed window.
• The subtracted data is stored in a BSB
2 Double-click the left mouse button. subdirectory in the same directory as the data file.
• The subtracted data file becomes the current data
file and is displayed in window [2].

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To use spectral libraries

To integrate and search peaks To search a single spectrum

Use the following procedure to integrate a total ion 1 In Data Analysis, load a data file. The TIC is displayed.
chromatogram and automatically generate a library 2 Select a spectrum. The selected spectrum appears in
search report for each peak detected. a window below the chromatogram.
1 In Data Analysis, load a data file. The TIC is displayed. 3 Initiate the library search by double-clicking the right
mouse button in the window containing the spectrum.
2 Select Spectrum / Library Search Report.
When the search is complete, the search results
3 When the Library Search Report Options dialog box appear on the screen. The spectrum for the unknown,
appears, select the options you want for the library the reference spectrum you select from the list of
search report: hits, and, if available, the chemical structure of the
• Select either Summary or Detailed to determine reference compound is displayed.
the report format. 4 To view other spectral data:
• Select one or more destinations (Screen, Printer, • Click on another compound in the hit list to display
and File). a different reference spectrum.
• Select an Integration Parameter File (leave the • Select the Difference checkbox to display the
field blank to autointegrate using the ChemStation difference between the unknown and the reference
integrator). spectra.
• Select which spectrum from each peak to use 5 To view other information:
(Apex, Apex - Start of Peak, Apex - Background at
time, or Peak Average). • Click the Statistics button to display information
about the quality of each hit found in the list.
4 Click OK to initiate the search. • Click the Text button to view the header
The chromatogram is integrated and a spectrum information stored in the library for the current
from each peak is searched. The results of the reference spectrum.
integration appear on the screen. The library search 6 Click the Print button to print a copy of the displayed
report is sent to the destinations selected in Step 4. spectra.
5 Select Chromatogram / Integration Results to view 7 Click the Done button to clear the library search
the tabulated integration results. results from the screen.

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Maintenance Schedule

Maintenance tasks are described in the hardware Safety warnings

manuals supplied with your system. How often
you need to perform system maintenance may
vary for your system. Keep a maintenance record. WA R N IN G
Do not perform maintenance with the MSD on or
Every day connected to its power source unless specifically
instructed to by documentation supplied with the MSD.
Check, and if necessary, replace the septum.
Check the tightness of the injection port liners.
Check the tightness of the column nuts. WA R N IN G
The GC/MSD interface can be on and at a dangerously
Every week high temperature even though the MSD is off. After it is
Check the foreline pump fluid level. turned off, the GC/MSD interface cools very slowly.
Make sure all parts have cooled before handling them.
Change the injection port liners and O-rings.

Every month WA R N IN G
Clean the split/splitless inlet vent line trap. Be careful when working behind the GC. During
Check for leaks (inlet, column connections). cool-down cycles, the GC will emit hot exhaust that
could cause burns.
Every three months
Replace gas cylinders (when below 500 psig). WA R N IN G
The oil trap provided for your foreline pump stops only
Every six months foreline pump oil. If you are analyzing toxic chemicals or
Replace the foreline pump fluid. using toxic solvents, remove the oil trap and use a hose
Check, and if necessary, refill the calibration vial. to route the foreline pump exhaust out of your
laboratory.
Every year
Check, and if necessary, replace the diffusion WA R N IN G
pump fluid. Use chemical-resistant gloves and safety glasses when
Recondition or replace internal and external replacing pump fluid. Avoid all contact with the fluid.
traps and chemical filters on the GC.

As needed WA R N IN G
Tune the MSD. The insulation around the inlets, detectors, valve box,
and insulation cups is make of refractory ceramic fibers
Clean the ion source. (RCF). Avoid inhalation of RCF particles. Ventilate your
Replace the carrier gas trap. work area, wear long sleeves, gloves, safety glasses, and
Replace worn out parts (filaments, EM, etc.). a disposable respirator. Dispose of insulation in a
Replace the column. sealed plastic bag. Wash your hands with mild soap and
Lubricate seals. cold water after handling RCFs.

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Operating Tips

o Back up your data and methods regularly to o For a new column, check that the column nuts
avoid loss of data if the files are accidentally are still tight after the first few oven
overwritten or deleted, or if a hardware temperature cycles.
problem develops with your disk drive.
o Use the Config Status keys on the GC keypad
o Make sure the tune file you are using is to set the 3 display items most important
appropriate for your samples. to you (time remaining, oven temp, etc.).
These are then always visible regardless of
o Save Tune reports in a notebook for future which ChemStation view is on top.
reference.
o Rinse and refill autosampler wash vials. Do
o Perform system maintenance as indicated not add more solvent to a partially full vial.
by the maintenance schedule in the GC and
MSD hardware documentation. Keep a o Use the following table as a guide to using
record of all maintenance performed. the SIM or Scan acquisition modes.

o When venting the MSD, take advantage of Task Mode

the cool GC to do maintenance such as
replacing inlet liners, septa, etc. Analyze a mixture with unknown Scan
components.
o After pumpdown, wait at least 2 hours for Analyze a mixture with known Scan or
the MSD to reach thermal equilibrium before components in unknown SIM
tuning or acquiring data. amounts (quantitate).

