Thermo Fisher Scientific QuantStudio User Manual

QuantStudio™ 6 Pro Real-Time PCR System and QuantStudio™ 7 Pro Real-Time PCR System
USER GUIDE
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.
The information in this guide is subject to change without notice.
DISCLAIMER: T
O 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
Updat
ed 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
D.0 7 January 2020 v1.2.1
C.0 3 December 2019 v1.2.0
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.
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 Ct to Cq in description of instrument verification.
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)
B.0 22 August 2019 v1.1.0
3 December 2019
Added Security, Auditing, and Esignature (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.
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:
Cq Export 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 pr
oducts 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
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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
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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
Contents
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
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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
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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
Contents
CHAPTER 9 Use the instrument with the Security, Auditing, and
Esignature (SAE) v2.0 module ................................................. 136
Overview of the Security, Auditing, and Esignature (SAE) v2.0 module components ... 137
Overview of the instrument features when the SAE module is enabled ............... 137
Security, Auditing, and Esignature (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 Esignature (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
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Contents
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
10
View the instrument details ..................................................... 166
View the license agreement .................................................... 167
View the privacy policy for the Connect cloud-based platform ...................... 167
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Configure the instrument settings ............................................... 168
Enable or disable demonstration mode ...................................... 168
Edit the instrument name (administrator only) ................................ 168
Set the date and the time .................................................. 168
Configure the heated cover settings ......................................... 169
Adjust the speaker volume ................................................. 169
Configure the network ..................................................... 169
Select the region for the Connect platform ................................... 170
Select a disk storage management mode .................................... 171
Enable and edit automatic sign-out ......................................... 171
Set an access key for external software to connect to the instrument ............ 171
Reset the access key for external software to connect to the instrument ......... 172
Configure maintenance and service settings ...................................... 172
Request technical support with Smart Help .................................. 172
Request instrument service with Smart Help ................................. 173
Perform and view self-verification tests ..................................... 173
View the instrument log ................................................... 178
Export the instrument log .................................................. 179
View the instrument statistics .............................................. 179
Enable or disable remote monitoring ........................................ 180
Update the software ...................................................... 180
Repair the software ....................................................... 181
Back up the instrument .................................................... 181
Restore a backup of the instrument ........................................ 182
Upload a certificate for a TaqMan™ Array Plate with RFID ...................... 182
Overview of an instrument reset (restore factory default) ....................... 183
Reset the instrument (restore factory default) ................................. 183
Request remote support ....................................................... 183
Configure the instrument for the hands-free features .............................. 185
Manage the run history ........................................................ 185
Manage the file name convention of the data file .................................. 185
View the notifications .......................................................... 186
Enable and disable home screen notifications .................................... 186
Set up email notifications ...................................................... 187
Clear the notifications ......................................................... 187
APPENDIX A Instrument specifications and layout ........................... 188
Instrument dimensions ........................................................ 188
Instrument and computer clearances ........................................ 189
Configured system dimensions ............................................ 190
Light guidelines .......................................................... 191
Electrical requirements ........................................................ 191
Environmental requirements .................................................... 192
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Contents
APPENDIX B Connect the instrument to a network .......................... 193
Connect the computer to the instrument directly or to a LAN ....................... 193
Connect the instrument to a wired network ....................................... 194
Connect the instrument to a wireless network .................................... 195
Instrument and computer connections ........................................... 196
Download and install the desktop software ....................................... 197
Computer requirements for the desktop software ............................. 197
Download the desktop software ............................................ 197
Install the desktop software ................................................ 198
Networking ................................................................... 198
Supported options for instrument and computer connections .................. 198
Control and monitor networked instruments .................................. 200
Networking guidelines and best practices ................................... 200
Firewall ports that must be open ............................................ 200
Ethernet port overview .................................................... 201
Third-party software ...................................................... 201
APPENDIX C Detailed procedures for preparation of a TaqMan
Array Card ........................................................................ 202
Guidelines for preparation of a card ............................................. 202
TaqMan™ Array Card diagram .................................................. 203
Load the PCR reaction mix ..................................................... 204
Centrifuge the card ............................................................ 204
Seal the card ................................................................. 206
APPENDIX D Parts and materials .............................................. 209
Kits, consumables, accessories, and reagents .................................... 209
96-well 0.2 mL consumables ................................................... 209
96-well 0.1 mL consumables ................................................... 210
384-well consumables ......................................................... 210
TaqMan™ Array Card consumables .............................................. 211
Accessories ................................................................. 212
APPENDIX E Safety .............................................................. 213
12
Symbols on this instrument .................................................... 213
Standard safety symbols .................................................. 214
Additional safety symbols ................................................. 215
Location of safety labels .................................................. 215
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Control and connection symbols ........................................... 219
Conformity symbols ...................................................... 219
Safety information for instruments not manufactured by Thermo Fisher Scientific ..... 220
Instrument safety ............................................................. 220
General ................................................................. 220
Physical injury ............................................................ 221
Electrical safety .......................................................... 222
Laser safety .............................................................. 223
Cleaning and decontamination ............................................. 224
Instrument component and accessory disposal .............................. 224
Safety and electromagnetic compatibility (EMC) standards ......................... 224
Safety standards ......................................................... 225
EMC standards ........................................................... 225
Environmental design standards ............................................ 226
Radio compliance standards ............................................... 226
RF transceiver specifications ............................................... 228
Chemical safety .............................................................. 229
Biological hazard safety ....................................................... 231
APPENDIX F Documentation and support ..................................... 232
Related documentation ........................................................ 232
Customer and technical support ................................................ 233
Limited product warranty ...................................................... 233
Index ..................................................................................... 234
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Product information

