QuantStudio™ Absolute Q™ Digital PCR

System
INSTALLATION, USE, AND MAINTENANCE

Catalog Number A52864

Publication Number MAN0025621
Revision E.0

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

 Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256
For descriptions of symbols on product labels or product documents, go to thermofisher.com/symbols-definition.

Revision history: MAN0025621 E.0 (English)

Revision Date Description

E.0 11 April 2023 • The manufacturing site address was updated to Singapore.

• The recommended equipment and a link to the recommended kits for nucleic acid isolation were added
(“Recommended materials not supplied” on page 10).
• Information on nucleic acid isolation was added (see “Nucleic acid isolation” on page 19).

• The optical dyes were revised to identify the recommended dyes.

• Translations were added to safety information (see “Installation and environmental requirements” on
page 84 and Appendix G, “Safety”).

D.0 31 August 2022 • New filter feature is available for filtering runs by run type, status, and instrument when selecting a run.

• Instructions were added for using the keyboard shortcuts for zooming in and out on pages (“Software
features” on page 37).
• Instructions were added for preparing DNA samples (“Prepare the DNA samples” on page 19).

• Instructions were revised for preparing the dPCR reagent mix (“Prepare the dPCR reaction mix” on
page 22).
• Instructions were added for creating a custom protocol using the Absolute Q™ Starter or other existing
protocols (“Create a custom protocol” on page 29) .
• Instructions were revised for editing the sample plate area (“Load the plate and run the protocol” on
page 32).
• Instructions were revised for editing the sample plate area to modify the run name, select and name
samples, and manage groups and group sets (“SETUP page” on page 39).
• Instructions were added for deleting a group set (“Delete group sets” on page 53).

• Instructions were added for changing a group set name (“Edit group set names” on page 52).

• Instructions were revised for navigating plots (“View plots” on page 63).

• Instructions were revised for manually setting thresholds (“Set thresholds” on page 66).

• Instructions were added for overlaying sample plots with identical thresholds (“Overlay samples” on
page 68).
• Instructions were added for updating the instrument software (“Update the instrument software” on
page 87).
• Instructions were revised for adding e-Signatures for plate setup and run results (“Sign data in the software”
on page 99).
• Instructions were revised for installing the SAE Administrator Console software and Absolute Q™ application
profile (“Install the SAE Administrator Console and Absolute Q™ application profile” on page 93).
• Information was added and revised regarding auditing at the SAE Administrator Console (“Use audit
functions” on page 97).
• Information was added to describe the information regarding e-Signature data that is captured at the SAE
Administrator Console (“View and review e-Signatures” on page 99).
• Information was added regarding system dye calibration (“Maintenance” on page 113).

• Information was added regarding troubleshooting actions to take if the connection to the SAE Administrator
Console is lost (Appendix E, “Troubleshooting”).
• Instructions were added for using FSA files for troubleshooting run and instrument issues (“Field Service
Archive files” on page 116).
 Revision Date Description
C.0 29 September • Added an appendix documenting the use of Security, Auditing, and E‑signature (SAE) v2.2 software with
2021 QuantStudio™ Absolute Q™ Digital PCR Software (Appendix C, “Use the software with Security, Auditing,
and E‑signature (SAE) v2.2”).
• Information was added regarding the Security, Auditing, and E‑signature (SAE) v2.2 software (“Software
description” on page 11).
• Information was added for the use of the Security, Auditing, and E‑signature (SAE) v2.2 software for system
security (“QuantStudio™ Absolute Q™ Digital PCR Software security” on page 17).
• Instructions were revised for placing MAP plate gasket strips on the MAP plate (“Load the reagent mix into
the MAP plate” on page 23).

B.0 13 September • Updated graphics in the Analysis page section with optical dye channel information.
2021
• Instructions were revised for preparing the dPCR reagent mix with steps to thaw or equilibrate reagents
before use and to vortex Absolute Q™ DNA Digital PCR Master Mix (5X) and Digital PCR assay (“Prepare the
dPCR reaction mix” on page 22).

A.0 1 September 2021 New publication documenting instrument functions and data analysis features of the QuantStudio™ Absolute Q™
Digital PCR System.

The information in this guide is subject to change without notice.

DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE
LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR
ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.
Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these
products, you accept the terms and conditions of all applicable Limited Use Label Licenses.
TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. Windows is
a trademark of Microsoft Corp.. Dell is a trademark of Dell, Inc.. CY is a registered trademark of Global Life Sciences Solutions Germany
GmbH.
©2021-2023 Thermo Fisher Scientific Inc. All rights reserved.
 Contents

■ CHAPTER 1 Product information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Product description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Instruments, kits, consumables, and accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Digital PCR Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Required materials not supplied . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Recommended materials not supplied . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Software description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Instrument hardware description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Overview of the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
QuantStudio™ Absolute Q™ MAP16 Digital PCR Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
QuantStudio™ Absolute Q™ MAP16 Digital PCR Plate compatibility . . . . . . . . . . . . . . 16
Network and password security requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Network configuration and security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Password security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
QuantStudio™ Absolute Q™ Digital PCR Software security . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

■ CHAPTER 2 Prepare and run an experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Prepare the DNA samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Nucleic acid isolation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Quality of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Quantity of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Sample dilution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Determine the optimal dilution when the target is known . . . . . . . . . . . . . . . . . . . . . . . . 20
Determine the optimal dilution when the target is unknown . . . . . . . . . . . . . . . . . . . . . . 21
Prepare the dPCR reaction mix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Load the reagent mix into the MAP plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Run digital PCR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Power on the instrument and computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Create a custom protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Select a protocol for a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Load the plate and run the protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Download a protocol from the Instrument page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

4 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Contents

■ CHAPTER 3 Analyze data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Software features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Runs page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Select a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
SETUP page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Change the run name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Sample selection and names . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Hide samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Download a protocol from the SETUP page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Manage groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Manage group sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
ANALYSIS page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
View by samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
View by groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Plot types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Set thresholds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Overlay samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Show array images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Export data from the ANALYSIS page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
RESULTS page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
View results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Export data from the RESULTS page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Generate reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Export and import runs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Export a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Import a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Delete a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

■ APPENDIX A Modify protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

■ APPENDIX B Install, update, and move the QuantStudio™ Absolute Q™

Digital PCR System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

Installation and environmental requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

Install the QuantStudio™ Absolute Q™ Digital PCR System . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Download and install the desktop software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Computer requirements for the desktop software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Download the desktop software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Install the desktop software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Update the instrument software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Moving the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Install the shipping lock screw . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Uninstall the shipping lock screw . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 5
Contents

■ APPENDIX C Use the software with Security, Auditing, and

E‑signature (SAE) v2.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

Overview of the SAE Administrator Console components . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

Overview of the QuantStudio™ Absolute Q™ Digital PCR Software
functionality when SAE functions are enabled . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Recommendations for SAE passwords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
SAE functions not supported by the QuantStudio™ Absolute Q™ Digital
PCR Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Enable SAE functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Install the SAE Administrator Console and Absolute Q™ application profile . . . . . . . . 93
Connect to the SAE server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Enable SAE functions in QuantStudio™ Absolute Q™ Digital PCR Software . . . . . . . . 94
Sign into QuantStudio™ Absolute Q™ Digital PCR Software using an SAE account . . . . . . 94
Sign out of the software using an SAE account . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Change your SAE account password . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Default permissions and roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Use audit functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Specify audit reason . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
View audit records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Export audit records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Sign data in the software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
View and review e-Signatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Review plate setup e-Signature information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Review plate results e-Signature information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Disable SAE functions in QuantStudio™ Absolute Q™ Digital PCR Software . . . . . . . . . . . 112

■ APPENDIX D Maintain the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

Clean the instrument and plate nest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

■ APPENDIX E Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114

Field Service Archive files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116

Capture and transfer data and log FSA files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Capture and transfer system FSA files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117

■ APPENDIX F Product Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118

QuantStudio™ Absolute Q™ Digital PCR Instrument specifications . . . . . . . . . . . . . . . . . . . 118

Dedicated computer requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
QuantStudio™ Absolute Q™ Digital PCR Instrument Optical Configuration . . . . . . . . . . . . 119

6 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Contents

■ APPENDIX G Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120

Symbols on this instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121

Standard safety symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Control and connection symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Conformity symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Safety information for instruments not manufactured by Thermo Fisher Scientific . . . . . 123
Instrument safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
General . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Hot Surface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Air inlet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Physical injury . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Electrical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Cleaning and decontamination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Instrument component and accessory disposal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Safety and electromagnetic compatibility (EMC) standards . . . . . . . . . . . . . . . . . . . . . . . . . 127
Safety standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
EMC standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Chemical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
Biological hazard safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130

■ APPENDIX H Documentation and support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131

Related documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131

Customer and technical support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Limited product warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 7
 1 Product information

■ Product description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
■ Instruments, kits, consumables, and accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
■ Digital PCR Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
■ Required materials not supplied . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
■ Recommended materials not supplied . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
■ Software description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
■ Instrument hardware description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
■ QuantStudio™ Absolute Q™ MAP16 Digital PCR Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
■ Network and password security requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
■ QuantStudio™ Absolute Q™ Digital PCR Software security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

IMPORTANT! Before using this product, read and understand the information in the “Safety” appendix
in this document.

Product description
The QuantStudio™ Absolute Q™ Digital PCR System enables precision quantification of target nucleic
acid sequences. Using patented microfluidic array technology, QuantStudio™ Absolute Q™ MAP16
Digital PCR Plates (MAP plates) are loaded with digital PCR (dPCR) reagents and then processed by the
QuantStudio™ Absolute Q™ Digital PCR Instrument. Depending on the protocol, results can be provided
in less than 90 minutes. The resulting data are visualized with the QuantStudio™ Absolute Q™ Digital
PCR Software. The QuantStudio™ Absolute Q™ Digital PCR System is for research use only, not for use
in diagnostic procedures.

8 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 1 Product information
Instruments, kits, consumables, and accessories 1

Instruments, kits, consumables, and accessories

The following table describes the products covered in this user guide.
Catalog numbers that appear as links open the web pages for those products.

Instrument system

Item Cat. No. Amount

QuantStudio™ Absolute Q™ Digital PCR System: A52864 1 instrument, 1 desktop

• QuantStudio Absolute Q Digital PCR Instrument
™ ™ computer and monitor

• Dell™ OptiPlex XE3 Tower computer with monitor, keyboard,

and mouse

Instrument accessories

Item Catalog No. Amount

QuantStudio™ Absolute Q™ MAP16 Plate Kit includes: A52865 1

• 12 QuantStudio Absolute Q MAP16 Digital PCR Plates
™ ™

• 60 QuantStudio™ Absolute Q™ MAP plate gasket strips

• 3 mL QuantStudio™ Absolute Q™ Isolation Buffer

QuantStudio™ Absolute Q™ Digital PCR Starter Kit

[1]
A52732 1

Reagents

Item Catalog No. Amount

Absolute Q™ DNA Digital PCR Master Mix (5X) A52490 200 reactions

QuantStudio™ Absolute Q™ Isolation Buffer A52730 (1) 3 mL bottle

[1] The kit is required for system installation. See QuantStudio™ Absolute Q™ Digital PCR Starter Kit User Guide (Pub No. MAN0025653).

Digital PCR Assays

Pre-designed and custom dPCR assays are available for use in dPCR experiments. For more
information contact your local sales representative or go to http://www.thermofisher.com/dpcr-
assays.html.
For information on the use of pre-designed dPCR assays, see the documentation provided with the
assay available at http://www.thermofisher.com/dpcr-assays.html.
Use this guide to perform experiments with custom dPCR assays ordered from Thermo Fisher Scientific
or with your unique custom assay protocols.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 9
 Chapter 1 Product information
1 Required materials not supplied

Required materials not supplied

Unless otherwise indicated, all materials are available through thermofisher.com. "MLS" indicates that
the material is available from fisherscientific.com or another major laboratory supplier.

Item Source

Equipment

Centrifuge, table top MLS

Pipettes, P10, P20, and P200 MLS

Filter pipette tips, P10, P20, and P200 MLS

Other consumables

Low bind microcentrifuge tubes MLS

Microcentrifuge tube rack MLS

Nuclease-Free Water MLS

Microfiber or optical lens cleaning cloth MLS

70% ethanol in water MLS

Recommended materials not supplied

Note: For information on the recommended kits for nucleic acid isolation, see http://
thermofisher.com/magmax.

Unless otherwise indicated, all materials are available through thermofisher.com. "MLS" indicates that
the material is available from fisherscientific.com or another major laboratory supplier.

Item Source

Spectrophotometer MLS

Qubit™ Flex Fluorometer Q33327

KingFisher™ Apex with 24 Combi Head 5400940

KingFisher™ Apex with 96 Deep-Well Head 5400930

10 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 1 Product information
Software description 1

Software description
The QuantStudio™ Absolute Q™ Digital PCR System uses the following software:
• QuantStudio™ Absolute Q™ Digital PCR Software—Controls the instrument, performs user-defined
experiments, analyzes data generated by the experiment. Parameters such as plate format, optical
channels, and thermal conditions for an experiment can be modified as needed prior to the start of
data generation. The software lets you to perform the following tasks:
– Define the experiment, including sample types, sample groups, replicates, pool sample,
experiment notes, and names
– Create and edit protocols
– Run and monitor protocols
– View system status
– View data in plot and tables
– Generate run reports
– Export data and reports
– Insert and remove MAP plates
– Install the shipping lock screw for transport of the instrument
• ThermoFisher Connect Transfer Software (Optional)—Data transmission feature that collects
instrument run data to send to Thermo Fisher Scientific to be used for improving the product
and user experience.
• Security, Auditing, and E‑signature (SAE) v2.2 (Optional)—Controls security and user access to the
software and specific features. See Appendix C, “Use the software with Security, Auditing, and
E‑signature (SAE) v2.2”.

The software is installed during system installation. See “Download and install the desktop software” on
page 86.

Instrument hardware description

Overview of the instrument
The instrument is an integrated processing system compatible with QuantStudio™ Absolute Q™ MAP16
Digital PCR Plates.
A dedicated computer provided with the instrument uses the QuantStudio™ Absolute Q™ Digital PCR
Software to operate the instrument and analyze data.
For information on installing the instrument, see Appendix B, “Install, update, and move the
QuantStudio™ Absolute Q™ Digital PCR System”.
For information on maintaining the instrument, see Appendix D, “Maintain the instrument”.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 11
 Chapter 1 Product information
1 Instrument hardware description

4 5

1 Shipping lock screw

2 Status indicator light
3 Plate presentation tray open/close button
4 Power switch, power port, USB port
5 Plate presentation tray

The instrument has the following features and functions:

• The plate presentation tray is controlled using a button on the front panel or from within the
software. Once a MAP plate is loaded into the tray, it is retracted into the instrument for automated
processing.
• An internal barcode scanner verifies the barcodes on the MAP plates.
• An internal compressor and pneumatic subsystem drives the microfluidic array
compartmentalization directly within the MAP plate using positive pressure.
• Liquid never contacts any parts in the instrument, so minimal maintenance and cleaning are
required.
• The plate nest is thermally controlled to perform PCR thermal cycling.
• The fluorescent optical system is mounted above the MAP plate and scans the MAP plate in up to
5 optical channels before and after PCR.
• Each optical channel is associated with a color and a supported dye. See “QuantStudio™ Absolute
Q™ Digital PCR Instrument Optical Dyes” on page 13.
• A computer integrated into the instrument manages critical runtime activities and stores recent data
that have not yet been analyzed.
• During an experiment run, positive pressure is applied to drive and separate the reagent mix into
pico-scale microreaction chambers on the MAP plate before starting PCR. PCR occurs in parallel
across the entire MAP plate. Each microreaction chamber contains a discrete reaction.
• The microreaction chamber arrays are scanned for fluorescence before and after PCR and are used
for data analysis.

12 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 1 Product information
Instrument hardware description 1

Instrument indicator status light key

The vertical bars of the Q symbol on the front of the instrument display the instrument status.

Appearance Color Status Meaning

White Flashing On, initializing – not ready.

White Steady On, not connected to software.

Blue Steady On, ready.

Blue Pulsing Running protocol.

Yellow Brief flashing Plate door open button pushed while door is locked.

Red Steady Error, see Appendix E, “Troubleshooting”.

