Thermo Scientific Applied Biosystems QuantStudio 6 Pro User manual

For Research Use Only. Not for use in diagnostic procedures.
QuantStudio™6 Pro Real-Time PCR System
and QuantStudio™7 Pro Real-Time PCR
System
USER GUIDE
Publication Number MAN0018045
Revision G.0

Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256
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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.
Revision history: Pub. No. MAN0018045
Revision Date Description
G.0 17 February 2021 v1.4.0
Updated centrifuges for the TaqMan™Array Card.
F.0 6 November 2020 v1.4.0
•Specified that the instrument and the desktop software must be connected to the same SAE server
for an account password to be updated on both applications.
•Provided the option of a static IP address or a dynamic IP address to connect to the SAE server.
•Corrected standards on 384-well RNase P plate (Figure 14 on page 105).
•Added a TaqMan™Array Card block, including system template file names, calibration workflow,
instructions to edit the plate file, and instructions to load and unload from the instrument
(QuantStudio™7 Pro System only).
•Added instructions to review the calibration status in the QuantStudio™Design and Analysis
Software v2.
•Added a peripheral self-test and updated the previous self-verification test to a hardware test.
•Added instructions to upload a certificate for a TaqMan™Array Plate with RFID.
•Added the option of a voice recording for Smart Help.
•Added remote support.
•Updated the RFID labels (Figure 27 on page 215 and Figure 28 on page 216).
E.0 27 April 2020 v1.3.0
•Added protein thermal shift experiments to the instrument functions.
•Added a 96-well 0.1-mL block.
•Updated instructions to export data files when setting up a run and added instructions to import or
delete export settings.
•Updated instructions to save an edited run method.
•Updated instructions to add or edit reagents and then to apply the reagents to the plate.
•Updated instructions to view the amplification plot after a run.
•Added instructions to view QC Check status after the run.
•Added information about a locked template file.
•Added functions for using the instrument with the SAE Administrator Console.
D.0 7 January 2020 v1.2.1
•Added information about position to set up facial authentication and to sign in with facial
authentication.
•Added instructions to test the connection to the Connect cloud-based platform and to view the
privacy policy for the Connect platform.
•Added instructions to repair the software after a software update.
•Changed port 7000 to 7443 for the instrument-to-computer connection.
•Corrected Ctto Cqin description of instrument verification.
C.0 3 December 2019 v1.2.0
•Added a 384-well plate block.
•Updated instructions to set up facial authentication.
•Added a new voice command for calibration.
•Added custom melt curve run calibration.

Revision Date Description
C.0
(continued)
3 December 2019 •Added Security, Auditing, and E‑signature (SAE) v2.0 module.
•Added instructions to generate and reset an access key for external software to connect to the
instrument.
•Added instructions to import an Assay Information File.
•Corrected that a Connect profile is required for the instrument schedule and Smart Help.
•Added new radio compliance standards.
B.0 22 August 2019 v1.1.0
•Corrected the text on the buttons for the following items:
–Add facial authentication to an existing instrument profile.
–View the license agreement.
–Reset the instrument (restore factory default).
•Added the following items:
–TET™dye as a system dye.
–Information about sleep mode.
–Information about the automatic sign-out feature.
–The option to configure the instrument so that sign-in is required (guest access is not
permitted).
–Instructions to set up email notification.
–Information about the speaker volume for each user.
–Instructions to back up the instrument and to restore a backup of the instrument.
–Information about multiple instruments and email notification in the comparison of a local
instrument profile and a Connect profile.
–Instructions to unlink a Connect profile.
–Instructions to update a PIN for a Connect profile.
–Lighting guidelines for facial authentication.
–Radio compliance standards and RF transceiver specifications.
•Corrected the following items:
–Indicators for voice commands.
–Voice commands are only available in select countries.
–Instructions to remove VeriFlex™Zones and the Auto Delta setting.
–Excitation and emission wavelengths of the filters in the calibration instructions.
–Add a four-digit PIN when signing into the instrument for the first time using a Connect
profile.
–Add a four-digit PIN when linking a local instrument profile to a Connect profile.
–Select a region for the Connect cloud-based platform.
–A run cannot be started if a block has never been calibrated on the instrument.
–The options after a calibration run is complete.
–The example files for the desktop software are embedded in the software and do not need to
be downloaded.
•Updated the following items:
–CqExport checkbox is selected as the default.
–Instructions to sign in with facial authentication.
A.0 18 April 2019 New document (v1.0.1).
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.
NOTICE TO PURCHASER: DISCLAIMER OF LICENSE: Purchase of this software product alone does not imply any license under any
process, instrument or other apparatus, system, composition, reagent or kit rights under patent claims owned or otherwise controlled by
Thermo Fisher Scientific, either expressly, or by estoppel.