o Optimum sensitivity generally occurs at Identify the presence of a few SIM

known compounds at low levels
column flow rates of 1.2 ml/minute or less.
within a mixture.
o When injecting volumes greater than one
microliter, use the pulsed splitless mode and o When choosing masses for SIM, use the
increase the initial oven temperature exact mass printed in the Tabulation report,
10 – 20°C. not the nominal mass annotated on the
spectrum display. This provides more
o For splitless injections, pulsed splitless mode accurate data.
gives more quantitative sample transfer onto
the column. A pulse pressure of twice the
o When doing SIM analysis, use low resolution
mode unless you are trying to determine the
initial inlet pressure is typical.
ratios of masses one amu apart. Low
o Selecting Constant Flow mode will provide resolution provides maximum sensitivity and
the most efficient separation in most cases. repeatability.
It also results in constant sensitivity
throughout the temperature program.
o Choose the narrowest scan range that still
produces good library search results. This
allows more spectra across the peak and
better quantitation.

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Troubleshooting Tips

MSD is on, but status flashing “Server not Peaks with split tops
found! Check LAN connection”
1 Bad injection technique
This is normal when the MSD is initially turned 2 Injection too large
on. It means the ChemStation has not yet
established contact with the MSD. If the
flashing continues after the pumpdown is Rising baseline
initiated:
1 Column bleed
1 Temporary power failure interrupted 2 Other contamination
communications
2 Bad connection between the MSD and the
ChemStation and/or the hub Retention time (RT) drift
1 Column has been shortened (shorter RT)
No peaks 2 Old column (shorter RT)
1 Incorrect sample concentration 3 Active sites in sample path (longer RT)
2 No analytes present 4 Reduced column flow (longer RT)
3 Syringe missing or not installed correctly 5 Injection port leak (longer RT)
(ALS only) 6 Initial oven temperature changed (up =
4 Empty sample vial shorter RT, down = longer RT)
5 Injection in split mode instead of splitless
mode
Poor sensitivity

Tailing peaks 1 Incorrect tuning

2 Tune file does not match type of analysis
1 Active sites in sample path 3 Incorrect temperatures
2 Injection too large 4 Incorrect sample concentration
3 Injection port too cool 5 Leaking injection port
4 Column flow too low 6 Incorrect split ratio
5 GC/MSD interface or ion source too cool 7 Purge off time in splitless mode too short
8 Excessive pressure in the MSD
Peaks with flat tops 9 Dirty ion source
10 Air leak
1 Solvent delay time too short
11 Detector is not working correctly
2 Display scale is wrong
12 Poor filament operation
3 Injection too large
13 Incorrect mass filter polarity
4 Electron multiplier voltage too high

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Poor repeatability Isotopes missing or isotope ratios incorrect

1 Dirty syringe needle 1 Incorrect tuning
2 Leaking injection port 2 Dirty ion source
3 Mismatched injection port liner and injection 3 High background
size 4 Electron multiplier voltage too high
4 Loose column connections 5 Repeller voltage too high
5 Variations in pressure, column flow, and 6 High scan speed (Scan mode)
temperature
7 Low dwell time (SIM mode)
6 Dirty ion source
8 Peaks too wide or too narrow
7 Loose connections in the analyzer
9 Repeller and ion focus leads have been
8 Ground loop reversed

Inconsistent peakwidths Foreline or vacuum manifold pressure

too high
1 Incorrect tuning
2 No PFTBA in calibration vial 1 Excessive column flow
3 Calibration valve failure 2 Air leak
4 Dirty ion source 3 Diffusion pump fluid level too low
5 Worn out electron multiplier 4 Diffusion pump fluid is contaminated
6 MSD has not had enough time to reach 5 Foreline pump oil level too low
thermal equilibrium 6 Foreline pump oil is contaminated
7 Large variations in the temperature of the lab 7 Constricted foreline hose (this would cause
the vacuum manifold pressure to be too high
but the foreline pressure to be too low)
High background in mass spectra
1 Air leak
2 Foreline or vacuum manifold pressure too high
3 Other contamination

Ions at m/z 18, 28, 32, and 44 Refer to the Troubleshooting the MSD section of
the online help for more detailed information.
1 Detector vented recently (residual air and
water)
2 Air leak

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What’s in this Book

What’s New in Revision D.01.00, 2

Using Online Help, 3
5973 MSD with a 6890 GC, 4
GC Keypad, 5
Instrument Control View, 6
Software Menus (Enhanced Mode), 8
Data Analysis Toolbar Buttons, 16
To vent (shut down) the MSD, 18
To pump down (start up) the MSD, 19
To tune your MSD, 20
To acquire data, 21
To analyze MS data, 22
To use spectral libraries, 23
Maintenance Schedule, 24
Operating Tips, 25
Troubleshooting Tips, 26

Document History

First Edition, 9/03

G1701DA MSD ChemStation
Rev. D.01.00

*G1701-90050*
*G1701-90050*
Copyright © 2003
Manual Part Number Agilent Technologies
G1701-90050 Printed in U.S.A. 9/03