QuantStudio™ Absolute Q™ Digital PCR Instrument Optical Dyes

The following optical dyes are supported for use when selecting optical channels when analyzing
experiment runs.
For more information on optical configuration, see “QuantStudio™ Absolute Q™ Digital PCR Instrument
Optical Configuration” on page 119.

Channel color System dyes

Blue FAM™ dye

Green VIC™ dye (recommended)

HEX™ dye

Yellow ABY™ dye

Red ROX™ dye

Dark Red CY™5 dye (recommended)

JUN™ dye

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 13
 Chapter 1 Product information
1 QuantStudio™ Absolute Q™ MAP16 Digital PCR Plates

QuantStudio™ Absolute Q™ MAP16 Digital PCR Plates

The QuantStudio™ Absolute Q™ Digital PCR Instrument uses QuantStudio™ Absolute Q™ MAP16 Digital
PCR Plates (MAP plates) for loading samples and running experiments.

IMPORTANT! When disposing of plates, follow all applicable waste regulations controlling the
chemicals used in the experiment.

Each MAP plate has the following features:

• Contains 16 wells, 4 columns of 4 wells each, and each experiment must use at least one full
column (4 samples).
• Contains 16 digital PCR microreaction chamber arrays that each contain 20,480 fixed volume
microreaction chambers where dPCR is performed.
• Can be used in up to 4 experiments, depending on the number of columns used in each
experiment. A MAP plate with unused columns can be used with subsequent experiments until
all 4 columns have been used.
• Has a standard microtiter plate footprint and is compatible with most plate and liquid handlers.
• Has a label that includes a barcode, product number, and unique serial number. The instrument
automatically reads the barcode when the MAP plate is inserted, and the unique serial number is
tracked in the results.
• Requires 1 MAP plate gasket strip be placed on each column before insertion into the instrument,
regardless of whether the column is being used for the experiment.

Note: MAP plate gasket strips can only be used once per MAP plate.

1 2 3 4 X

2
3
C

Figure 1 MAP plate without MAP plate gasket strips

1 Columns 1–4 and column X
2 A–D represents wells A1–D1 associated with column 1
3 Microreaction chamber associated with well 4C

14 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 1 Product information
QuantStudio™ Absolute Q™ MAP16 Digital PCR Plates 1

Figure 2 MAP plate gasket strip

1 This end of the MAP plate gasket strip is placed on row A of the MAP plate
2 This end of the MAP plate gasket strip is placed on row D of the MAP plate

1 2 3 4 X

Figure 3 MAP plate with MAP plate gasket strips in place

1 MAP plate gasket strips on columns 1–4 and column X

The following figure shows the dimensions of a MAP plate.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 15
 Chapter 1 Product information
1 Network and password security requirements

128 mm (5 in.)

A1
85.5 mm (3.4 in.)

Figure 4 MAP plate dimensions

QuantStudio™ Absolute Q™ MAP16 Digital PCR Plate compatibility

IMPORTANT! The instrument is only compatible with QuantStudio™ Absolute Q™ MAP16 Digital PCR
Plates. The instrument can malfunction with third-party plates, which could result in contamination of
the instrument.

• For best results, we strongly recommend that you use Absolute Q™ DNA Digital PCR Master Mix
(5X) and QuantStudio™ Absolute Q™ Isolation Buffer.
• MAP plates are made of injection molded thermoplastic commonly used in other PCR vessels
and are generally compatible with most existing reagent kits and components available from third
parties. Compatibility of any untested third-party reagent is not guaranteed. Contact technical
support for more information on tested reagents (see Appendix H, “Documentation and support”).

Network and password security requirements

Network configuration and security
The network configuration and security settings of your laboratory or facility (such as firewalls, anti-
virus software, network passwords) are the sole responsibility of your facility administrator, IT, and
security personnel. This product does not provide any network or security configuration files, utilities, or
instructions.
If external or network drives are connected to the software, it is the responsibility of your IT personnel
to ensure that such drives are configured and secured correctly to prevent data corruption or loss. It
is the responsibility of your facility administrator, IT, and security personnel to prevent the use of any
unsecured ports (such as USB, Ethernet) and ensure that the system security is maintained.

16 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 1 Product information
QuantStudio™ Absolute Q™ Digital PCR Software security 1

Password security
Thermo Fisher Scientific strongly recommends that you maintain unique passwords for all accounts in
use on this product. All passwords should be reset upon first sign in to the product. Change passwords
according to your organization's password policy.
It is the sole responsibility of your IT personnel to develop and enforce secure use of passwords.

QuantStudio™ Absolute Q™ Digital PCR Software security

By default, the QuantStudio™ Absolute Q™ Digital PCR Software does not require login credentials to
access the software nor does it restrict access to functions within the software.
To require login credentials and modify access by user roles, see Appendix C, “Use the software with
Security, Auditing, and E‑signature (SAE) v2.2”.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 17
 2 Prepare and run an experiment

This chapter provides a general protocol for preparing experiments using custom dPCR assays ordered
on http://www.thermofisher.com/dpcr-assays.html or with your unique custom dPCR assays. For
predesigned dPCR assays, follow the instructions in the user guide for your particular assay.

Workflow
This workflow represents running a single experiment on the QuantStudio™ Absolute Q™ Digital PCR
Instrument.

Note: The procedure for sample preparation can vary depending on application and reagents.

Experiment workflow

Prepare the DNA samples (page 19)

Prepare the dPCR reaction mix (page 22)

Load the reagent mix into the MAP plate (page 23)

Run digital PCR (page 28)

Analyze data (page 37)

Finish

18 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 2 Prepare and run an experiment
Prepare the DNA samples 2

Prepare the DNA samples

We recommend the following best practices for the preparation of DNA template (genomic DNA (gDNA)
or complementary DNA (cDNA)) for use in digital PCR (dPCR) experiments. Because dPCR experiment
strategy and methodology can vary significantly, sample preparation and template quality must be
assessed on an individual basis.

Nucleic acid isolation

Determine the extraction procedure that is optimal for your workflow. High-quality nucleic acids can be
isolated from various sample types. Different procedures can be used for downstream dPCR analysis,
depending on your workflow. Each procedure obtains nucleic acid at a different concentration, and the
concentration of the nucleic acid must be within the dynamic range of the instrument.
For more information on recommended kits for nucleic acid isolation, see “Recommended materials not
supplied” on page 10.

Quality of DNA
Use a gDNA or cDNA template that meets the following criteria:
• Is extracted from the raw material that you are testing with an optimized protocol.

Note: Salting-out procedures and crude lysates are not recommended.

• Does not contain PCR inhibitors
• Has an A260/230 and A260/280 ratio between 1.7 and 1.9

The ratio of absorbency at 260 nm and 280 nm is used to assess the purity of DNA and RNA. A ratio of
~1.8 is generally accepted as “pure” for DNA. A ratio of ~2.0 is generally accepted as “pure” for RNA.
If the ratio is appreciably lower in either case, it may indicate the presence of protein, phenol, or other
contaminants that absorb strongly at or near 280 nm.
The ratio of absorbency at 260 nm and 230 nm is used as a secondary measure of nucleic acid
purity. The 260/230 values for “pure” nucleic acid are often higher than the respective 260/280 values.
Expected 260/230 values are commonly in the range of 2.0–2.2. If the ratio is appreciably lower than
expected, it may indicate the presence of contaminants that absorb at 230 nm.

Quantity of DNA
The quantity of DNA template added to a dPCR reaction depends on the following factors:
• Concentration of gDNA or cDNA present in each sample
• Expected number of copies of the target sequence present in the genome or cDNA of your
samples

Before performing digital PCR experiments, consider quantifying the amount of gDNA or cDNA in each
sample.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 19
 Chapter 2 Prepare and run an experiment
2 Prepare the DNA samples

We recommend one of the following methods for quantification, see “Recommended materials not
supplied” on page 10.
• Quant-iT™ 1X dsDNA Assay Kit, High Sensitivity using the Qubit™ Flex Fluorometer
• Spectrophotometer

Sample dilution
If a target is present at a sufficiently high concentration in the sample of interest, it is possible that all
reaction replicates will be positive, thereby preventing the determination of the target concentration. In
this case, the sample must be diluted prior to running the dPCR experiment.

Determine the optimal dilution when the target is known

In a dPCR experiment, gDNA samples are diluted to a limiting quantity, to the extent that most
individual PCR reactions contain either zero or one target molecule. If the target copy number per
genome is known, dilute the extracted DNA to the optimal input range as described in the following
sections.
• “Determine the target copy number per genome” on page 20
• “Dilute the extracted genomic DNA to the ideal input range” on page 21

Determine the target copy number per genome

This section provides examples of calculations for determining the target copy number per genome.
Other calculation methods can be used. For information on the human genome, see On the length,
weight and GC content of the human genome, Piovesan et al. BMC Res Notes (2019) 12:106 https://
www.ncbi.nlm.nih.gov/pmc/articles/PMC6391780/pdf/13104_2019_Article_4137.pdf.

1. If the source or species of the gDNA is known, using a genome size checker tool, determine the
size of the genome.
http://www.thermofisher.com/DNA-calculator
The size checker estimate of the single human genome is 3.2 × 109 bp (haploid).

2. Using the size of the genome determined in step 1, calculate the genome mass using the following
formula:
m = (n) (1.096 × 10-21 g/bp), where m is the genome mass, and n is the genome size in base pairs
The following example calculates the mass of the human genome using the estimate of 3.2 × 109
bp (haploid) for (n).
m = (3.2 × 109 bp) (1.096 × 10-21 g/bp)
m = 3.5 × 10-12 gram (g) or 3.5 picogram (pg)

3. Using the mass of the genome calculated in step 2, refer to a public database of genomic
variants to identify the copies of the target sequence per single genome. For example, http://
dgv.tcag.ca/dgv/app/home.
The following example determines the genomic copy ratio to the mass of the human genome
of the RNase P gene (single exon RPPH1 gene) located on chromosome 14 cytoband 14q11.2.
(chr.14:20343370 on build GRCh38).
RNase P gene copies per haploid human genome mass: 1 copy/3.5 pg

20 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 2 Prepare and run an experiment
Prepare the DNA samples 2

In other words, 1 copy of the RNase P target sequence can be found in every 3.5 pg of human
DNA. This example is relevant to any gene that is present at the normal rate of one copy per
haploid genome (two copies per diploid genome) and provides a basis to perform a dPCR
experiment to determine the optimal digital range.

Dilute the extracted genomic DNA to the ideal input range

Based on the known target copy number per genome, dilute the samples so that each reaction well
contains approximately 0.6 to 1.6 copies of the target sequence.
Sample dilution = target copy number ÷ microchamber volume
For example, if 3.5 pg represents 1 copy of the target sequence in a 432 pL microchamber, dilute the
stock human gDNA of the sample to 8.1 ng/µl (3.5÷0.432) in the final dPCR reaction.
The expected result in the dPCR is ~1 copy gene target per reaction well.

Determine the optimal dilution when the target is unknown

If the target copy number per genome is unknown (e.g., for a locus of unknown copies per genome or
RNA of unknown expression level), we recommend that you determine the optimal dilution by preparing
a dilution series of the sample that includes three to four data points above and below the expected
digital range. This ensures that one of the data points is within the optimal digital range.
The Cq value is a function of concentration therefore 1 copy target sequence in different reaction
volumes produces different Cq values. Additionally, the actual Cq value in real time PCR always
depends on the primary analysis parameters set by the user, baseline, threshold, etcetera.
If tested using real-time PCR, the quantification cycle (Cq) values can be used to estimate the target
molecule input for the points of the dilution series prior to dPCR.
• 1 copy in total of 20 µL produces Cq of ~38—96-well plate
• 1 copy in total of 10 µL produces Cq of ~37—384-well plate
• 1 copy in total of 1.5 µL produces Cq of ~34.5—TaqMan™ Array Card
• 1 copy in total of 33 nL produces Cq of ~29—OpenArray™ Plate

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 21
 Chapter 2 Prepare and run an experiment
2 Prepare the dPCR reaction mix

Prepare the dPCR reaction mix

This section provides general information for using the Absolute Q™ DNA Digital PCR Master Mix (5X)
and your dPCR assay to prepare a dPCR reaction mix.
For information on preparing the dPCR reaction mix for a pre-designed Absolute Q™ dPCR assay, see
the documentation provided with the assay.

Note: Other dPCR reagents are compatible with the MAP plates and can be used to create the dPCR
reagent mix. For more information on specific applications, contact technical support (see Appendix H,
“Documentation and support”).

Gather the following materials:

• Absolute Q™ DNA Digital PCR Master Mix (5X)
• Nuclease-free water
• Digital PCR assay (40X or 20X)

IMPORTANT!
· Throughout this procedure, protect reagents from light when not in use.
· For best results, perform the run within one hour of reaction preparation.

1. Thaw and equilibrate all reagents to room temperature before use.

Note:
· Store reagents on ice when not in use.
· Limit number of reagent freeze/thaw cycles.

2. Pulse vortex the Absolute Q™ DNA Digital PCR Master Mix (5X) and dPCR assay (40X or 20X) at
high speed for 10 seconds.

3. Using a benchtop centrifuge, centrifuge the DNA sample at 10,000 × g or the highest speed
available for 1 minute, then transfer the supernatant to the reaction mix as indicated in step 4.

22 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 2 Prepare and run an experiment
Load the reagent mix into the MAP plate 2

4. Combine the following reagents in the order listed.

Volume per reaction with

Reagent Final Concentration Volume per reaction
10% overage[1]
Nuclease-free water – Fill to 9 μL Fill to 10 μL
Absolute Q™ DNA Digital 1X 1.8 μL 2 μL
PCR Master Mix (5X)
Digital PCR assay (40X or 1X 0.23 μL (40 X) 0.25 μL (40 X)
20X)[2] or or
0.45 μL (20X) 0.50 μL (20X)
DNA Sample 1–11,000 copies/ μL[3] Variable Variable
Total – 9 μL 10 μL
[1] After calculating the number of reactions required, prepare the dPCR mix for the appropriate number of reactions and scale
those components by 10% for overage. Dilute the assay accordingly to avoid pipetting less than 1 μL volumes.
[2] If you are using a dPCR assay with a stock concentration other then 40X or 20X you must manually calculate the volumes
based on the concentration you are using.
[3] A DNA copy and dilution calculator can be found at http://www.thermofisher.com/DNA-calculator.

5. Mix the dPCR reagents well by performing one of the following actions:
• Pipette mix 10–20 times, or
• Pulse vortex 3–5 times for 1 second each.

6. Centrifuge at 1,000 × g for up to 1 minute.

7. Perform the run within one hour of reaction preparation.

Load the reagent mix into the MAP plate

At a clean lab bench, gather the following materials:
• P10 or P20 pipette and filter pipette tips
• Prepared dPCR reaction mix
• QuantStudio™ Absolute Q™ Isolation Buffer
• MAP plate with sufficient unused columns for the experiment
• MAP plate gasket strips (unused)

IMPORTANT! At least 1 column of the MAP plate must be run at a time. Columns cannot be reused,
but a MAP plate with unused columns can be used for subsequent experiments. When the experiment
is complete, if the MAP plate has unused columns, place it back into its pouch for storage.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 23
 Chapter 2 Prepare and run an experiment
2 Load the reagent mix into the MAP plate

1. Just prior to use, remove the MAP plate from its package.

Note:
· Leave the MAP plate in the package until ready to load sample.
· Be careful to handle the MAP plate by its frame.
· Place the MAP plate back into the package when not in use.

1 2 3 4 X

2
3
C

Figure 5 MAP plate without MAP plate gasket strips

1 Columns 1–4 and column X
2 A–D represent wells A1–D1 associated with column 1
3 Array associated with well 4C

2. Place the MAP plate on a level, dust-free, dry surface.

24 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 2 Prepare and run an experiment
Load the reagent mix into the MAP plate 2

3. Using a new pipette tip for each well, at a 45° angle, load 9 μL of the dPCR reagent mix to the
bottom of the well. Pipette the mixture only to the first stop to prevent bubble formation.
IMPORTANT! Do not contact bottom of well with the pipette tip or puncture the thin film at the
bottom of the well.