Trademarks: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. TaqMan is
a registered trademark of Roche Molecular Systems, Inc., used under permission and license. Cy is a registered trademark of GE
Healthcare. Amazon, Alexa, and all related logos are trademarks of Amazon.com, Inc. or its aliates. Windows is a trademark of
Microsoft Corporation. Chrome is a trademark of Google LLC. Pentium is a trademark of Intel Corporation or its subsidiaries in the U.S.
and/or other countries. Macintosh is a trademark of Apple Inc., registered in the U.S. and other countries.
©2021 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 Product information ................................................ 14
Network and password security requirements ..................................... 14
Network configuration and security .......................................... 14
Password security ......................................................... 14
Instrument hardware description ................................................. 15
Overview of the instrument .................................................. 15
Features of each instrument ................................................. 16
Instrument filters and supported dyes ........................................ 16
Overview of data collection ................................................. 18
VeriFlex™Zones ........................................................... 18
AutoDelta settings ......................................................... 19
Parts of the instrument ..................................................... 20
Instrument status indicator .................................................. 22
Hands-free features ............................................................ 22
Facial authentication ....................................................... 22
Voice commands .......................................................... 22
Indicators for the hands-free features ........................................ 23
Software description ........................................................... 24
Parts of the home screen ................................................... 24
Connect and Cloud definitions .............................................. 26
Instrument, desktop software, and Connect platform features ................... 26
Overview of file locations and files ........................................... 27
Components of the files .................................................... 30
Third-party software ....................................................... 31
Network connection options ................................................ 31
Types of runs .................................................................. 31
Standard curve run ........................................................ 31
Relative standard curve run ................................................. 32
Comparative Ct(DDCt) run .................................................. 32
Genotyping run ............................................................ 33
Presence/absence run ...................................................... 33
Melt curve run ............................................................. 33
QuantStudio™6 Pro Real-Time PCR System and QuantStudio™7 Pro Real-Time PCR System User Guide 5

System template file names ..................................................... 34
System template file names for the 96-well 0.2-mL block ....................... 34
System template file names for the 96-well 0.1-mL block ....................... 35
System template file names for the 384-well block ............................. 37
System template file names for the TaqMan™Array Card block .................. 38
Workflow ..................................................................... 40
■CHAPTER 2 Get started .......................................................... 41
Precautions for use ............................................................. 41
Installation and instrument verification ............................................ 42
Overview of guest access ....................................................... 42
Use the instrument as a guest ............................................... 42
Power on the instrument ........................................................ 43
Sign in ........................................................................ 43
Sign in with a PIN .......................................................... 43
Sign in with facial authentication ............................................. 44
Enable or disable the microphone ................................................ 44
Use voice commands .......................................................... 45
Sign out ...................................................................... 46
■CHAPTER 3 Create and run plates on the instrument ......................... 47
Options to run a plate .......................................................... 47
Create and run a plate from a system template or a saved plate file .............. 47
Repeat the last run ......................................................... 49
Overview of customized data export .............................................. 50
(Optional) Scan a barcode using a barcode scanner ................................ 51
Load a plate into the instrument .................................................. 51
Load a TaqMan™Array Card into the instrument ................................... 52
Unload a plate or a TaqMan™Array Card from the instrument ........................ 52
■CHAPTER 4 Edit a plate before starting a run .................................. 54
Overview of a template file with restricted editing .................................. 54
Options to edit the properties of a plate file ........................................ 55
Import a sample setup ..................................................... 55
Import an auto export setting ................................................ 55
Delete an auto export setting ................................................ 55
Options to edit the method of a plate file .......................................... 56
Method elements .......................................................... 57
Edit the method ........................................................... 57
Add or remove steps ....................................................... 58
Add or remove stages ...................................................... 58
Add or remove data collection locations ...................................... 58
Contents
6QuantStudio™6 Pro Real-Time PCR System and QuantStudio™7 Pro Real-Time PCR System User Guide