1
Network and password security requirements ............................................ 14
Instrument hardware description ....................................................... 15
Hands-free features ................................................................... 22
Software description .................................................................. 24
Types of runs ........................................................................ 31
System template file names ............................................................ 34
Workflow ............................................................................ 40

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.

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.
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QuantStudio™ 6 Pro Real-Time PCR System and QuantStudio™ 7 Pro Real-Time PCR System User Guide

Instrument hardware description

Overview of the instrument

The Applied Biosystems™ QuantStudio™ 6 Pro and 7 Pro Real-Time PCR Systems use fluorescent­based polymerase chain reaction (PCR) reagents to perform the following functions:
Quantitative detection of target nucleic acid sequences (targets)
Qualitative detection of targets (endpoint analysis)
Qualitative analysis of the PCR product (post-PCR target nucleic acid sequences melt curve analysis)
Protein thermal shift experiments
Chapter 1 Product information
Instrument hardware description
1
Each instrument is available with an interchangeable block. The following blocks are available:
96-well 0.2-mL block
96-well 0.1-mL block
384-well block
TaqMan™ Array Card block (QuantStudio™ 7 Pro System only)
The instrument can be used directly from the touchscreen to create and start runs. To design runs or to analyze data, the instrument can be integrated with the desktop software or the Connect platform.
Each instrument has the following features:
Sign-in with facial authentication
An interchangeable block
Microphone for voice commands
Speakers for feedback from voice commands and for instructional videos
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Chapter 1 P
1
Instrument hardware description
roduct information
Smart Help to request technical support or instrument service directly from the instrument
Barcode scanner for tracking plates or TaqMan™ Array Cards