1 Microfluidic channel to the microreaction chamber array

2 Reagent remains in the well until the instrument pushes it into the microreaction chamber array during the run

4. Using a new pipette tip for each well, at a 45° angle, load 15 μL of the Absolute Q™ Isolation Buffer
on the side of the well above the top of the reagent mix. Carefully overlay the buffer on top of the
reagent mix to prevent mixing or bubble formation. Pipette only to the first stop.
The isolation buffer sits on top of the reagent, preventing contamination and evaporation.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 25
 Chapter 2 Prepare and run an experiment
2 Load the reagent mix into the MAP plate

5. Place a total of 5 MAP plate gasket strips on all 4 columns of wells and the X-shaped posts on the
column X on the right side of the plate. Orient the MAP plate gasket strip so that the side labeled
A–D aligns with rows A–D marked on the plate. Be sure to cover the columns completely and press
the MAP plate gasket strips firmly into place.
IMPORTANT! MAP plate gasket strips must be placed on all columns, including unused columns.
Failure to do so can produce poor results.

Figure 6 MAP plate gasket strip

1 Place this end of the MAP plate gasket strip on row A
2 Place this end of the MAP plate gasket strip on row D

26 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 2 Prepare and run an experiment
Load the reagent mix into the MAP plate 2

Figure 7 Press the MAP plate gasket strips firmly into place

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 27
 Chapter 2 Prepare and run an experiment
2 Run digital PCR

1 2 3 4 X

Figure 8 MAP plate with MAP plate gasket strips in place

1 MAP plate gasket strips on columns 1–4 and column X

6. Move the MAP plate to the instrument.

IMPORTANT! Do not tip, invert, or shake the filled MAP plate.

Run digital PCR

Power on the instrument and computer
IMPORTANT! Prior to powering on the QuantStudio™ Absolute Q™ Digital PCR Instrument, confirm
that the shipping lock screw has been removed. Failure to do so can damage the instrument. See
“Uninstall the shipping lock screw” on page 89.

1. Confirm that the power cable is connected to an appropriate power source.

2. Confirm that the USB cable is connected from the instrument to the dedicated computer.

3. Power on the dedicated computer and monitor, then start the software.

4. Power on the instrument by moving the power switch located on the left side near the back of the
instrument to the I position.

Note: The instrument makes a humming noise as it charges the internal compressor.

The bars of the instrument symbol flash white to indicate that the system is initializing. This takes
approximately 30 seconds.
The instrument is ready when the status lights are a steady blue and a ready status appears under
the instrument on the Instrument page in the QuantStudio™ Absolute Q™ Digital PCR Software.

28 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 2 Prepare and run an experiment
Run digital PCR 2

Create a custom protocol

The QuantStudio™ Absolute Q™ Digital PCR Software is pre-configured with the Absolute Q™ Starter
(default) protocol to use as a template for creating your first custom protocol. Protocols created from
this default protocol can be edited or used as templates to create additional custom protocols.
For information on protocol settings for a pre-designed Absolute Q™ dPCR assay, see the
documentation provided with the assay.

Note: The default protocol cannot be edited.

Protocols define the following run information:

• Dyes used in each active optical channel
• PCR parameters

1. In the left pane, click to access the Instrument page.

2. In the PROTOCOL pane, click PROTOCOL, then in the Protocols screen, select a protocol.

Note: For your first custom protocol, select the default protocol.

3. Click to create a copy of the protocol.

A copy of the protocol is added to the protocol list.

4. (Optional) Use the following options to make changes to a protocol.

Option Action
Rename the protocol. 1. Select the protocol, then click .
2. In the name field, type a new name and press Enter.

Delete a protocol. Select the protocol, then click .

Copy a protocol. Select the protocol, then click .

5. Select the new protocol, then click LOAD.

6. In the PROTOCOL pane, click .

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 29
 Chapter 2 Prepare and run an experiment
2 Run digital PCR

7. In the Channels area, set the optical channels as needed.

Parameter Action
Active optical channel Select the check box for each optical channel to be used.
Target dye for active channel For each active optical channel, select the drop-down to choose the
target dye.

1
2

Figure 9 Optical channel dyes

1 Dye channel check box
2 Dye channel name

8. Modify PCR parameters as needed.

Parameter Actions
Temperature • Enter a value in the temperature fields.
• Drag the slider bars to adjust the temperature.

Dwell times Enter in seconds or minutes and seconds in mm:ss format.

Cycles Set the number of cycles by entering a value into the Cycles field.
RNA-RT Select RNA-RT to add an extra temperature step for RNA reverse transcription
to cDNA for RNA samples. Not required for DNA samples.
Preheat Select Preheat to add a preheat step. Sometimes called hot start, preheating
the samples before PCR helps to reduce non-specific binding at lower
temperatures.

30 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 2 Prepare and run an experiment
Run digital PCR 2

(continued)
Parameter Actions
Two or three-step Select the Two Step drop-down to select 2 or 3 step cycling.
cycling
Two-stage PCR cycle Select Two Stage PCR to add a second PCR cycle stage.

6 5 4 3

Figure 10 Protocol parameters

1 Temperature settings fields and slider bar
2 Time fields and cycles field
3 Two-stage PCR setting
4 Two or three step cycling option
5 Preheat setting
6 RNA-RT setting

9. Select SAVE.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 31
 Chapter 2 Prepare and run an experiment
2 Run digital PCR

Select a protocol for a run

1. In the left pane of the QuantStudio™ Absolute Q™ Digital PCR Software, select to access the
Instrument page.

2. Select PROTOCOL, then perform one of the following tasks:

Task Actions
Select an existing 1. Select PROTOCOL.
protocol.
2. Select a protocol from the Protocols list.
3. Select LOAD.

Edit the loaded 1. In the PROTOCOL pane, click .

protocol.
2. Modify the optical channels and PCR parameters as needed. See
Appendix A, “Modify protocols”.
3. Select SAVE.

Create a custom See “Create a custom protocol” on page 29.

protocol
Import a protocol. 1. Select PROTOCOL.
2. In the Protocols list area click .
3. Select IMPORT FILE, then navigate to the location of the protocol file.
4. Select the file, then select Open.
5. Select the imported protocol from the Protocols list.
6. Select LOAD.

Load the plate and run the protocol

IMPORTANT! You must clean the plate nest before each run. See “Clean the instrument and plate
nest” on page 113.

IMPORTANT! Before running the protocol, make sure your protocol parameters are defined correctly.
Protocol parameters cannot be changed after the run. See “Select a protocol for a run” on page 32 or
Appendix A, “Modify protocols”.

1. In the left pane, click to access the Instrument page.

2. In the sample plate area, use the check boxes above the plate to select the columns to be used in
the run.
IMPORTANT! Failure to deselect the columns that are not in use will prevent them from being
used in a subsequent run.

32 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 2 Prepare and run an experiment
Run digital PCR 2

3. Use the following options to manage samples for the run.

Option Actions
Edit a sample 1. In the sample plate area, click the on the sample well, then enter a sample
name. name.
2. Perform one of the following actions to save the sample name.
• Click away from the sample name field.
• Press enter to save the edit and open to the next sample name in the same
column for editing.

Modify an 1. Below the sample plate area, select EDIT GROUPS to open the groups dialog
existing group box.
or create
2. Select NEW GROUP in the Group list to add a new group.
additional
groups. 3. In the Group name field, enter or change the name for the group
4. In the Target DNA fields, enter or change the name of the DNA target for each
active optical channel.
5. From the Analysis drop-down, select the analysis type for each optical channel.
6. From the SAMPLES area, select one of the following sample grouping options:
• Individual
• Replicates
• Pooling
7. Select SAVE in the groups dialog box.

4. Assign samples to a group by performing the following actions.

a. In the sample plate area select one or more samples to be included in a group.
Previously defined groups appear above the sample plate grid.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 33
 Chapter 2 Prepare and run an experiment
2 Run digital PCR

b. Select the group for these samples.

1 Group list area

5. (Optional) To reset the plate to default values at any time during the plate loading process, select
RESET PLATE.

6. (Optional) In the Notes field, enter information regarding this run, then click ADD NOTE.

7. Click the START button under the instrument icon.

The instrument door opens to receive the loaded MAP plate.
IMPORTANT! Confirm that gaskets are placed on all columns of the MAP plate, including unused
columns. Failure to do so can produce poor results.

8. When prompted, verify that gaskets have been placed on all wells and on the column X posts on
the far right as shown on the screen.

Note: See callout 5 in the following figure for the location of column X.

34 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 2 Prepare and run an experiment
Run digital PCR 2

9. Carefully load the MAP plate in the plate nest.

IMPORTANT! Be sure to load the MAP plate gently to avoid damage to the plate nest.

10. Select CLOSE DOOR.

The door closes and the MAP plate bar code is scanned and is displayed in the Run name dialog
box.

Note: If the instrument cannot scan the barcode, it can be manually added in the Plate Barcode
field of Run name dialog box.

11. When prompted, enter a Run name.

12. Click RUN.

• The run status displays in the left sidebar.
• While processing the run, the instrument lights slowly pulse blue.
• When the run is complete, the instrument lights are a steady blue.
• Data populates the ANALYSIS tab on the Runs page as it becomes available.

13. When the Run complete dialog displays, select the run name to view the final data in the Runs
page.
For more information on analyzing experiment results, see Chapter 3, “Analyze data”.

Download a protocol from the Instrument page

You can save a protocol that you have created or modified to use on another computer using the
QuantStudio™ Absolute Q™ Digital PCR Software by using the download option on the Instrument
page.

1. In the left pane, click to access the Instrument page.

2. Select PROTOCOL, then select a protocol from the Protocols list.

3. Above the Channels list, click .

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 35
 Chapter 2 Prepare and run an experiment
2 Run digital PCR

4. Select one of following options.

• Download Protocol to download the protocol AQUA file.
• Download PNG to download a graphic representation of the protocol.

5. When prompted, navigate to the location where you want to save the file, then select Save.

36 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 3 Analyze data

■ Software features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
■ Runs page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
■ SETUP page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
■ ANALYSIS page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
■ RESULTS page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
■ Export and import runs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
■ Delete a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Software features
QuantStudio™ Absolute Q™ Digital PCR Software has the following pages:
• The Runs page lets you see experiment results organized by plate run and provides access to the
SETUP, ANALYSIS, and RESULTS pages for analyzing and viewing experiment results. See “Runs
page” on page 38.
• The SETUP page for a run provides controls for analysis options such as sample and target names,
sample groups, replicate statistics, pooling, and copy number calculations. See “SETUP page” on
page 39.
• The ANALYSIS page for a run displays relevant information by samples or groups and provides
different options for viewing the data. See “ANALYSIS page” on page 55.
• The RESULTS page for a run shows a summary of the run data and provides reporting and data
exporting options. See “RESULTS page” on page 73.

You can zoom in or zoom out on any page using the following keyboard shortcuts:
• ctrl+ + to zoom in
• ctrl+ - to zoom out

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 37
 Chapter 3 Analyze data
3 Runs page

Runs page
The Runs page lets you see experiment results organized by plate run. Recently completed runs require
a few minutes to complete the data analysis. The progress of the analysis is displayed in the Analyzed
column. A green check mark indicates that the analysis is complete.

Figure 11 Runs page overview

1 Runs page
2 Filter run criteria
3 Import run
4 Run analysis shortcut menu

When a run is being analyzed, the ANALYSIS and RESULTS pages periodically update with new
information.
Run data can be exported for analysis on another computer running the QuantStudio™ Absolute Q™
Digital PCR Software and imported from runs generated on a different instrument. See “Export and
import runs” on page 77.

Select a run
1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list.

3. (Optional) Use the filter option to find and select a run.

a. Click located above the run list.

38 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
SETUP page 3

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

Proceed to the SETUP page (see “SETUP page” on page 39), ANALYSIS page (see “ANALYSIS page”
on page 55}, and RESULTS page (see “RESULTS page” on page 73) to continue with the data
analysis of the run.

SETUP page
The SETUP page within the run lets you perform the following tasks:
• Change the run name. See “Change the run name” on page 39.
• Name the samples and set the analysis type. See “Name a sample” on page 41.
• Create and assign groups. See “Manage groups” on page 45.
• Save or load previously defined groups. See “Manage group sets” on page 50.
• Download the PCR thermal protocol or an image of the protocol. See “Download a protocol from
the SETUP page” on page 43.

Sample names and group analysis can be done before or during the run in the Instrument page or after
the run in Runs4SETUP page.

Change the run name

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the SETUP page.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 39
 Chapter 3 Analyze data
3 SETUP page

3. (Optional) Use the filter option to find and select a run, then select the SETUP page.
a. Click located above the run list.

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the upper-right corner of the sample plate area, click to enable editing.

5. Click next to the run name field, then enter the new name.

6. Click SAVE.

Sample selection and names

Sample names are user-assigned identifiers for the contents of each loaded well of a plate.
Groups determine what type of analysis is applied to all samples within a group.
Selecting a sample displays the analysis of that single sample.

Select samples
1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the SETUP page.

3. (Optional) Use the filter option to find and select a run, then select the SETUP page.
a. Click located above the run list.

40 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
SETUP page 3

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the upper-right corner of the sample plate area, click to enable editing.

5. In the sample plate area use the following options to select samples.

Option Actions
Select a single sample. 1. Select the sample check box.
2. Click anywhere in the sample area to select it.

Select multiple samples. 1. Click and drag through samples to select multiple samples at once.

6. Click SAVE.

Name a sample
1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the SETUP page.

3. (Optional) Use the filter option to find and select a run, then select the SETUP page.
a. Click located above the run list.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 41
 Chapter 3 Analyze data
3 SETUP page

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the upper-right corner of the sample plate area, click to enable editing.

5. In the sample plate area, click the on the sample well, then enter a sample name.

6. Perform one of the following actions to save the sample name.

• Click away from the sample name field.
• Press enter to save the edit and open to the next sample name in the same column for editing.

7. Click SAVE.

Hide samples
When samples are hidden, they are treated as if they were never run.
Hidden samples can be revealed. No data is lost by hiding a sample.
Hiding samples can be useful if there is an issue with the reagents, loading, or integrity of the sample.
Hiding samples has the following effect on the information that is included for display:
• No analysis results are shown for the samples.
• The samples are removed from the RESULTS page.
• The samples are excluded from reports.
• The samples are excluded from calculations for replicates or pooled results.

42 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
SETUP page 3

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the ANALYSIS page.

3. (Optional) Use the filter option to find and select a run, then select the ANALYSIS page.
a. Click located above the run list.

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the plot area, click .

5. On the sample to be hidden, click to hide the sample.

6. To reveal a hidden sample, click on the sample.

7. Click Save.

Download a protocol from the SETUP page

You can save a protocol that you have created or modified to use on another computer using the
QuantStudio™ Absolute Q™ Digital PCR Software by using the download option on the SETUP page.

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the SETUP page.

3. (Optional) Use the filter option to find and select a run, then select the SETUP page.
a. Click located above the run list.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 43
 Chapter 3 Analyze data
3 SETUP page

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the Protocol area, click .

5. Select one of following options.

• Download Protocol to download the protocol AQUA file.
• Download PNG to download a graphic representation of the protocol.

6. When prompted, navigate to the location where you want to save the file, then select Save.

44 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
SETUP page 3

Manage groups
After a run is completed, groups are used to define the analysis and results type for reporting for
individual samples or sets of samples. Once defined, a group can be edited or deleted.

Note: Only groups without samples can be deleted.

When samples are assigned to a group, they will all have the same definition for the following
characteristics of the sample:
• The target DNA associated with each fluorescent dye.
• The analysis type for each optical channel:
– CNV (Copy Number Variation)—Reporting ratio of CNV/CNV Ref
– CNV Ref (Copy Number Variation Reference)—The reference target for CNV

Note: The reference target is a gene of known and stable copy number used to calculate the
copy number for the gene of interest.

– Signal—Absolute quantification
– Not Used—Ignored in analysis
• Grouping options:
– Individual—Each sample has a separate result entry.
– Replicates—The results show the Mean, Standard Deviation, and the CV% of the
concentration for all the samples in the group.
– Pooling—The results treat all of the samples in the group as one large sample.

See the following sections for more information:

• To create groups, see “Create groups” on page 45.
• To edit groups, see “Edit groups” on page 47.
• To delete groups, see “Delete groups” on page 48.
• To add samples to groups, see “Assign samples to groups” on page 49.
• To save group sets, see “Save group sets” on page 50.
• To load group sets, see “Load group sets” on page 51.
• To edit group set names, see “Edit group set names” on page 52.
• To delete group sets, see “Delete group sets” on page 53.

Create groups
1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the SETUP page.

3. (Optional) Use the filter option to find and select a run, then select the SETUP page.
a. Click located above the run list.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 45
 Chapter 3 Analyze data
3 SETUP page

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the upper-right corner of the sample plate area, click to enable editing.