Set up or remove VeriFlex™Zones ........................................... 59
Set up or remove the Auto Delta feature ...................................... 61
Configure ramp rates ....................................................... 62
Add or remove a pause ..................................................... 62
Options to edit the well details of a plate file ....................................... 62
Options to view a plate layout ............................................... 63
Assign or edit a well for a plate .............................................. 65
Assign or edit a well for a TaqMan™Array Card ................................ 66
Add or edit the reagent details for a plate ..................................... 66
Apply the reagents to a plate ................................................ 67
Delete the reagent details ................................................... 67
Add or edit the reagent details for a TaqMan™Array Card ....................... 68
Apply the reagents to a TaqMan™Array Card .................................. 68
Edit a passive reference dye ................................................ 68
Import an Assay Information File (AIF) ........................................ 69
■CHAPTER 5 Options for a run .................................................... 70
Screens available during a run ................................................... 70
Edit a plate file during a run ..................................................... 71
Pause an instrument run ........................................................ 72
Stop an instrument run ......................................................... 72
View the method during a run ................................................... 73
View real-time data and plots during a run ........................................ 73
Adjust the display of real-time plots during a run ............................... 74
View the time remaining during a run ............................................. 74
Lock the touchscreen during a run ............................................... 74
Unlock the touchscreen during a run ............................................. 75
Instrument Schedule ........................................................... 75
Overview of the instrument schedule ......................................... 75
Schedule a run ............................................................ 75
Cancel a scheduled run .................................................... 75
■CHAPTER 6 View and manage files ............................................. 77
Manage plate files .............................................................. 77
Copy plate files ............................................................ 77
Delete plate files ........................................................... 78
Manage data files .............................................................. 78
View QC Check status after a run ............................................ 78
View an amplification plot after a run ......................................... 80
Transfer a data file immediately after a run .................................... 81
Transfer data files at a later time ............................................. 81
View the list of data files on the instrument .................................... 82
Delete data files from the instrument ......................................... 82
Contents
QuantStudio™6 Pro Real-Time PCR System and QuantStudio™7 Pro Real-Time PCR System User Guide 7

■CHAPTER 7 Calibrate and verify instrument performance ..................... 84
Instrument and block calibration ................................................. 84
Calibration and verification schedule ............................................. 85
Calibration descriptions ......................................................... 86
View the calibration status and set reminders ...................................... 87
View the calibration status on the instrument .................................. 87
Set calibration frequency and reminders on the instrument ...................... 88
View calibration status and set reminders on the Connect platform .............. 88
Review calibration status ................................................... 89
Export a calibration report ....................................................... 89
Perform ROI/uniformity, background, and dye calibrations for plate blocks ............ 89
Calibration workflow ....................................................... 90
Prepare a calibration plate .................................................. 90
Perform calibrations ........................................................ 91
View the calibration images ................................................. 93
Transfer calibration results .................................................. 94
Transfer calibration data files ................................................ 94
Troubleshoot calibration failure .............................................. 95
Identify contamination ...................................................... 95
Create a background plate (optional) ......................................... 96
Perform ROI/uniformity, background, dye, and normalization calibrations for the
TaqMan™Array Card block .................................................... 97
Calibration workflow ....................................................... 97
Prepare a calibration TaqMan™Array Card .................................... 98
Perform calibrations ....................................................... 100
View the calibration images ................................................ 101
Troubleshoot normalization calibration failure ................................ 102
Perform verification using RNase P plates ........................................ 103
Instrument verification description .......................................... 104
RNase P instrument verification plate ....................................... 104
Performance specifications pass criteria ..................................... 105
Prepare an RNase P plate ................................................. 105
Perform RNase P verification ............................................... 106
Troubleshoot verification failure ............................................. 107
Perform verification using RNase P with a TaqMan™Array Card ..................... 108
RNase P instrument verification TaqMan™Array Card ......................... 109
Prepare an RNase P TaqMan™Array Card ................................... 110
Perform RNase P verification ............................................... 112
Calibrate custom dyes ......................................................... 113
Overview of custom dyes .................................................. 113
Use a dilution series to determine an optimal custom dye concentration ......... 114
Calibrate the custom dye .................................................. 117
Calibrate for a custom melt curve run ............................................ 120
Contents
8QuantStudio™6 Pro Real-Time PCR System and QuantStudio™7 Pro Real-Time PCR System User Guide