Features of each instrument

Feature
Filter set
[1]
VeriFlex™ Zones
TaqMan™ Array Card block
Security, Auditing, and Esignature (SAE) v2.0 module
[1]
S
ee “System dyes” on page 16.
[2]
See “VeriFlex™ Zones” on page 18.
[3]
See Chapter 9, “Use the instrument with the Security, Auditing, and Esignature (SAE) v2.0 module”.
Instrument filt
System dyes
The QuantStudio™ 6 Pro Real-Time PCR System has a coupled five-color filter set.
The QuantStudio™ 7 Pro Real-Time PCR System has a decoupled six-by-six color filter set.
For more information about available spectral dye calibration kits, contact Support.
QuantStudio™ 6 Pro System QuantStudio™ 7 Pro System
Coupled five-color filter set Decoupled six-by-six color filter set
[2]
Three VeriFlex™ Zones Six VeriFlex™ Zones
Available
Available
ers and supported dyes
[3]
Filter wavelength (nm)
Peak filter Color
[1]
System dyes Example custom dyes
Excitation Emission
x1-m1 Blue 470 ± 15 520 ± 15
x2-m2 Green 520 ± 10 558 ± 11 VIC™ dye
x3-m3 Yellow 550 ± 11 586 ± 10
FAM™ dye, SYBR
GREEN™ dye
NED™ dye, TAMRA
dye, ABY™ dye
SYT09
JOE™ dye, HEX™ dye,
TET™ dye
Cy®3 dye
x4-m4 Orange 580 ± 10 623 ± 14 ROX™ dye, JUN™ dye Texas Red™ dye
x5-m5 Red 640 ± 10 682 ± 14
x6-m6 Deep-Red 662 ± 10 711 ± 12 None
[1]
T
he central wavelengths are the optimized wavelengths.
[2]
The HEX™ dye and TET™ dye from Thermo Fisher Scientific fall within the emission wavelength range of the system, therefore they can be added and adapted for use on the instrument.
[3]
This filter set currently does not support any dyes supplied by Thermo Fisher Scientific.
MUSTANG PURPLE
dye, Cy®5
[3]
LIZ™ dye
Cy®5.5 dye
[2]
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Filters
Wavelength
(nm)
1 2
3
4
5
x1-m1 x2-m2
x3-m3
x4-m4
x5-m5 x6-m6
Emission Spectra
Chapter 1 P
Instrument hardware description
roduct information
1
x1-m1—FAM™ dye, S
1
x2-m2—VIC™ dye
2
x3-m3—ABY™ dye, NED™ dye, Cy®3, T
3
YBR GREEN™ dye
AMRA™ dye
x4-m4—JUN™ dye, RO
4
x5-m5—Cy® 5, MUS
5
X™ dye, Texas Red™ dye
TANG PURPLE™ dye
Custom dyes
The instrument can run assays designed with custom dyes. Custom dyes include the following options:
Dyes that are not supplied by Thermo Fisher Scientific.
Dyes or formulations of dyes that are not system dyes for the instrument.
To use a custom dye on the instrument, review the following requirements.
Calibrate the instrument for the custom dye (see “Calibrate custom dyes” on page 113).
Ensure that the custom dye excites between 455–672 nm and emits between 505–723 nm.
Select a custom dye that does not overlap with other dyes used in the run (see “System dyes” on
page 16).
The custom dye for use in calibration must be attached to the 5' end of a short DNA oligonucleotide consisting of the first two bases of the probe sequence without a quencher at the 3' end.
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Chapter 1 Product information
1
Instrument hardware description

Overview of data collection

The instrument collects raw fluorescence data at dierent points during the PCR cycle, depending on the type of run performed.
When you create a plate file, you can customize the optical filter channels through which the instrument collects data. You can specify a filter channel set for all PCR thermal protocols and for melt curve stages.
Run type Run type Data collection point
Real-time
Standard curve
Relative standard curve
Comparative Ct (DDCt)
Melt curve
During the thermal cycling protocol.
Typical timing is to collect data at each cycle of a PCR stage or continuously during a melt stage.
Post-PCR (endpoint)

VeriFlex™ Zones

VeriFlex™ Z control over your real-time PCR runs.
The independent zones are ideal for real-time PCR optimization. They also provide the ability to perform multiple runs at the same time. Unlike standard gradients which give a sigmoidal temperature curve across the columns, blocks with VeriFlex™ Zones help deliver accurate temperatures across every zone.
The QuantStudio™ 6 Pro System has three VeriFlex™ Zones (Figure 1 on page 19). The QuantStudio™ 7 Pro System has six VeriFlex™ Zones (Figure 2 on page 19).
Note: VeriFlex™ Zones are only applicable for the 96-well 0.2-mL block and the 96-well 0.1-mL block.
ones provide independent temperature zones that oer enhanced functionality and precise
Genotyping
Presence/absence
After thermal cycling is completed. For Presence/Absence and Genotyping analysis,
data collection before the PCR cycle is optional, but recommended.
(Optional) During the thermal cycling protocol. Collecting data during the run can confirm
genotyping results by viewing traces in allelic discrimination plots or viewing genotyping calls at earlier cycles.
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Chapter 1 P
Instrument hardware description
roduct information
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Figure 1 Three VeriFlex™ Z
Figure 2 Six VeriFlex™ Z
Note: Plate files are not compatible between the QuantStudio™ 6 Pro System and the QuantStudio™ 7
Pro System. For more information, see “Compatibility of plate files” on page 29.