5. Below the sample plate area, select EDIT GROUPS to open the groups dialog box.

6. Select NEW GROUP in the Group list.

7. In the Group name field, enter a name for the group.

8. In the Target DNA fields, enter the name of the DNA target for each active optical channel.

9. From the Analysis drop-down, select the analysis type for each optical channel.

10. From the SAMPLES area, select one of the following sample grouping options:
• Individual
• Replicates
• Pooling

11. Select SAVE in the groups dialog box.

12. Select SAVE on the SETUP page.

46 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
SETUP page 3

Edit groups
1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the SETUP page.

3. (Optional) Use the filter option to find and select a run, then select the SETUP page.
a. Click located above the run list.

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the upper-right corner of the sample plate area, click to enable editing.

5. Below the sample plate area, select EDIT GROUPS to open the groups dialog box.

6. Select the group in the Name list.

7. Edit group settings as needed.

8. Select SAVE in the groups dialog box.

9. Select SAVE on the SETUP page.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 47
 Chapter 3 Analyze data
3 SETUP page

Delete groups
Only groups that do not contain samples can be deleted.

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the SETUP page.

3. (Optional) Use the filter option to find and select a run, then select the SETUP page.
a. Click located above the run list.

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the upper-right corner of the sample plate area, click to enable editing.

5. Below the sample plate area, select EDIT GROUPS to open the groups dialog box.

6. Select the group in the Name list.

7. Click .

8. Select SAVE in the groups dialog box.

9. Select SAVE on the SETUP page.

48 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
SETUP page 3

Assign samples to groups

Assigning samples to groups defines the analysis and results type for reporting for individual samples or
sets of samples.

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the SETUP page.

3. (Optional) Use the filter option to find and select a run, then select the SETUP page.
a. Click located above the run list.

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the upper-right corner of the sample plate area, click to enable editing.

5. In the sample plate area select one or more samples to be included in a group.
Pre-defined groups appear above the sample plate grid.

6. Select the group for these samples.

7. Select SAVE.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 49
 Chapter 3 Analyze data
3 SETUP page

Manage group sets

All the groups defined for a plate can be saved as a named group set.
Saved group sets can be loaded into other runs.
Each group set contains the following information:
• All the groups created in a run, even if they are not applied to a sample
• The location of the samples applied to each group
• The name and color of each group
• The target DNA names in each group
• The analysis type for each target
• The analysis for samples as individual, replicates, or pooling

Group sets do not include the sample names and dye names which will be unaffected by loading a
group set.
The QC channel in a run is never changed by loading a group set. For information on the QC channel,
see “View by samples” on page 58.
To save a group set, see “Save group sets” on page 50.
To load a group set, see “Load group sets” on page 51.
To edit a group set name, see “Edit group set names” on page 52.
To delete a group set, see“Delete group sets” on page 53.

Save group sets

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the SETUP page.

3. (Optional) Use the filter option to find and select a run, then select the SETUP page.
a. Click located above the run list.

50 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
SETUP page 3

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the upper-right corner of the sample plate area, click to enable editing.

5. From the sample plate grid, select the groups to be included in the Group Set.

6. In the upper-right corner of the page, click .

7. In the Save Group Set dialog, enter a name for the Group Set, then select SAVE.

8. Select SAVE on the SETUP page.

Load group sets

When a group set is loaded, the following items apply:
• All existing groups in the run are replaced by the groups in the set and applied to the samples as
defined by the group set.
• The targets in each group are assigned to the closest channel matching the run that the group set
originated from.
• When a group set containing only a single column is applied to a multi-column run, the group
pattern is repeated for each column.

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the SETUP page.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 51
 Chapter 3 Analyze data
3 SETUP page

3. (Optional) Use the filter option to find and select a run, then select the SETUP page.
a. Click located above the run list.

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the upper-right corner of the page, click

5. In the Load Group Set dialog, choose a group set from the list, then select LOAD.

Edit group set names

When a group set is loaded:
• All existing groups in the run are replaced by the groups in the set and applied to the samples as
defined by the group set.
• The targets in each group are assigned to the closest channel matching the run that the group set
originated from.
• When a group set containing only a single column is applied to a multi-column run, the group
pattern is repeated for each column.

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the SETUP page.

3. (Optional) Use the filter option to find and select a run, then select the SETUP page.
a. Click located above the run list.

52 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
SETUP page 3

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the upper-right corner of the page, click

5. In the Load Group Set dialog, select a group set, then .

6. Edit the group set name, then select .

Delete group sets

When a group set is loaded:
• All existing groups in the run are replaced by the groups in the set and applied to the samples as
defined by the group set.
• The targets in each group are assigned to the closest channel matching the run that the group set
originated from.
• When a group set containing only a single column is applied to a multi-column run, the group
pattern is repeated for each column.

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the SETUP page.

3. (Optional) Use the filter option to find and select a run, then select the SETUP page.
a. Click located above the run list.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 53
 Chapter 3 Analyze data
3 SETUP page

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the upper-right corner of the page, click

5. In the Load Group Set dialog, choose a group set from the list, then select .

54 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
ANALYSIS page 3

ANALYSIS page
The ANALYSIS page displays relevant information by samples or groups and provides different options
for viewing the data.

1 2 3 4

5 6 7 8 9

Figure 12 ANALYSIS page overview

1 View by samples
2 View by groups
3 View QC channel
4 Export sample data
5 View data by optical channel
6 Select EDIT ANALYSIS to edit plot information
7 Toggle Show Rejects to show microreaction chambers automatically rejected from analysis and results
8 Toggle to display array view
9 Toggle between 1D Scatter plot, Histogram, and 2D Scatter plot views

Viewing by samples puts the color channel information into rows for comparison across the color
channels. You can view or download data plots for each sample. See “View by samples” on page 58.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 55
 Chapter 3 Analyze data
3 ANALYSIS page

1 2 3

Figure 13 View by samples

1 View by samples
2 ANALYSIS page
3 Color channels for the selected sample
4 1D Scatter plots with positive and negative threshold

QC channel data is provided for each sample.

56 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
ANALYSIS page 3

1 2

Figure 14 View QC channel data for a sample

1 QC channel toggle
2 QC channel window

Viewing by GROUPS lets you compare color channels across the sample. You can view or download
data plots for each group. See “View by groups” on page 60.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 57
 Chapter 3 Analyze data
3 ANALYSIS page

1 2 3

Figure 15 View by groups

1 View by groups
2 Row for each sample in the selected group
3 Color channel selection
4 Toggle Overlay Sample to see all data from a sample target within a group in single plot

View by samples
1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the ANALYSIS page.

3. (Optional) Use the filter option to find and select a run, then select the ANALYSIS page.
a. Click located above the run list.

58 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
ANALYSIS page 3

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. On the ANALYSIS page, select SAMPLES.

The information is displayed in the results area using the 1D Scatter plot type.

5. (Optional) Use these options to change the results view:

Option Description
1D Scatter plot type
Show Rejects
Histogram plot type
2D Scatter plot type
2D Scatter plot type with heatmap
Show Arrays

For information about plots, see “Plot types” on page 62 and “View plots” on page 63.
For information about showing arrays, see “Show array images” on page 70.

6. (Optional) Toggle the QC window by selecting the QC toggle.

The QC window displays the plot and array image for the QC channel (usually ROX™).This quality
control data ensures that only properly filled microreaction chambers are used for analysis by
evaluating the ROX™ signal for each microreaction chamber.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 59
 Chapter 3 Analyze data
3 ANALYSIS page

The top and bottom thresholds are automatically set but can be manually adjusted. The QC plot
should have a single level band indicating uniform filling.

7. (Optional) Manually adjust the threshold using the function.

For more information about adjusting thresholds, see “Set thresholds” on page 66.

View by groups
1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the ANALYSIS page.

3. (Optional) Use the filter option to find and select a run, then select the ANALYSIS page.
a. Click located above the run list.

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. On the ANALYSIS page, select GROUPS.

The information is displayed in the results area using the 1D Scatter plot type.

60 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
ANALYSIS page 3

5. (Optional) Use these options to change the results view.

Option Description
1D Scatter plot type
Show Rejects
Histogram plot type
2D Scatter plot type
2D Scatter plot type with heatmap
Show Arrays

For more information on plots, see “Plot types” on page 62 and “View plots” on page 63.
For more information on showing arrays, see “Show array images” on page 70.

6. (Optional) Manually adjust the threshold using the function.

For more information on adjusting thresholds, see “Set thresholds” on page 66.

7. (Optional) Overlay sample targets with common thresholds within a group, see “Overlay samples”
on page 68.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 61
 Chapter 3 Analyze data
3 ANALYSIS page

Plot types
There are three plot options:

Option Description

1D scatter (signal versus index)

Histogram

2D Scatter, with optional heatmap (color versus color) — use the Heatmap to display scatter
plots as a heatmap. Brighter areas indicate a higher density of plots.

Show Rejects ( ): display or hide microreaction chambers that have been rejected from the
analysis results. Showing rejects does not impact the analysis or results calculations.

1 2 3

Figure 16 View 1D Scatter plot

1 EDIT ANALYSIS option
2 Show Rejects option
3 1D Scatter option

Figure 17 View Histogram plot

1 Histogram plot option

62 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
ANALYSIS page 3

Figure 18 View 2D Scatter plot

1 2D Scatter plot option

View plots
View plot information by zooming in on an area of interest or enlarging the plot.
For information on adjusting thresholds, see “Set thresholds” on page 66.

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the ANALYSIS page.

3. (Optional) Use the filter option to find and select a run, then select the ANALYSIS page.
a. Click located above the run list.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 63
 Chapter 3 Analyze data
3 ANALYSIS page

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. Use the following options to view a plot.

Option Actions
Filter plot area By default all channels are displayed in the plot area.
by channel. • To view to a specific channel, click on the channel name in the upper-left corner
of the plot area.

Zoom in on an 1. Hover over a plot, then click and drag the cursor on the area of interest.
area of a plot.
2. (Optional) To download the selected area of the plot as a PNG image or
download data from the plot, click .
3. (Optional) To return the plot to the original scale, click .

Enlarge a plot. 1. Hover over a plot, then click .

2. Use the left and right arrows to navigate between the channels.
3. (Optional) Hover over the enlarged plot, then click and drag the cursor on an
area of interest.
4. (Optional) To download the plot as a PNG image or download data from the
plot, click .
5. (Optional) To return the plot to the original scale, click .

64 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
ANALYSIS page 3

Figure 19 Zoom in on a section of a plot

1 Click and drag to zoom in on a selection

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 65
 Chapter 3 Analyze data
3 ANALYSIS page

Set thresholds
Thresholds on all plots are automatically set during the initial analysis based on the data distribution.
Automatic (default) thresholds have a single grey line indicating the barrier between positive and
negative data points.
Thresholds that have been adjusted have a single blue line indicating the barrier between positive and
negative data points.

Figure 20 Adjust thresholds

1 Blue line indicates threshold has been adjusted.

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the ANALYSIS page.

3. (Optional) Use the filter option to find and select a run, then select the ANALYSIS page.
a. Click located above the run list.

66 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
ANALYSIS page 3

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. To enable editing in the plot area, click .

The following options are available in the plot area.

Option Description
Enable editing of the Analysis page.
SAVE Save changes and exit edit mode.
CANCEL Discard all changes and exit edit mode.
Autoscale to return the plot to return the original scale.
AUTO Auto-threshold to return the plot to the original threshold.
Enlarge the plot.

5. (Optional) Filter the plot area by channel by selecting the channel name in the upper-left corner of
the plot area.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 67
 Chapter 3 Analyze data
3 ANALYSIS page

6. Adjust the thresholds on a plot by using one of the following options.

Option Action
Manually enter Adjust the threshold hold number using the following actions.
the threshold • Click in the threshold value field above the plot, then enter the new value.
values.
• Hover over the threshold value field above the plot, then click the up or down
arrows to adjust the value.

Drag the 1. Hover over the threshold line until the threshold value appears.
threshold bar.
2. Click on the threshold value, then drag the threshold bar up or down to adjust
the value.
Note: Clicking on the threshold line (not the value) results in a zoom action.

Note: For samples that have been grouped, adjusting a channel threshold changes the threshold
value for all samples in the group to the same value.

7. (Optional) To revert to the original threshold value automatically calculated by the system, click
AUTO.

Note: Auto-threshold reverts all the samples that have had thresholds adjusted back to their
original system-generated auto-threshold values. Samples in groups that have not been adjusted
will not be changed.

8. (Optional) To discard all changes and exit the edit mode, click CANCEL.

9. To save the changes and exit the edit mode, click SAVE.
The system recalculates the thresholds and refreshes the page to display the adjusted thresholds.

Overlay samples
Using the GROUPS view on the ANALYSIS page, you can overlay sample plots when you want to see
all the data from a sample target within a group in a single plot. For example, sample overlay in the 2D
plots allows for clustering with a larger microreaction chamber population so it can help provide more
confidence in the clustering results (especially when some samples have low positive count) and allows
you to apply a common threshold to the entire group at once.

Note: All analysis editing and plot view features are available for use with overlayed samples.

To overlay samples within a target, all samples within that target in the sample group must have a
common threshold. For information on adjusting thresholds, see “Set thresholds” on page 66.

1. Use the search fields to find a run or select a run from the list, then select the ANALYSIS page.

2. (Optional) Use the filter option to find and select a run, then select the ANALYSIS page.
a. Click located above the run list.

68 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
ANALYSIS page 3

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

3. Select GROUPS, then in the sample plate area, select the group of interest.

Note: If the toggle is not available, the sample targets in the selected group do
not have common thresholds. To adjust the thresholds, see “Set thresholds” on page 66.

4. In the plot area, select .

The page refreshes to display the overlayed plots for each sample channel.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 69
 Chapter 3 Analyze data
3 ANALYSIS page
2

Show array images

The Show Arrays ( ) option toggles the display of array images for all channels of a sample.
Microreaction chambers with positive data points are colored. Microreaction chambers with negative
and rejected data points are gray scale. Often they have a low signal and appear black.

Figure 21 View channel array images

1 Show arrays option
2 Channel array images

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the ANALYSIS page.

3. (Optional) Use the filter option to find and select a run, then select the ANALYSIS page.
a. Click located above the run list.

70 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
ANALYSIS page 3

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. On the ANALYSIS page, select a sample, then click .

5. Select an array to view an enlarged image.

6. Use the left and right arrows to navigate between arrays.

Export data from the ANALYSIS page

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the ANALYSIS page.

3. (Optional) Use the filter option to find and select a run, then select the ANALYSIS page.
a. Click located above the run list.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 71
 Chapter 3 Analyze data
3 ANALYSIS page

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. To export data, perform one of the following tasks:

Option Actions
Export table data. 1. From the ANALYSIS page, in the optical channel table area, click .
2. Select an export option.
• Copy to Clipboard — copies the data in HTML format
• Download CSV — downloads the data in CSV format
3. When prompted, navigate to the location to save the file and select Save.

Export plot data. 1. From the ANALYSIS page, in the plots area, hover over a plot and click .
2. Select an export option.
• Download Plot
• Download Data
3. When prompted, navigate to the location to save the file and select Save.

72 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
RESULTS page 3

RESULTS page
The RESULTS page displays the results for all the samples in a single table. The values are plotted
together below the concentration table.
From the RESULTS page, you can:
• View statistical results from the run. See “View results” on page 73.
• View results plots from the run by sample or group. See “View results” on page 73.
• Copy the data to the clipboard in HTML format. See “Export data from the RESULTS page” on
page 75.
• Download the data table in CSV format. See “Export data from the RESULTS page” on page 75.
• Generate data reports. See “Generate reports” on page 76.

The presentation of the RESULTS page is based on the groups assigned in the SETUP page.

Figure 22 View Results

View results
1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the RESULTS page.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 73
 Chapter 3 Analyze data
3 RESULTS page

3. (Optional) Use the filter option to find and select a run, then select the RESULTS page.
a. Click located above the run list.

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. To view results, perform one of the following tasks:

Option Actions
View results for 1. From the list of active optical channels above the concentration table, select
all optical ALL to view all channels.
channels.
2. Use the scroll bar at the bottom of the concentration table to scroll through
concentration table data for all channels.
3. Use the scroll bar on the side of the page to scroll down to see the plot data for
all channels.
4. Toggle between SAMPLE and GROUP to change the display of the plot data.
5. Use the scroll bar at the bottom of the plot area to scroll through the plot data
for all channels.