■CHAPTER 8 Manage profiles ................................................... 122
Require sign-in ............................................................... 122
Recommended order to set up profiles .......................................... 123
Overview of local instrument profiles and Connect profiles ......................... 123
Connect instrument profile roles and functions ................................... 124
Test the connection to the Connect platform ..................................... 124
Link the instrument to your Connect account ..................................... 126
Create a new local instrument profile ............................................ 127
Link a local profile to a Connect profile .......................................... 127
Unlink a Connect account ...................................................... 129
If you link when you are signed in to the instrument ............................... 129
If you link when you are not signed in to the instrument ............................ 130
Manage individual instrument profiles ........................................... 131
Create an administrator instrument profile during initial start-up ................ 131
Set up facial authentication at the initial creation of an instrument profile ........ 131
Add facial authentication to an existing instrument profile ...................... 132
Change the PIN for an instrument profile .................................... 133
Change the PIN for a Connect profile ....................................... 133
Manage all instrument profiles as an administrator ................................ 133
View all instrument profiles ................................................. 133
Reset the PIN for a profile ................................................. 134
Add a profile ............................................................. 134
Enable or disable administrator privileges .................................... 135
Delete a profile ........................................................... 135
■CHAPTER 9 Use the instrument with the Security, Auditing, and
E‑signature (SAE) v2.0 module ................................................. 136
Overview of the Security, Auditing, and E‑signature (SAE) v2.0 module components ... 137
Overview of the instrument features when the SAE module is enabled ............... 137
Security, Auditing, and E‑signature (SAE) v2.0 module functions .................... 138
Functions that are controlled ............................................... 138
Functions that can be audited ............................................. 139
Functions that can be signed ............................................... 139
Security, Auditing, and E‑signature (SAE) v2.0 module roles ........................ 139
Dialog boxes in the SAE module ................................................ 140
Profiles when the SAE module is enabled ........................................ 141
SAE-enabled system components .............................................. 141
Compatibility between SAE-enabled and SAE-disabled components ............ 142
Contents
QuantStudio™6 Pro Real-Time PCR System and QuantStudio™7 Pro Real-Time PCR System User Guide 9

Enable SAE functions ......................................................... 143
Workflow: Enable SAE functions ............................................ 143
Configure SAE Administrator Console application profiles ..................... 143
Enable SAE on the instrument and specify the SAE server (administrator only) ... 143
Connect to the SAE server ................................................. 144
Enable SAE functions in QuantStudio™Design and Analysis Software v2 ........ 145
Disable SAE on the instrument (administrator only) ................................ 145
Sign in as a local administrator with SAE enabled ................................. 146
Sign in with SAE enabled ...................................................... 147
Sign out with SAE enabled ..................................................... 148
Change your SAE account password on the instrument ............................ 149
Sign a plate setup ............................................................. 150
Enter an audit reason .......................................................... 151
View signing records for a plate file .............................................. 152
View audit records ............................................................ 153
Use the instrument when the SAE server is oine ................................. 154
E-signature requirements to start a run .......................................... 154
Signing in after automatic screen locking ........................................ 155
SAE error messages and actions ................................................ 155
■CHAPTER 10 Maintain the instrument ......................................... 156
Install a block ................................................................ 156
Change the block ............................................................. 157
Remove the block ............................................................. 158
Decontaminate the sample block ............................................... 159
Materials required ........................................................ 159
Clean the sample block ................................................... 159
Detailed procedures for cleaning the sample block ............................ 160
Replace the instrument fuses ................................................... 161
Materials required ........................................................ 161
Replace the fuses ........................................................ 161
Power on or o, store, and move ................................................ 163
Enable and edit sleep mode ............................................... 163
Power on the instrument ................................................... 164
Power o the instrument ................................................... 164
Prepare the instrument to store, move, or ship ............................... 165
Move the instrument ...................................................... 165
■CHAPTER 11 Configure the instrument settings .............................. 166
View the instrument details ..................................................... 166
View the license agreement .................................................... 167
View the privacy policy for the Connect cloud-based platform ...................... 167
Contents
10 QuantStudio™6 Pro Real-Time PCR System and QuantStudio™7 Pro Real-Time PCR System User Guide