AutoDelta settings

AutoDelta enables an incremental increase or decrease in the temperature or time in a PCR cycle.
o use AutoDelta, specify a dierence in the time and the temperature. Specify the PCR cycle for this
T change to be applied.
ones
ones
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Chapter 1 Product information
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Instrument hardware description

Parts of the instrument

Figure 3 Front of the instrument
Cameras
1
Touchscreen
2
Microphones
3
USB port
4
Indicator light
5
Proximity sensor
6
Access door for block change
7
Speakers
8
Drawer
9
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Instrument hardware description
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Figure 4 Back of the instrument
USB ports
1
Wi-Fi dongle port
2
Ethernet port
3
Note: The instrument r
The USB ports at the rear of the instrument can be used for external devices, for example, a mouse or a k
eyboard.
ecognizes only one external storage device at a time for data transfer.
QuantStudio™ 6 Pro Real-Time PCR System and QuantStudio™ 7 Pro Real-Time PCR System User Guide
RS-232 port (service use only)
4
ON/OFF switch
5
Power inlet receptacle
6
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Chapter 1 Product information
1

Hands-free features

Instrument status indicator

Indicator
O Powered o
Blue light changing brightness slowly Powering on
Blue light changing brightness Standby
Blue light moving inwards towards middle of instrument
Blue light moving outwards towards side of instrument
Blue light moving back and forth Block is being changed
Blue light on Instrument is ready to start a run or is performing a
Amber blinking Error
Hands-free features
Instrument status
Sleep mode
Drawer opening
Drawer closing
run

Facial authentication

The instrument allows hands-free facial authentication to sign in a user. The instrument camera detects a face. The instrument will sign in the user after the face is matched to the photo associated with a
profile.

Voice commands

The instrument recognizes a set of commands for hands-free operation. For list of supported voice commands, see “Use voice commands” on page 45.
Voice commands are only available when a user is signed in with a Connect account. Voice commands are not available with a local instrument profile.
Voice commands are only available in select countries.
Voice commands use Amazon™ Alexa™ for Business.
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Indicators for the hands-free features

Indicators for facial authentication
Chapter 1 Product information
Hands-free features
1
Display
The Sign In screen displays . Facial authentication for the instrument is enabled.
The Sign In screen does not display .
Facial authentication for the instrument is disabled.
All users must sign in with a PIN.
Note: To enable facial authentication, see “Configure the instrument for the hands-free features” on page 185.
Status of facial authentication
Indicators for voice commands
For the location of the proximity sensor, see Figure 3 on page 20.
Display Status of voice commands
(Gray)
(Gray)
The voice command function is not available because the proximity sensor does not detect a person.
The voice command function is not available if any of these conditions is true:
The voice command function for the instrument is disabled by an administrator.
The user is signed in with a local profile.
The microphone was disabled by the user and the proximity sensor does not detect a person. The icon will return to a red state when the proximity sensor detects a person.
The instrument is preparing to accept voice commands.
(Amber)
(Blue)
(Red)
Note: The amber display is an intermediate state and will only appear for several seconds.
The voice command function is available if all of these conditions are true:
The voice command function for the instrument is enabled by an administrator.
The user is signed in with a Connect instrument profile.
The proximity sensor detects a person.
The microphone was disabled by the user (see “Enable or disable the microphone” on page 44).
To enable voice commands, see “Configure the instrument for the hands-free features” on page 185.
For more information about linking a local instrument profile to a Connect profile, see “Link the instrument to your Connect account” on page 126 and “If you link when you are signed in to the instrument” on page 129.
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Chapter 1 Product information
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Software description