View results for 1. From the list of active optical channels above the concentration table, select the
a specific desired channel.
optical
2. Use the scroll bar on the side of the page to scroll down to see the
channel.
concentration table data for the channel.
3. Use the scroll bar on the side of the page to scroll down to see the plot data for
the channel.
4. Toggle between SAMPLE and GROUP to change the display of the plot data.

74 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
RESULTS page 3

Export data from the RESULTS page

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the RESULTS page.

3. (Optional) Use the filter option to find and select a run, then select the RESULTS page.
a. Click located above the run list.

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 75
 Chapter 3 Analyze data
3 RESULTS page

4. To export data, perform one of the following tasks.

Option Actions
Export 1. From the RESULTS page, in the concentration table area, click .
concentration
2. Select an export option.
data.
• Copy to Clipboard — copies the data in HTML format.
• Download CSV — downloads the table data shown in CSV format.
• Multi-channel CSV — downloads table data not seen in the RESULTS
page that provides concentration data on target combinations in CSV
format.
3. When prompted, navigate to the location to save the file and select Save.

Export plot data. 1. From the RESULTS page, in the plots area, hover over a plot and click .
2. Select an export option.
• Download Plot — downloads plot data as a PNG file.
• Download Data — downloads the plot data in CSV format.
3. When prompted, navigate to the location to save the file and select Save.

Generate reports
The GENERATE REPORT option uses the Report Builder to create and export reports as PDF files.

Note: Hidden samples are excluded from reports. You must unhide any samples that you need
included in a report. To unhide a sample, see “Hide samples” on page 42.

1. In the left pane, click to access the Runs page.

2. Use the search fields to find a run or select a run from the list, then select the RESULTS page.

3. (Optional) Use the filter option to find and select a run, then select the RESULTS page.
a. Click located above the run list.

76 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
Export and import runs 3

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. From the RESULTS page, select GENERATE REPORT to open Report Builder.
The Report Builder dialog box opens and All Groups are selected by default to be included in the
report.

5. (Optional) Select Select Groups, then from the list of groups, select the check box next to each
group to be included in the report. Any combination of groups can be selected.

6. (Optional) Select QC Channel to include the QC channel data for all samples.

7. Select BUILD.

Export and import runs

Runs can be exported to a ZST file that can be transferred and imported into QuantStudio™ Absolute
Q™ Digital PCR Software running on a different computer.
The ZST run file contains all analysis options:
• Group details
• Sample names
• Thresholds

Run files are approximately 30 MB in size.

To export a run, see “Export a run” on page 78.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 77
 Chapter 3 Analyze data
3 Export and import runs

To import a run, see “Import a run” on page 79.

Export a run
1. In the left pane, click to access the Runs page.

2. Use the search fields to find the runs for export.

3. (Optional) Use the filter option to find and select runs for export.
a. Click located above the run list.

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the list of runs, select the check boxes of the runs to be included in the export.

5. In the upper-right side of the run list, click .

6. When prompted, enter a name for the export file and navigate to the locate where you want to save
the run, then select Save.

78 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Chapter 3 Analyze data
Delete a run 3

Import a run
1. In the left pane, click to access the Runs page.

2. In the upper-right corner of the Runs page click .

3. Perform one of the following options:

Option Action
Drag the ZST file into the Import your 1. Using Windows™ File Explorer, navigate to the location of
result file window from Windows™ File the ZST file to import.
Explorer.
2. Drag and drop the file into the Import your result file
window.

Navigate to the ZST file from the 1. Select IMPORT FILE and navigate to the location of the
Import your result file window. ZST file to import.
2. Select the file, then select Open.

Delete a run
IMPORTANT! Deleting a run is permanent. You cannot restore a deleted run.

1. In the left pane, click to access the Runs page.

2. Use the search fields to find the runs to be deleted.

3. (Optional) Use the filter option to find and select runs to be deleted.
a. Click located above the run list.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 79
 Chapter 3 Analyze data
3 Delete a run

b. Select one or many filters from the following list of filter options.

Note: If no filters are selected, all runs are displayed.

Filter Option
Run Type • Experiment—A typical user-generated run.
• System Calibration—A run performed by a Thermo Fisher representative to
calibrate the instrument.

Status • Active—A dye calibration run currently being used as the calibration for the
attached instrument.
• Available—An experiment run available in the software.
• Obsolete—A dye calibration run not currently being used as the calibration for
the attached instrument.
• Unknown—The status of a run cannot be determined because the instrument is
not currently attached, or does not contain the requisite data.

Instrument Instruments associated with the run data either generated in or imported into the
system.

c. Click away from the filter list to view the run list based on your filter selections.

d. (Optional) Click the on the filter name to remove a filter selection from the list of runs.

4. In the list of runs, select the check boxes of the runs to be deleted.

5. In the upper-right side of the run list, click .

6. When prompted to delete the run, select DELETE.

80 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 A Modify protocols

Existing protocols can be edited or used as templates to create additional custom protocols.
Protocols define the following run information:
• Dyes used in each active optical channel
• PCR parameters

1. In the left pane, click to access the Instrument page.

2. Use one of the following options to select a protocol.

Option Action
Select the loaded protocol. In the PROTOCOL pane, click to modify the
loaded protocol.
Select a protocol from the 1. In the PROTOCOL pane, click PROTOCOL.
list of available protocols.
2. In the Protocols screen, select a protocol, and click LOAD.
3. In the PROTOCOL pane, click to modify the
loaded protocol.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 81
 Appendix A Modify protocols
A Delete a run

3. Modify optical channels as needed.

Parameter Action
Active optical channel Select the check box for each optical channel to be used.
Target dye for active channel For each active optical channel, select the drop-down to choose the
target dye.

1
2

Figure 23 Optical channel dyes

1 Dye channel check box
2 Dye channel name

4. Modify PCR parameters as needed.

Parameter Actions
Temperature • Enter a value in the temperature fields.
• Drag the slider bars to adjust the temperature.

Dwell times Enter in seconds or minutes and seconds in mm:ss format.

Cycles Set the number of cycles by entering a value into the Cycles field.
RNA-RT Select RNA-RT to add an extra temperature step for RNA reverse transcription
to cDNA for RNA samples. Not required for DNA samples.
Preheat Select Preheat to add a preheat step. Sometimes called hot start, preheating
the samples before PCR helps to reduce non-specific binding at lower
temperatures.

82 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix A Modify protocols
Delete a run A

(continued)
Parameter Actions
Two or three-step Select the Two Step drop-down to select 2 or 3 step cycling.
cycling
Two-stage PCR cycle Select Two Stage PCR to add a second PCR cycle stage.

6 5 4 3

Figure 24 Protocol parameters

1 Temperature settings fields and slider bar
2 Time fields and cycles field
3 Two-stage PCR setting
4 Two or three step cycling option
5 Preheat setting
6 RNA-RT setting

5. Select SAVE.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 83
 B Install, update, and move the
QuantStudio™ Absolute Q™ Digital
PCR System

■ Installation and environmental requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

■ Install the QuantStudio™ Absolute Q™ Digital PCR System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
■ Download and install the desktop software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
■ Update the instrument software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
■ Moving the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

Installation and environmental requirements

The room where the instrument is installed must be kept within the following operational environment
conditions.

Condition Acceptable range

Installation site For indoor laboratory use only

(Applicable pollution degree 2)

Operating temperature and humidity 15-30°C (60-85°F), 0-80% RH

Storage temperature and humidity 5-40°C (40-105°F), 0-80% RH

Vibration Do not place the instrument adjacent to strong vibration sources.

Excessive vibration during use can affect instrument performance.

Altitude Up to 6,500 ft (2000 m)

Input voltage tolerance +/-10%

Over voltage category II

• Installation time: <10 minutes

• Required materials: scissors or a strap cutter
• Space requirement: The instrument is approximately 0.6 m (2 ft) cubed. The presentation drawer
must not be obstructed and extends approximately 200 mm (8 in) from the front panel of the
instrument when open. The power and USB connections are on the left side near the back of the
instrument.
• Ensure that the fan vents on the back and bottom of the instrument are not obstructed.

84 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix B Install, update, and move the QuantStudio™ Absolute Q™ Digital PCR System
Install the QuantStudio™ Absolute Q™ Digital PCR System B

IMPORTANT! Keep all packaging materials in good condition, as they are required if the instrument
needs to be returned for any reason.

WARNING! The instrument requires 2–3 people for moving. Moving the system alone may result in
serious injury.

AVERTISSEMENT ! Le déplacement de l’instrument nécessite 2 à 3 personnes. Si vous déplacez le

système seul, vous risquez de vous blesser gravement.

Install the QuantStudio™ Absolute Q™ Digital PCR System

IMPORTANT! Ensure that the installation location meets the power and environmental requirements
specified in “Installation and environmental requirements” on page 84.

1. With 2–3 people, carefully unbox the instrument by cutting the straps and lifting the top of the box
off using the hand holes.
Do not cut or damage any of the packaging. Keep all packaging as it is required for returns or
service requests.

2. Carefully place the instrument on a flat, stable surface with no adjacent vibration sources.

3. Position the instrument so that there is access to the power and USB connectors on the left side of
the system.

4. Once the instrument is in place, remove the shipping lock screw on the top of the instrument.
a. With the power off, unscrew the shipping lock screw on the top of the instrument.

b. Insert the provided white plastic cap into the screw hole.
For more information on removing the shipping lock screw, see “Uninstall the shipping lock
screw” on page 89.
IMPORTANT! To prevent damage to the instrument, the shipping lock screw must be
removed before powering on the instrument.

Keep the shipping lock screw in case the instrument needs to be moved or returned for service.

5. Confirm that the power switch is in the OFF, O, position and then connect the power cable to the
instrument and a suitable power source.

6. Set up the dedicated computer and monitor near the instrument.

7. Use the power cable to connect the dedicated computer to a suitable power source.

8. Connect the keyboard and mouse to the back of the dedicated computer.

9. Turn on the power to the dedicated computer.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 85
 Appendix B Install, update, and move the QuantStudio™ Absolute Q™ Digital PCR System
B Download and install the desktop software

10. Install the software onto the dedicated computer. See “Download and install the desktop software”
on page 86.

11. When the software installation is complete, use the USB cable to connect the instrument to the
dedicated computer.

12. Turn on the power to the instrument by moving the power switch located at the left side near the
back to the I position.
Wait approximately 30 seconds for the instrument to initialize.

13. Once connected to the software, check that there are no errors reported.

The system is ready for use.

Download and install the desktop software

Computer requirements for the desktop software
Install the QuantStudio™ Absolute Q™ Digital PCR Software on the computer provided by Thermo Fisher
Scientific, and use it to control the instrument. Thermo Fisher Scientific does not support the use of
customer-provided computers to control the instrument.
However, you can install the QuantStudio™ Absolute Q™ Digital PCR Software on a customer-provided
computer to use the software to import run data for analysis. Minimum requirements for a customer-
provided computer are:
• Operating system—Windows™ 10 (64‑bit)
• Dell™ OptiPlex XE3 Tower computer

Download the desktop software

1. Go to https://www.thermofisher.com/us/en/home/global/forms/life-science/quantstudio-
absolute-q-software.html.

2. Download each software package.

Install the desktop software

1. Use a Windows™ Administrator account to log in to the computer on which you are installing the
desktop software.

2. For each software package perform the following actions:

a. Unzip the downloaded software.

b. Double-click setup.exe

c. Follow the InstallShield Wizard prompts to install the software.

d. Select Typical as the setup preference, then click Next.

86 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix B Install, update, and move the QuantStudio™ Absolute Q™ Digital PCR System
Update the instrument software B

e. Click Finish.

3. Start the QuantStudio™ Absolute Q™ Digital PCR Software.

4. When prompted, accept the End User License Agreement.

5. When prompted, accept or decline the Privacy Statement that allows Thermo Fisher Scientific to
use the ThermoFisher Connect Transfer Software to collect instrument run data.
• If you accept, ThermoFisher Connect Transfer Software data transmission is activated.
• If you decline, ThermoFisher Connect Transfer Software data transmission is not activated.

Note: Connect Transfer can be deactivated at any time by a user with administrator privileges
within the QuantStudio™ Absolute Q™ Digital PCR Software by accessing the Help menu ( ),
opening the Privacy Statement, and declining data collection.

Update the instrument software

If the software and/or firmware on the instrument is not compatible with the desktop computer's
software, you are automatically prompted to update the instrument software.

1. In the left pane of the QuantStudio™ Absolute Q™ Digital PCR Software, select to access the
Instrument page.
A dialog box appears with the following message, Software update required to use this instrument.

2. Click UPDATE.

3. In the Absolute Q™ Instrument Setup dialog box, click Install.

Note: The instrument information and setup file are pre-populated and cannot be changed.

4. When the update is complete, click Finish.

Note: When the update is complete, the instrument automatically restarts.

Moving the instrument

IMPORTANT! When moving the instrument the shipping lock screw must be manually installed before
moving the unit, and manually removed after transport. Moving the instrument without the shipping lock
screw in place can cause damage to the instrument.

IMPORTANT! When moving the instrument, make sure there is no plate in the instrument as it can
become dislodged and jam mechanical parts during instrument transport.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 87
 Appendix B Install, update, and move the QuantStudio™ Absolute Q™ Digital PCR System
B Moving the instrument

Install the shipping lock screw

1. Power on the instrument.

2. Start the QuantStudio™ Absolute Q™ Digital PCR Software.

3. Open the plate door to ensure there is no plate loaded. If a plate is loaded, remove it.

4. Close the plate door.

5. In the left pane, select to access the Instrument page.

6. Click on the instrument and select Prepare for Shipping.

Wait until a message stating Ready for Shipping appears before proceeding.

7. Remove the white plastic plug from the shipping screw hole and place it in the bag attached to the
shipping screw.

8. Insert the shipping screw and screw it finger tight. Do not over tighten.

9. Close the software and power off the instrument.

1 Shipping lock screw

88 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix B Install, update, and move the QuantStudio™ Absolute Q™ Digital PCR System
Moving the instrument B

Uninstall the shipping lock screw

IMPORTANT! Perform this task before powering on the instrument.

1. Ensure that the power is off and the instrument is not plugged into a power source.

2. Unscrew the shipping lock screw from the top of the instrument.

1 Shipping lock screw

3. Insert the white plastic cap in the shipping lock screw hole.
The instrument is now ready for power-up and use.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 89
 C Use the software with Security,
Auditing, and E‑signature (SAE) v2.2

■ Overview of the SAE Administrator Console components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

■ Enable SAE functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
■ Sign into QuantStudio™ Absolute Q™ Digital PCR Software using an SAE account . . . . . . . . . . . 94
■ Sign out of the software using an SAE account . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
■ Change your SAE account password . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
■ Default permissions and roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
■ Use audit functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
■ Sign data in the software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
■ View and review e-Signatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
■ Disable SAE functions in QuantStudio™ Absolute Q™ Digital PCR Software . . . . . . . . . . . . . . . . 112

The Security, Auditing, and E‑signature (SAE) v2.2 software (SAE Administrator Console) is only
compatible with the QuantStudio™ Absolute Q™ Digital PCR System.
For more information on Security, Auditing, and E‑signature (SAE) v2.2, including definitions of accounts
and roles, see the SAE Administrator Console v2.0 or later User Guide for PCR systems (Pub. No.
MAN0017468).

Overview of the SAE Administrator Console components

The SAE Administrator Console includes three components:
• SAE Administrator Console that an administrator uses to configure the module.
• SAE server that stores settings, user accounts, and audit records.

Note: The SAE server and SAE Administrator Console software are installed simultaneously on the
same computer during installation.
• SAE screens in an application (sign in and audit that a user interacts with). QuantStudio™ Absolute
Q™ Digital PCR Software is an application.

90 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
Overview of the SAE Administrator Console components C

The SAE Administrator Console provides the following SAE functionality in the QuantStudio™ Absolute
Q™ Digital PCR Software:
• System security—Controls user sign in and access to functions.
• Auditing—Tracks changes and actions performed by users.
• E-signature—Allows users to provide an electronic signature (user name and password) when
performing certain functions.

Depending on the way that your SAE administrator configures these features:
• Some features and functions that are described in this guide may not be accessible to you.
• You may see dialog boxes and prompts when you use the software.

Overview of the QuantStudio™ Absolute Q™ Digital PCR Software

functionality when SAE functions are enabled
The following features are active when SAE functions are enabled in the QuantStudio™ Absolute Q™
Digital PCR Software:
• Users must sign in with an SAE user account to use QuantStudio™ Absolute Q™ Digital PCR
Software.
• Both audit objects and and audit actions are tracked in the SAE Administrator Console. Audit
actions are tracked automatically, audit objects are viewable when enabled.
• Run setup and software functions for a user are determined by the SAE application profile and user
account settings.

Recommendations for SAE passwords

Thermo Fisher Scientific recommends enabling a password policy for SAE user accounts with the
following minimum number of characters:
• Administrative users: 12 characters
• Non-administrative users: 8 characters

The use of a password manager is recommended in order to help to create secure passwords.

SAE functions not supported by the QuantStudio™ Absolute Q™ Digital PCR

Software
The following SAE functions are not supported by the QuantStudio™ Absolute Q™ Digital PCR Software.

Function Option not supported

System > Other • Open file from non-SAE system

Settings • Client offline sign in
• Offline sign in threshold

Audit history Instrument Run Records

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 91
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
C Enable SAE functions

(continued)

Function Option not supported

e-Signature • Ability to add e-Signature meanings

• Ability to delete e-Signature meanings
• Ability to configure actions that require e-Signature
• Ability to control/configure e-Signature rights by user role
• Ability to control reasons available for e-Signature
• Ability to control/configure data to be signed for each e-Signature meaning
• Ability to control/configure number of signatures (by role) for each action requiring
e-Signature

Enable SAE functions

Workflow

Enable SAE functions

Install the SAE Administrator Console and Absolute Q™ application

profile (page 93)

Connect to the SAE server (page 94)

Enable SAE functions in QuantStudio™ Absolute Q™ Digital PCR

Software (page 94)

92 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
Enable SAE functions C

Install the SAE Administrator Console and Absolute Q™ application profile

The following configurations of SAE server and SAE Administrator Console software are supported:
• SAE installed on a standalone computer that is connected to the Absolute Q™ dedicated computer
and optional Absolute Q™ companion computers
• SAE and Absolute Q™ software that is installed on the Absolute Q™ dedicated computer and is
connected to optional Absolute Q™ companion computers
• SAE and Absolute Q™ software that is installed on an Absolute Q™ companion computer that is
connected to the Absolute Q™ dedicated computer and other optional Absolute Q™ companion
computers

IMPORTANT! Before installing the application profile, see the release notes for compatibility
information to ensure you are installing the Absolute Q™ application profile that is compatible with
the version of Absolute Q™ software that you are using.

1. To download the SAE server and SAE Administrator Console software and Absolute Q™
application profile go to https://www.thermofisher.com/us/en/home/global/forms/life-science/
quantstudio-absolute-q-software.html.

2. Install the SAE server and SAE Administrator Console software a computer with a static IP address
(recommended) or a dynamic IP address.
a. Unzip the downloaded software.

b. Double-click setup.exe

c. Follow the InstallShield Wizard prompts to install the software.

d. Select Typical as the setup preference, then click Next.

e. Click Finish.

Note: The SAE server and SAE Administrator Console software are installed simultaneously during
installation.

3. At the SAE Administrator Console, an SAE administrator must install the application profile for the
Absolute Q™ software before SAE can be used.
The application profile contains default settings for the Absolute Q™ software.
For information on installing application profiles, see the SAE Administrator Console v2.0 or later
User Guide for PCR systems (Pub. No. MAN0017468).

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 93
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
C Sign into QuantStudio™ Absolute Q™ Digital PCR Software using an SAE account

Connect to the SAE server

1. In the QuantStudio™ Absolute Q™ Digital PCR Software, select System4SAE Connection
Settings.

2. Enter the IP address and port number of the SAE server.

Note: If using a dynamic IP address, enter the hostname instead of the IP address to prevent the
loss of a connection.

3. (Optional) Click Test Connection to confirm that the connection information is correct.

4. Click Save.

Enable SAE functions in QuantStudio™ Absolute Q™ Digital PCR Software

This procedure requires an SAE administrator account.
Before you enable SAE functions in the QuantStudio™ Absolute Q™ Digital PCR Software, you must
complete the following tasks:
• Connect to the SAE server (see “Connect to the SAE server” on page 94).
• Close all protocol or analyzed run files.

1. In the QuantStudio™ Absolute Q™ Digital PCR Software, select System4Enable Security.

2. Enter your SAE administrator account user name and password, then click Sign In.

The SAE administrator account is automatically signed into the software after SAE functions are
enabled. The SAE user name is displayed in the upper-right corner of the software menu bar. All users
must sign into the software while SAE functions are enabled.
To sign out of the SAE administrator account in the Absolute Q™ software, see “Sign out of the software
using an SAE account” on page 95.

Note: Signing out of the SAE administrator account does not disable SAE functions in the Absolute
Q™ software. To disable SAE functions in the Absolute Q™ software, see “Disable SAE functions in
QuantStudio™ Absolute Q™ Digital PCR Software” on page 112.

Sign into QuantStudio™ Absolute Q™ Digital PCR Software

using an SAE account
Sign in for the QuantStudio™ Absolute Q™ Digital PCR Software is only required if SAE functions are
enabled by an SAE administrator (see “Enable SAE functions in QuantStudio™ Absolute Q™ Digital PCR
Software” on page 94).

1. In the QuantStudio™ Absolute Q™ Digital PCR Software sign in screen, enter your SAE user name
and password.

2. Click Sign In.

94 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
Sign out of the software using an SAE account C

The user name of the SAE account that is signed in to the software appears in the menu bar.

Sign out of the software using an SAE account

1. In the lower-left corner of the left pane, click .

2. Click Sign Out.

Change your SAE account password

Note: External user account (External/Federated LDAP repository accounts) passwords cannot be
changed in the QuantStudio™ Absolute Q™ Digital PCR Software, they can only be changed in their
respective repository.

1. In the lower-left corner of the left pane, click .

2. Click Change Password.

3. Enter the password information, then click OK.

Default permissions and roles

The SAE Administrator Console provides the following default permissions and roles. You can use the
default roles when you create SAE user accounts or create custom roles in the SAE Administrator
Console v2.2 (see the SAE Administrator Console v2.0 or later User Guide for PCR systems
(Pub. No. MAN0017468)).
• Administrator • Technician
• Scientist • Service

IMPORTANT! SAE permissions for a role apply to all user accounts that are assigned to the role.

The roles and associated user-configurable permissions are listed in the following table. You can also
double‑click the role in the Roles tab to display the list of permissions.

Note: The No Privileges role is used by the software when you set up user repositories. Do not assign
this role to a user account.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 95
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
C Default permissions and roles

Role
Function Description
Administrator Scientist Technician Service

Miscellaneous

Service access Access to the instrument service No No No Yes

menu.

Application Access to application Yes No No Yes

administration administration menus.

Generate report Create analysis reports. Yes Yes Yes Yes

Instrument Control

Edit protocol Edit run protocols. Yes Yes No Yes

Start run Choose a protocol and start and Yes Yes Yes Yes
stop instrument runs.

Run analysis

Change thresholds Change channel thresholds. Yes Yes No Yes

Edit groups Edit group definitions. Yes Yes No Yes

Rename samples Change sample names. Yes Yes Yes Yes

Assign samples Assign samples to set groups or Yes Yes Yes Yes
load a group set.

Hide samples Show or hide samples from an Yes Yes No Yes

analysis.

Run management

Delete run Delete a run from the database. Yes No No Yes

e-sign run Place an electronic signature on Yes Yes No Yes

a run.

Import run Import and export runs to and Yes Yes No Yes
from ZST files.

Edit run Edit run features. Yes Yes No Yes

Security Configuration

Configure security and Configure security and auditing Yes No No No

auditing in the SAE Administrator
Console.

Audit History

View action records View action records. Yes No No No

96 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
Use audit functions C

(continued)

Role
Function Description
Administrator Scientist Technician Service

View system View system configuration Yes No No No

configuration records.

View application object View application object records. Yes No No No

records

View instrument run Edit run features. Yes No No No

records

Use audit functions

The following sections provide information on using SAE auditing functions.

Specify audit reason

Depending on how the audit settings are configured in the SAE Administrator Console, the Enter
Audit Reason screen may appear when you make changes to a protocol or an analyzed run in the
QuantStudio™ Absolute Q™ Digital PCR Software to prompt you to select an audit reason from the drop
down list, or add a custom reason.

Note: Custom Reason is not displayed if audit settings are configured to require users to select a
reason.

For more information on configuring audit settings, see the SAE Administrator Console v2.0 or later
User Guide for PCR systems (Pub. No. MAN0017468).

View audit records

For instructions to view audit action records for a protocol or an analyzed run, see the SAE
Administrator Console v2.0 or later User Guide for PCR systems (Pub. No. MAN0017468).
For a list of actions that are audited, see “Actions that are audited” on page 98.
For instructions to view audit object records of a specific run, see “View audit object records” on
page 98.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 97
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
C Use audit functions

View audit object records

Use the following steps to view the audit object record of a specific run by using the Run ID for the run.

1. In the QuantStudio™ Absolute Q™ Digital PCR Software, select the desired run.
For information on selecting a run, see “Select a run” on page 38.

2. In the upper-right corner of the Run screen, hover over the Run ID and click Copy to clipboard.

3. At the SAE Administrator Console perform the following steps:

a. Select Audit History > Application Object Records.

b. Select Enable Application Objects Filtering.

c. In the Object name field, paste the Run ID that you copied in step 2.

d. Click Search.

The information regarding the run appears in results area of the Audit History screen.

Note: For assistance in interpreting audit history data, contact your Thermo Fisher representative.

Actions that are audited

The actions are audited and listed in the action records regardless of whether audits are enabled or
disabled.
The following user actions are audited:
• Sign in success
• Sign out
• Sign in failure
• Start Run
• Stop Run
• Accept Calibration
• Reject Calibration

Export audit records

For information on exporting audit records for a protocol or an analyzed run, see the SAE Administrator
Console v2.0 or later User Guide for PCR systems (Pub. No. MAN0017468).

98 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
Sign data in the software C

Sign data in the software

An e-Signature can optionally be added for plate setup and run results.

1. Chose from the following options to provide an e-Signature for run setup, plate setup, and run
results.

Option Actions
Run setup, Instrument • In the left pane, click to access the Instrument page.
page
Plate setup, SETUP 1. In the left pane, click to access the Runs page.
page
2. Use the search fields to find a run or select a run from the list, then
select the SETUP page.

Run results, RESULTS 1. In the left pane, click to access the Runs page.
page
2. Use the search fields to find a run or select a run from the list, then
select the RESULTS page.

2. Depending on the page you are on, click one of the following options to add your e-Signature:
• RUN page —
• SETUP page —
• RESULTS page —

3. Select one of the following options from the drop-down list to indicate the meaning of the e-
Signature.
• Reviewed and Approved Plate Setup
• Reviewed and Approved Plate Results

4. Enter your user name and password.

5. Click Sign.

If a run is signed and unmodified, the signature appears on reports that are created using GENERATE
REPORT.
For information on how to view e-signature data in the SAE software, see View and report audit
and e-Signature records in the SAE Administrator Console v2.0 or later User Guide for PCR systems
(Pub. No. MAN0017468).

View and review e-Signatures

For information on how to view e-Signature data, see View and report audit and e-Signature records in
the SAE Administrator Console v2.0 or later User Guide for PCR systems (Pub. No. MAN0017468).

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 99
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
C View and review e-Signatures

The sections that follow provide detailed information for reviewing e-Signature data.
• For information on plate setup e-Signature data, see “Review plate setup e-Signature information”
on page 100.
• For information on plate results e-Signature data, see “Review plate results e-Signature
information” on page 107.

Review plate setup e-Signature information

The sections that follow provide descriptions of the information provided in the e-Signature plate setup
record. Optionally, this information can be printed.

Signature metadata
This section provides information regarding the signature metadata for each e-Signature plate setup
record.

Signature metadata

Object Description

Meaning E-Signature option selected

Signed Date Date of e-Signature

Signed By Name of user

Host ID Instrument name

Full Name User name

Status Status of the signature:

• CURRENT: Valid
• OBSOLETE: Invalid

Role The role assigned to the user who performed the run

Figure 25 Signature details

100 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
View and review e-Signatures C

Protocol information
This section provides information regarding the protocol section of the e-Signature plate setup record.

Protocol details

Object Description

ScanChannelOne – ScanChannelFive Up to five channels specified to scan. Each channel reflects the
optical dye used.
• FAM™ dye
• VIC™ dye (recommended) or HEX™ dye
• ABY™ dye
• ROX™ dye
• CY™5 dye (recommended) or JUN™ dye

RNAStep_Duration Duration of RNA-RT step (optional)

RNAStep_Temperature Temperature of RNA-RT step (optional)

PCRPreheat_Duration Duration of pre-heat step (optional)

PCRPreheat_Temperature Temperature of pre-heat step (optional)

PCR_Stage(1/2)_Step(1/2/3)_Duration Duration of indicated stage and step

PCR_Stage(1/2)_Step(1/2/3)_Temperature Temperature of indicated stage and step

Name Name of protocol

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 101
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
C View and review e-Signatures

Figure 26 Plate setup — protocol

102 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
View and review e-Signatures C

Plate channel information for each sample

This section provides information regarding the channels used in the plate section of the e-Signature
plate setup record. If the channel was not used, the detail will reflect None in all data points. The figure
that follows depicts a partial record.

For each color — blue, green, yellow, red, and dark red

Object Description

Channel Name of the target

ChannelType Channel analysis setting

ChannelMaximum For red only, (QC) maximum QC channel value

ChannelMinimum For red, (QC) minimum QC channel value

For other colors, the threshold dividing positive and negative numbers

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 103
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
C View and review e-Signatures

Figure 27 Plate channel detail by channel color

104 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
View and review e-Signatures C

Additional plate information

This section provides information regarding the additional information provided in the plate section of
the e-Signature plate setup record.

Other plate information

Object Description

CNVReferenceNumber If CNV statistics are used for this channel, the reference factor specified, otherwise
None.

Name Sample name

Group Group name

GroupType Group analysis setting

Hidden Sample hidden in analysis:

• TRUE
• FALSE

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 105
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
C View and review e-Signatures

Figure 28 Plate information

Run metadata
The section provides information regarding the run name section of the e-Signature plate setup record.

Run metadata

Object Description

run name The name given to the run at the instrument

106 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
View and review e-Signatures C

Figure 29 Run name

Review plate results e-Signature information

The sections that follow provide descriptions of the information provided in the e-Signature plate results
record. Optionally, this information can be printed.

Signature metadata
This section provides information regarding the signature metadata for each e-Signature plate results
record.

Signature metadata

Object Description

Meaning E-Signature option selected.

Signed Date Date of e-Signature

Signed By Name of user

Host ID Instrument name

Status Status of the signature:

• CURRENT: Valid
• OBSOLETE: Invalid

Figure 30 Signature information

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 107
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
C View and review e-Signatures

Results by group
This section provides information regarding the groups section of the e-Signature plate results record.
A column is included for each dye used.

For each group, for each dye

Object Description

name Group name

std_conc Concentration standard deviation of analysis group

cv_conv Coefficient of variation of analysis group (where 100% = 1.00)

CI_95 95% percent confidence interval for concentration for analysis group

Total One of the following options:

• If replicates, this is the group average of microchambers
• If pooled, this is the total pooles microchambers

Positive Group positive microchambers

percent_cv Coefficient of variation of analysis group (where 100% = 100)

cp_num Calculated copy number (if available)

cp_CI_95 95% confidence interval of calculated copy number (if available)

Conc.(cp./uL) Group concentration in copies per microliter

108 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
View and review e-Signatures C

Figure 31 Plate results by group

Results for samples

This section provides information regarding the samples section of the e-Signature plate results record.
A column is included for each dye used.

For each sample, for each dye

Object Description

name Sample name

std_conc Concentration standard deviation of analysis group

cv_conv Coefficient of variation of analysis group (where 100% = 1.00)

CI_95 95% percent confidence interval for concentration for analysis group

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 109
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
C View and review e-Signatures

For each sample, for each dye (continued)

Object Description

Total One of the following options:

• If replicates, this is the group average of microchambers
• If pooled, this is the total pooled microchambers

Positive Group positive microchambers

percent_cv Coefficient of variation of analysis group (where 100% = 100)

cp_num Calculated copy number (if available)

cp_CI_95 95% confidence interval of calculated copy number (if available)

Conc.(cp./uL) Group concentration in copies per microliter

110 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
View and review e-Signatures C

Figure 32 Plate results by samples

Run metadata
The section provides information regarding the run name section of the e-Signature plates result
record.

Run metadata

Object Description

run name The name given to the run at the instrument

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 111
 Appendix C Use the software with Security, Auditing, and E‑signature (SAE) v2.2
C Disable SAE functions in QuantStudio™ Absolute Q™ Digital PCR Software

Figure 33 Run name

Disable SAE functions in QuantStudio™ Absolute Q™ Digital

PCR Software
This procedure requires an SAE administrator account.
Close all plate files and data files.

1. In QuantStudio™ Absolute Q™ Digital PCR Software, select System4Disable Security.

2. Enter the password of the SAE administrator account, then click Sign In.

112 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 D Maintain the instrument

Clean the instrument and plate nest

All surfaces should be dry and free of dust and lint before operation.
Clean the outside of the instrument with a damp, lint-free cloth using one of the following solutions:
• Mild soap
• 70% ethanol in water

Clean the plate nest surface gently with a lint-free cloth (microfiber cloth or optical lens cleaning cloth)
using 70% ethanol in water. Do not wipe the grooves that surround the plate nest.

IMPORTANT! The plate nest is covered in a thin graphite sheet. This sheet is susceptible to scratches
and may impact results if it is damaged. It is important to only wipe the graphite surface with lint-free
wipes or use air-dusters. Contact technical support if this surface becomes damaged (see Appendix H,
“Documentation and support”.

Maintenance
For best results when using the instrument, the following practices are recommended:
• The plate nest must be cleaned before each run.
• Ensure that the fan vents on the back and bottom of the instrument are not obstructed.
• Ensure that system dyes are calibrated on a yearly basis.

Note: A warning message appears on the Instrument page 45 days prior to dye calibration
expiration. If the dyes are not calibrated within that time frame, a warning message appears
indicating that the calibration has expired and remains on the Instrument page until the dyes are
calibrated.

IMPORTANT! System dye calibration must only be performed by qualified field service engineers.
Attempting to calibrate dyes without the assistance of a field service engineer may compromise run
data for analysis.

For information on maintenance and service plans, contact technical support (see Appendix H,
“Documentation and support”).

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 113
 E Troubleshooting

Observation Possible cause Recommended action

QuantStudio™ Absolute Q™ Software connection error. Power cycle system using power switch on the
Digital PCR Software is not side of the instrument.
connecting, front panel LEDs
Uninstall and re-install the software.
are white
QuantStudio™ Absolute Q™ Poor USB cable connection. Power off the instrument. Unplug the power
Digital PCR Software is not and USB cables from the instrument. Wait
connecting, front panel LEDs 10 seconds. Plug the power and USB cables
are blue back in to the instrument and dedicated
computer. Power on and connect.
Front panel LEDs are red Instrument error. Power cycle the instrument using the power
switch.
The Run status displays as Port 8000 is blocked. If a firewall or other application is using port
DISCONNECTED 8000, remove it or use a different port.
Pressure leak error Missing or damaged gaskets. Make sure that all 5 columns of gaskets are
present.
Replace any damaged gaskets.
Instrument makes noise and Instrument firmware startup Power off the instrument. Unplug the power
LEDs are white one minute error. cable from the instrument. Wait 10 seconds.
after power up Plug the power cable back in and power on
the instrument.
Barcode not found Plate in backwards. Well A1 should be at the top left of the plate
tray.
Missing or unreadable barcode Enter the barcode manually if it is human
label. readable.
Connection to the standalone Power outage. Restore power to the SAE Administrator
SAE Administrator Console is Console.
lost
Cables have become Confirm all cables are properly connected.
disconnected.

114 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix E Troubleshooting
Maintenance E

Observation Possible cause Recommended action

Connection to the standalone Hardware failure of the SAE Uninstall and reinstall the QuantStudio™
SAE Administrator Console is Administrator Console. Absolute Q™ Digital PCR Software to continue
lost use of the QuantStudio™ Absolute Q™ Digital
(continued) PCR System without SAE.
1. Consult with your organization's policies
and procedures regarding operation
without SAE enabled before continuing.
2. At the desktop computer, shut down the
QuantStudio™ Absolute Q™ Digital PCR
Software.
3. Uninstall the QuantStudio™ Absolute Q™
Digital PCR Software.
IMPORTANT! To prevent data loss,
select Keep during uninstall to preserve
the exising database.
4. Install the QuantStudio™ Absolute Q™
Digital PCR Software, see “Install the
desktop software” on page 86.
IMPORTANT! To prevent data loss,
select Update during installation of
the software to preserve the existing
database.
Communication between the Another application may be Ensure that only the QuantStudio™ Absolute
instrument and the Absolute causing a communication Q™ Digital PCR Software and if applicable
Q™ computer is interrupted or conflict. SAE Administrator Console are installed on
inconsistent the dedication computer. Uninstall any other
applications.
Hardware failure. Confirm all cables are properly connected
Confirm that both devices have power.
Contact thermofisher.com/support.
1. Confirm all cables are properly
connected..
2. Confirm that both devices have power.
3. Contact thermofisher.com/support.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 115
 Appendix E Troubleshooting
E Field Service Archive files

Field Service Archive files

Field Service Archive (FSA) files contain information regarding runs and instrument usage that can
be used for troubleshooting unexpected run results and instrument performance. The following table
provides information on the FSA files that can be captured from the QuantStudio™ Absolute Q™ Digital
PCR System.

File type and file name format Description

Data • Used for troubleshooting issues with a run

{run_name}_{short_run_id}_{YYYY_MM_DD}_data.fsa • Contains raw images and the run ZST file
• Automatically created with each run
• File size can be large, >1GB
• 20 most recent files retained

Log • Used for troubleshooting issues with a run

{run_name}_{short_run_id}_{YYYY_MM_DD}_logs.fsa • Contains logs from the QuantStudio™ Absolute Q™
Digital PCR Software
• Contains logs from the instrument computer software
and hardware not related to the camera
• Automatically created with each run
• File size is ~120 MB
• 70 most recent files retained

System • Used for troubleshooting system issues not related to a

run
{YYYY_MM_DD}_system.fsa
• Contains logs from the desktop computer and
instrument computer at the time of capture
• Created on demand
• File size is ~120 MB
• The file is not automatically deleted

Capture and transfer data and log FSA files

Data and log FSA files are used for troubleshooting unexpected results or instrument failure during a
run.

Note: Only use these instructions when instructed by a Thermo Fisher support representative.

1. On the desktop computer, open the Start Menu.

2. Find the shortcut to the QuantStudio Absolute Q 6 Field Service Archives folder by performing
one of the following actions.
• In the search field, type QuantStudio • Scroll through the application list.
Absolute Q 6 Field Service Archives.

116 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix E Troubleshooting
Field Service Archive files E

3. Click on the shortcut to open the archive files folder, then select the data and log files for the run in
question.
For example:
• Absolute Q Starter Chemistry Run 31_8ea5ccfc_2022_04_01_data.fsa
• Absolute Q Starter Chemistry Run 31_8ea5ccfc_2022_04_01_logs.fsa

4. Send the files to your Thermo Fisher support representative for analysis using a file transfer
program of your choosing.

Capture and transfer system FSA files

System FSA files are used for troubleshooting system issues not related to a run, for example if the
plate tray is malfunctioning. A system FSA file is created on demand using the QuantStudio™ Absolute
Q™ Digital PCR Software.

Note: Only use these instructions when instructed by a Thermo Fisher support representative.

1. In the QuantStudio™ Absolute Q™ Digital PCR Software, select System4Download System

Logs.
The system log file is created and a File Explorer window opens with the system log file name
pre-populated in the file name field.

2. Navigate to a folder of your choice, then click Save.

3. Send the files to your Thermo Fisher support representative for analysis using a file transfer
program of your choosing.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 117
 F Product Specifications

■ QuantStudio™ Absolute Q™ Digital PCR Instrument specifications . . . . . . . . . . . . . . . . . . . . . . . . 118

■ Dedicated computer requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
■ QuantStudio™ Absolute Q™ Digital PCR Instrument Optical Configuration . . . . . . . . . . . . . . . . . . 119

QuantStudio™ Absolute Q™ Digital PCR Instrument

specifications
Dimensions (unpacked) 620 mm (l) x 600 mm (w) x 540 mm (h)
24.5 in (l) x 23.5 in (w) x 21.2 in (h)

Dimensions (packaged) 860 mm (l) x 860 mm (w) x 790 mm (h)

33.5 in (l) x 34 in (w) x30 (h)

Weight Approximately 60 kg, 132 lbs

Connections Power, USB 3.0 (to dedicated computer)

Cooling mode Forced convection

Illumination Rax, Blue, Phosphor Green high-power LED

Optical channels 5 (fixed configuration)

Power input 100-240 V, 50-60Hz

Power rating 1200-1600 W

Rated current 12 A (110V), 8.5 A (230 V)

Maximum noise level 70 dB

Dedicated computer requirements

Operating system Windows™ 10 (64-bit) or later

Computer Dell™ OptiPlex XE3 Tower

118 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix F Product Specifications
QuantStudio™ Absolute Q™ Digital PCR Instrument Optical Configuration F

QuantStudio™ Absolute Q™ Digital PCR Instrument Optical

Configuration
The QuantStudio™ Absolute Q™ Digital PCR Instrument comes in a single optical configuration and is
pre-calibrated during manufacturing. It can be field calibrated for enhanced spectral compensation.

Note: HEX™ dye is not supported for field calibration.

Note: A warning message appears on the Instrument page 45 days prior to dye calibration expiration.
If the dyes are not calibrated within that time frame, a warning message appears indicating that the
calibration has expired and remains on the Instrument page until the dyes are calibrated.

# Color Excitation filter peak Emission filter peak System dyes

1 Blue 466 520 FAM™ dye

2 Green 514 560 VIC™ dye (recommended)

HEX™ dye

3 Yellow 549 589 ABY™ dye

4 Red 589 625 ROX™ dye

5 Dark Red 630 684 CY™5 dye (recommended)

JUN™ dye

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 119
 G Safety

■ Symbols on this instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121

■ Safety information for instruments not manufactured by Thermo Fisher Scientific . . . . . . . . . . . . 123
■ Instrument safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
■ Safety and electromagnetic compatibility (EMC) standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
■ Chemical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
■ Biological hazard safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130

WARNING! GENERAL SAFETY. Using this product in a manner not specified in the user
documentation may result in personal injury or damage to the instrument or device. Ensure that
anyone using this product has received instructions in general safety practices for laboratories and
the safety information provided in this document.

· Before using an instrument or device, read and understand the safety information provided in the
user documentation provided by the manufacturer of the instrument or device.
· Before handling chemicals, read and understand all applicable Safety Data Sheets (SDSs) and use
appropriate personal protective equipment (gloves, gowns, eye protection, and so on). To obtain
SDSs, visit thermofisher.com/support.

AVERTISSEMENT ! SÉCURITÉ GÉNÉRALE. L’utilisation de ce produit d’une manière non spécifiée

dans le manuel d’utilisation peut entraîner des blessures ou endommager l’instrument ou l’appareil.
Assurez-vous que toute personne utilisant ce produit est formée aux pratiques générales de sécurité
pour les laboratoires et aux informations de sécurité fournies dans le présent document.

· Avant d’utiliser un instrument ou un dispositif, lisez et assimilez les informations de sécurité figu­
rant dans le manuel d’utilisation fourni par le fabricant de l’instrument ou du dispositif.
· Avant de manipuler des produits chimiques, lisez et assimilez toutes les fiches de données de
sécurité (FDS) applicables et utilisez les équipements de protection individuelle appropriés (gants,
blouses, lunettes de protection, etc.). Pour consulter les fiches de données de sécurité, rendez-
vous sur le site thermofisher.com/support.

120 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix G Safety
Symbols on this instrument G

Symbols on this instrument

Symbols may be found on the instrument to warn against potential hazards or convey important safety
information. In this document, the hazard symbol is used along with one of the following user attention
words.
• CAUTION!—Indicates a potentially hazardous situation that, if not avoided, may result in minor or
moderate injury. It may also be used to alert against unsafe practices.
• WARNING!—Indicates a potentially hazardous situation that, if not avoided, could result in death or
serious injury.
• DANGER!—Indicates an imminently hazardous situation that, if not avoided, will result in death or
serious injury.

Standard safety symbols

Symbol and description

CAUTION! Risk of danger. Consult the manual for further safety information.

CAUTION! Caution, air inlet.

CAUTION! Hot surface.

CAUTION! Potential biohazard.

Symbole et description

MISE EN GARDE ! Risque de danger. Consulter le manuel pour d’autres renseignements de

sécurité.

MISE EN GARDE ! Risque de choc électrique.

MISE EN GARDE ! Surface chaude.

MISE EN GARDE ! Danger biologique potentiel.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 121
 Appendix G Safety
G Symbols on this instrument

Control and connection symbols

Symbols and descriptions

On (Power)

Off (Power)

Protective conductor terminal (main ground)

Conformity symbols
Conformity
Description
mark

Indicates conformity with the WEEE Directive 2012/19/EU.

CAUTION! To minimize negative environmental impact from disposal of electronic

waste, do not dispose of electronic waste in unsorted municipal waste. Follow local
municipal waste ordinances for proper disposal provision and contact customer
service for information about responsible disposal options.

MISE EN GARDE ! Pour réduire l’empreinte écologique résultant de l’élimination

des composants électroniques, ne les jetez pas dans les déchets municipaux non
triées. Respectez les réglementations locales en matière de déchets pour un traite­
ment approprié et contactez le service clientèle pour en savoir plus sur les solutions
responsables.

122 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix G Safety
Safety information for instruments not manufactured by Thermo Fisher Scientific G

Safety information for instruments not manufactured by

Thermo Fisher Scientific
Some of the accessories provided as part of the instrument system are not designed or built by Thermo
Fisher Scientific. Consult the manufacturer's documentation for the information needed for the safe use
of these products.

Instrument safety
General

CAUTION! Do not remove instrument protective covers. If you remove the protective instrument
panels or disable interlock devices, you may be exposed to serious hazards including, but not limited
to, severe electrical shock, laser exposure, crushing, or chemical exposure.

MISE EN GARDE ! Ne retirez pas les couvercles de protection de l’instrument. Si vous retirez
les panneaux de protection des instruments ou si vous désactivez les dispositifs de verrouillage, vous
risquez de courir de graves dangers, comme, par exemple, un choc électrique, une exposition au
laser, un écrasement ou une exposition à des produits chimiques.

Hot Surface

CAUTION! Hot surface. During instrument operation, the temperature of the plate nest can be as
high as 100°C. The instrument has a software interlock to prevent the door from opening if the plate
nest temperature is over 45°C, but if the system appears to be malfunctioning use caution when
operating near the plate nest.

MISE EN GARDE ! Surface chaude. En cours de fonctionnement, la température des plaques peut
atteindre 100°C. L’instrument est doté d’un logiciel de verrouillage qui empêche l’ouverture de la
porte si la température des plaques est supérieure à 45°C. Toutefois, si le système semble présenter
un dysfonctionnement, soyez prudent lorsque vous travaillez à proximité des plaques.

Air inlet

CAUTION! Air inlet. Air inlet is only suitable for atmospheric air and not pressurized gas. Do not
connect flammable gas to the air inlet port. Do not restrict air inlet port.

MISE EN GARDE ! Arrivée d’air. L’arrivée d’air ne convient qu’à l’air atmosphérique et non aux
gaz sous pression. Ne raccordez pas de gaz inflammable à l’orifice d’arrivée d’air. Veillez à ne pas
obstruer l’orifice d’arrivée d’air.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 123
 Appendix G Safety
G Instrument safety

Physical injury

CAUTION! Moving and Lifting Injury. Improper lifting can cause painful and permanent back injury.
Things to consider before lifting or moving the instrument or accessories:
· Depending on the weight, moving or lifting may require two or more persons.
· If you decide to lift or move the instrument after it has been installed, do not attempt to do so
without the assistance of others, the use of appropriate moving equipment, and proper lifting
techniques.
· Ensure you have a secure, comfortable grip on the instrument or accessory.
· Make sure that the path from where the object is to where it is being moved is clear of
obstructions.
· Do not lift an object and twist your torso at the same time. Keep your spine in a good neutral
position while lifting with your legs.
· Participants should coordinate lift and move intentions with each other before lifting and carrying.
· For smaller packages, rather than lifting the object from the packing box, carefully tilt the box on its
side and hold it stationary while someone else slides the contents out of the box.

MISE EN GARDE ! Blessures causées par le déplacement et le soulèvement. Soulever de

manière inappropriée peut provoquer des lésions dorsales douloureuses et permanentes.
Éléments à prendre en compte avant de soulever ou de déplacer l’instrument ou ses accessoires:
· Selon le poids, deux personnes ou plus peuvent être nécessaires pour déplacer ou soulever
l’instrument.
· Si vous décidez de soulever ou de déplacer l’instrument après son installation, n’essayez pas de le
faire seul, sans un équipement approprié et sans avoir recours à des techniques appropriées.
· Assurez-vous d’avoir une prise sûre et confortable sur l’instrument ou l’accessoire.
· Assurez-vous que le chemin entre l’endroit où se trouve l’objet et l’endroit où il est déplacé est
libre de tout obstacle.
· Ne soulevez pas un objet et ne pivotez pas votre torse en même temps. Tenez votre colonne
vertébrale dans une position bien droite en vous relevant.
· Les participants doivent coordonner leurs mouvements avant de soulever et de porter.
· Pour les petits colis, au lieu de soulever l’objet de son emballage, inclinez soigneusement le carton
sur le côté et maintenez-le immobile pendant que quelqu’un d’autre fait glisser le contenu hors du
carton.

124 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix G Safety
Instrument safety G

Electrical safety

WARNING! Ensure appropriate electrical supply. For safe operation of the instrument:
· Plug the system into a properly grounded receptacle with adequate current capacity.
· Ensure the electrical supply is of suitable voltage.
· Never operate the instrument with the ground disconnected. Grounding continuity is required for
safe operation of the instrument.

AVERTISSEMENT ! Veiller à utiliser une alimentation électrique appropriée. Pour garantir le

fonctionnement de l’instrument en toute sécurité :

· Brancher le système sur une prise électrique correctement mise à la terre et de puissance adéqua­
te.
· S’assurer que la tension électrique est convenable.
· Ne jamais utiliser l’instrument alors que le dispositif de mise à la terre est déconnecté. La continui­
té de la mise à la terre est impérative pour le fonctionnement de l’instrument en toute sécurité.

WARNING! Power Supply Line Cords. Use properly configured and approved line cords for the
power supply in your facility.

AVERTISSEMENT ! Cordons d’alimentation électrique. Utiliser des cordons d’alimentation adap­

tés et approuvés pour raccorder l’instrument au circuit électrique du site.

WARNING! Disconnecting Power. To fully disconnect power either detach or unplug the power
cord, positioning the instrument such that the power cord is accessible.

AVERTISSEMENT ! Déconnecter l’alimentation. Pour déconnecter entièrement l’alimentation, dé­

tacher ou débrancher le cordon d’alimentation. Placer l’instrument de manière à ce que le cordon
d’alimentation soit accessible.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 125
 Appendix G Safety
G Instrument safety

Cleaning and decontamination

CAUTION! Cleaning and Decontamination. Use only the cleaning and decontamination methods
that are specified in the manufacturer user documentation. It is the responsibility of the operator (or
other responsible person) to ensure that the following requirements are met:

· No decontamination or cleaning agents are used that can react with parts of the equipment or with
material that is contained in the equipment. Use of such agents could cause a HAZARD condition.
· The instrument is properly decontaminated a) if hazardous material is spilled onto or into the
equipment, and/or b) before the instrument is serviced at your facility or is sent for repair,
maintenance, trade-in, disposal, or termination of a loan. Request decontamination forms from
customer service.
· Before using any cleaning or decontamination methods (except methods that are recommended by
the manufacturer), confirm with the manufacturer that the proposed method will not damage the
equipment.

MISE EN GARDE ! Nettoyage et décontamination. Utiliser uniquement les méthodes de nettoya­

ge et de décontamination indiquées dans la documentation du fabricant destinée aux utilisateurs.
L’opérateur (ou toute autre personne responsable) est tenu d’assurer le respect des exigences sui­
vantes:

· Ne pas utiliser d’agents de nettoyage ou de décontamination susceptibles de réagir avec certaines

parties de l’appareil ou avec les matières qu’il contient et de constituer, de ce fait, un DANGER.
· L’instrument doit être correctement décontaminé a) si des substances dangereuses sont renver­
sées sur ou à l’intérieur de l’équipement, et/ou b) avant de le faire réviser sur site ou de l’envoyer
à des fins de réparation, de maintenance, de revente, d’élimination ou à l’expiration d’une période
de prêt (des informations sur les formes de décontamination peuvent être demandées auprès du
Service clientèle).
· Avant d’utiliser une méthode de nettoyage ou de décontamination (autre que celles recomman­
dées par le fabricant), les utilisateurs doivent vérifier auprès de celui-ci qu’elle ne risque pas
d’endommager l’appareil.

Instrument component and accessory disposal

CAUTION! To minimize negative environmental impact from disposal of electronic waste, do not
dispose of electronic waste in unsorted municipal waste. Follow local municipal waste ordinances for
proper disposal provision and contact customer service for information about responsible disposal
options.

MISE EN GARDE ! Pour réduire l’empreinte écologique résultant de l’élimination des composants
électroniques, ne les jetez pas dans les déchets municipaux non triées. Respectez les réglementa­
tions locales en matière de déchets pour un traitement approprié et contactez le service clientèle
pour en savoir plus sur les solutions responsables.

126 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix G Safety
Safety and electromagnetic compatibility (EMC) standards G

Safety and electromagnetic compatibility (EMC) standards

The instrument design and manufacture complies with the following standards and requirements for
safety and electromagnetic compatibility.

Safety standards
Reference Description

EU Directive 2011/65/EU European Union “RoHS Directive” – Restriction of hazardous substances in electrical
& Commission Delegated and electronic equipment
Directive (EU) 2015/863

IEC 61010-1 Safety requirements for electrical equipment for measurement, control, and laboratory
use – Part 1: General requirements

IEC 61010-2-010 Safety requirements for electrical equipment for measurement, control and laboratory
use – Part 2-010: Particular requirements for laboratory equipment for the heating of
materials

IEC 61010-2-081 Safety requirements for electrical equipment for measurement, control and laboratory
use – Part 2-081: Particular requirements for automatic and semi-automatic laboratory
equipment for analysis and other purposes

EMC standards
Reference Description

EMC EN 61326-1 Electrical Equipment for Measurement, Control and Laboratory Use – EMC Requirements –
Part 1: General Requirements

FCC Class A This device complies with Part 15 of the FCC rules. Operation is subject to the following two
equipment Caution conditions:

1. This device may not cause harmful interference, and

2. This device must accept any interference received, including interference that may cause
undesired operation.

FCC Part 15 U.S. Standard Radio Frequency Devices

Subpart B (47
This equipment has been tested and found to comply with the limits for a Class A digital
CFR)
device, pursuant to part 15 of the FCC Rules. These limits are designed to provide reasonable
protection against harmful interference when the equipment is operated in a commercial
environment. This equipment generates, uses, and can radiate radio frequency energy and,
if not installed and used in accordance with the instruction manual, may cause harmful
interference to radio communications. Operation of this equipment in a residential area is likely
to cause harmful interference in which case the user will be required to correct the interference
at his own expense.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 127
 Appendix G Safety
G Chemical safety

Chemical safety
WARNING! GENERAL CHEMICAL HANDLING. To minimize hazards, ensure laboratory personnel
read and practice the general safety guidelines for chemical usage, storage, and waste provided
below. Consult the relevant SDS for specific precautions and instructions:

· Read and understand the Safety Data Sheets (SDSs) provided by the chemical manufacturer
before you store, handle, or work with any chemicals or hazardous materials. To obtain SDSs, see
the "Documentation and Support" section in this document.
· Minimize contact with chemicals. Wear appropriate personal protective equipment when handling
chemicals (for example, safety glasses, gloves, or protective clothing).
· Minimize the inhalation of chemicals. Do not leave chemical containers open. Use only with
sufficient ventilation (for example, fume hood).
· Check regularly for chemical leaks or spills. If a leak or spill occurs, follow the manufacturer
cleanup procedures as recommended in the SDS.
· Handle chemical wastes in a fume hood.
· Ensure use of primary and secondary waste containers. (A primary waste container holds the
immediate waste. A secondary container contains spills or leaks from the primary container.
Both containers must be compatible with the waste material and meet federal, state, and local
requirements for container storage.)
· After emptying a waste container, seal it with the cap provided.
· Characterize (by analysis if needed) the waste generated by the particular applications, reagents,
and substrates used in your laboratory.
· Ensure that the waste is stored, transferred, transported, and disposed of according to all local,
state/provincial, and/or national regulations.
· IMPORTANT! Radioactive or biohazardous materials may require special handling, and disposal
limitations may apply.

AVERTISSEMENT ! PRÉCAUTIONS GÉNÉRALES EN CAS DE MANIPULATION DE PRODUITS

CHIMIQUES. Pour minimiser les risques, veiller à ce que le personnel du laboratoire lise attentive­
ment et mette en œuvre les consignes de sécurité générales relatives à l’utilisation et au stockage
des produits chimiques et à la gestion des déchets qui en découlent, décrites ci-dessous. Consulter
également la FDS appropriée pour connaître les précautions et instructions particulières à respecter :

· Lire et comprendre les fiches de données de sécurité (FDS) fournies par le fabricant avant de
stocker, de manipuler ou d’utiliser les matériaux dangereux ou les produits chimiques. Pour obtenir
les FDS, se reporter à la section « Documentation et support » du présent document.
· Limiter les contacts avec les produits chimiques. Porter des équipements de protection appropriés
lors de la manipulation des produits chimiques (par exemple : lunettes de sûreté, gants ou vête­
ments de protection).
· Limiter l’inhalation des produits chimiques. Ne pas laisser les récipients de produits chimiques
ouverts. Ils ne doivent être utilisés qu’avec une ventilation adéquate (par exemple, sorbonne).
· Vérifier régulièrement l’absence de fuite ou d’écoulement des produits chimiques. En cas de fuite
ou d’écoulement d’un produit, respecter les directives de nettoyage du fabricant recommandées
dans la FDS.
· Manipuler les déchets chimiques dans une sorbonne.

128 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 Appendix G Safety
Chemical safety G

· Veiller à utiliser des récipients à déchets primaire et secondaire. (Le récipient primaire contient les
déchets immédiats, le récipient secondaire contient les fuites et les écoulements du récipient pri­
maire. Les deux récipients doivent être compatibles avec les matériaux mis au rebut et conformes
aux exigences locales, nationales et communautaires en matière de confinement des récipients.)
· Une fois le récipient à déchets vidé, il doit être refermé hermétiquement avec le couvercle fourni.
· Caractériser (par une analyse si nécessaire) les déchets générés par les applications, les réactifs et
les substrats particuliers utilisés dans le laboratoire.
· Vérifier que les déchets sont convenablement stockés, transférés, transportés et éliminés en res­
pectant toutes les réglementations locales, nationales et/ou communautaires en vigueur.
· IMPORTANT ! Les matériaux représentant un danger biologique ou radioactif exigent parfois une
manipulation spéciale, et des limitations peuvent s’appliquer à leur élimination.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 129
 Appendix G Safety
G Biological hazard safety

Biological hazard safety

WARNING! Potential Biohazard. Depending on the samples used on this instrument, the surface
may be considered a biohazard. Use appropriate decontamination methods when working with
biohazards.

AVERTISSEMENT ! Risque biologique potentiel. En fonction des échantillons utilisés sur cet
instrument, la surface peut être considérée comme présentant un risque biologique. Utilisez des mé­
thodes de décontamination appropriées lorsque vous travaillez en présence de risques biologiques.

WARNING! BIOHAZARD. Biological samples such as tissues, body fluids, infectious agents,
and blood of humans and other animals have the potential to transmit infectious diseases.
Conduct all work in properly equipped facilities with the appropriate safety equipment (for example,
physical containment devices). Safety equipment can also include items for personal protection,
such as gloves, coats, gowns, shoe covers, boots, respirators, face shields, safety glasses, or
goggles. Individuals should be trained according to applicable regulatory and company/ institution
requirements before working with potentially biohazardous materials. Follow all applicable local,
state/provincial, and/or national regulations. The following references provide general guidelines when
handling biological samples in laboratory environment.

· U.S. Department of Health and Human Services, Biosafety in Microbiological and Biomedical
Laboratories (BMBL), 6th Edition, HHS Publication No. (CDC) 300859, Revised June 2020
www.cdc.gov/labs/pdf/CDC-BiosafetymicrobiologicalBiomedicalLaboratories-2020-P.pdf
· Laboratory biosafety manual, fourth edition. Geneva: World Health Organization; 2020 (Laboratory
biosafety manual, fourth edition, and associated monographs)
www.who.int/publications/i/item/9789240011311

AVERTISSEMENT ! RISQUE BIOLOGIQUE. Les échantillons biologiques tels que les tissus, les
fluides corporels, les agents infectieux et le sang de l’homme et d’autres animaux sont suscepti­
bles de transmettre des maladies infectieuses. Effectuez tous vos travaux dans des installations
correctement équipées et dotées du matériel de sécurité approprié (par exemple, des dispositifs de
confinement physique). L’équipement de sécurité peut également inclure des articles de protection
personnelle, tels que des gants, des manteaux, des blouses, des couvre-chaussures, des bottes,
des respirateurs, des masques faciaux, des lunettes de sécurité ou des lunettes de protection. Les
personnes doivent être formées conformément aux exigences réglementaires applicables et aux
exigences de l’entreprise ou de l’institution avant de travailler avec des matières potentiellement
dangereuses. Respectez toutes les réglementations locales, nationales et/ou provinciales applicables.
Les références suivantes proposent des recommandations générales pour la manipulation d’échantil­
lons biologiques dans un environnement de laboratoire.

· U.S. Department of Health and Human Services, Biosafety in Microbiological and Biomedical
Laboratories (BMBL), 6th Edition, HHS Publication No. (CDC) 300859, révision de juin 2020
www.cdc.gov/labs/pdf/CDC-BiosafetymicrobiologicalBiomedicalLaboratories-2020-P.pdf
· Laboratory biosafety manual, fourth edition. Genève: Organisation mondiale de la santé; 2020
(Laboratory biosafety manual, fourth edition, et monographies associées)
www.who.int/publications/i/item/9789240011311

130 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
 H Documentation and support

Related documentation
Publication
Document Description
number

QuantStudio™ Absolute Q™ Digital MAN0025653 Describes the setup, use, and analysis of runs
PCR Starter Kit User Guide using the QuantStudio™ Absolute Q™ Digital
PCR Starter Kit assay. (Catalog No. A52732)

QuantStudio™ Absolute Q™ Digital MAN0026431 Describes the site preparation required for
PCR System Site Preparation Guide installing the QuantStudio™ Absolute Q™ dPCR
System.

SAE Administrator Console v2.0 or MAN0017468 Describes the setup and use of the Security,
later User Guide for PCR systems Auditing, and E-signature (SAE) module.

Note: For additional documentation, see “Customer and technical support” on page 131.

Customer and technical support

Visit thermofisher.com/support for the latest service and support information.
• Worldwide contact telephone numbers
• Product support information
– Product FAQs
– Software, patches, and updates
– Training for many applications and instruments
• Order and web support
• Product documentation
– User guides, manuals, and protocols
– Certificates of Analysis
– Safety Data Sheets (SDSs; also known as MSDSs)

Note: For SDSs for reagents and chemicals from other manufacturers, contact the
manufacturer.

QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide 131
 Appendix H Documentation and support
H Limited product warranty

Limited product warranty

Life Technologies Corporation and/or its affiliate(s) warrant their products as set forth in the
Life Technologies' General Terms and Conditions of Sale at www.thermofisher.com/us/en/home/
global/terms-and-conditions.html. If you have any questions, please contact Life Technologies at
www.thermofisher.com/support.

132 QuantStudio™ Absolute Q™ Digital PCR System Installation, Use, and Maintenance Guide
QuantStudio Absolute Q Digital PCR UG_RUO_v6.2_MAN0025621-v10-GUID-
C7926563-6DA7-46A2-9A5B-47D1EC1FA818-2023/03/06 14:01:00 en
20:08:16.5+01:00
thermofisher.com/support | thermofisher.com/askaquestion
thermofisher.com

11 April 2023