Software description

Parts of the home screen

Figure 5 Home screen
Instrument name
1
Instrument calendar
2
Microphone
3
Help
4
Eject
5
Status dial
6
Table 1 Parts of the home screen
Element of the home
scr
een
Block installed
7
Current user
8
Connectivity icons
9
Buttons to access plate files
10
Instrument settings
11
Function
Instrument name Set by the administrator to identify the instrument.
Calendar Schedule time for a run or see runs that are scheduled.
Microphone Shows the status of the microphone (see “Indicators for voice commands” on
page 23 and “Enable or disable the microphone” on page 44).
Help Access the Help.
Eject Open or close the drawer to insert or remove a plate or a TaqMan™ Array Card.
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Table 1 Parts of the home screen (continued)
Chapter 1 P
roduct information
Software description
1
Element of the home
screen
Status dial
When the instrument is not in use—Displays Set up run.
When the instrument is in use—Displays the sample block temperature, the
Function
elapsed run time, and the run status.
When the instrument is locked while in use—Displays Locked within the status dial.
When a run is complete—Displays Run complete.
Block type The block that is installed on the instrument.
If applicable, the following items are noted:
If there is no block and heated cover set installed.
If the block and heated cover are mismatched.
Current user Displays the current signed-in user.
Guest is displayed if no user is signed in.
Connectivity Only the icons that apply to the connectivity status of the instrument at the time are
displayed.
—The instrument is wirelessly connected.
—The instrument is connected to a wired network.
—A USB drive is plugged into the instrument.
—The instrument is connected to a network drive.
—The instrument is connected to a Connect account.
Buttons to access plate
[1]
files
Access a plate file to edit it or start a run.
Set up run—Open a system template or a saved plate file.
(Load plate file)—Open a system template or a saved plate file.
(Run last)—Open the last plate file that was used to start a run. The last plate
file is specific to the profile.
Instrument settings
[1]
P
late files are applicable to TaqMan™ Array Cards.
QuantStudio™ 6 Pro Real-Time PCR System and QuantStudio™ 7 Pro Real-Time PCR System User Guide
Edit the file name convention.
View the run history, and transfer or delete data files.
Install, change, or remove the block and the heated cover.
Configure the instrument settings.
Configure the maintenance and service settings.
View notifications.
Configure hands-free operation.
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Chapter 1 Product information
1
Software description
Connect and Cloud definitions
The terms Connect, Cloud, Thermo Fisher Connect, and Thermo Fisher Cloud are used interchangeably on the instrument touchscreen. The term Connect is used in this document.
The following icons are used interchangeably on the instrument touchscreen:
The icon is used in this document.

Instrument, desktop software, and Connect platform features

The instrument and the software include the features described below.
Note: System templates cannot be edited. They can be edited, then saved as a separate plate file.
Feature Instrument Desktop Connect
Use as guest (no sign in)
Schedule a run
Open system templates
Open system templates, edit them, and save them as plate files
Open plate files created on the desktop software
Open plate files created on the Connect platform
Open plate file created on the instrument
Send plate files to the instrument run queue
Access the plate file associated with last run on the instrument
Load plate in instrument
Start run
View real-time data during a run
View results after a run is complete
26
See instrument status (run in progress)
Send email notifications
Check calibration status
Analyze and export results
QuantStudio™ 6 Pro Real-Time PCR System and QuantStudio™ 7 Pro Real-Time PCR System User Guide
(Limited)
Chapter 1 Product information
Software description
(continued)
Feature Instrument Desktop Connect
View analysis of results
1
Set calibration reminders
Review exported calibration or RNase P verification results
Overview of file locations and files
Note: The term plate file is applicable to both plates and TaqMan™ Array Cards.
File locations
File location
Run queue Plate files sent from the desktop software.
Public
Templates
Description and function
Plate files saved by guest users are stored in this folder.
Data files from runs started by guest users are stored in this folder.
System templates are stored in this folder.
System templates cannot be edited. They must be saved as a separate plate file and stored in a dierent folder.
Data files cannot be saved in this folder.
(RNase P only)
Connect
Network drive
USB drive
My instrument
Plate files can be retrieved from a Connect profile.
Data files can be saved to a Connect profile.
You must have a Connect profile.
Plate files can be retrieved from a network drive.
Data files can be saved to a network drive.
The instrument must be connected to a network or a computer.
Plate files can be retrieved from a USB drive.
Data files can be saved to a USB drive.
A USB drive must be inserted into the instrument.
This location is only available to a user who is signed in. Guest users cannot access this location to retrieve plate files or save data files.
This location is specific to a user. Files are not accessible to any other users, except for administrators.
Plate files can be retrieved from this location.
Data files are always saved to this location.
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Chapter 1 Product information
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Software description
(continued)
File location
Post-read
Description and function
In endpoint PCR, the pre-read data is saved in this folder for post-read analysis.
Files
IMPORTANT! Plate files and data files are not included in a back-up of the instrument and are not
restored when a backup of the instrument is restored.
Plate files and data files must be transferred separately. See Chapter 6, “View and manage files”. System templates are included in the back-up and are restored when a backup of the instrument is restored.
All file types ar
Item Description and function Supported in
System template
e applicable to both plates and TaqMan™ Array Cards.
A non-editable t
Accessed from (only system templates are stored in this folder).
Accessed from the Set up run button.
Is saved as a separate plate file if it is edited.
Contains the thermal protocol for the real-time PCR.
Does not contain the sample information.
Does not contain the target information.
Sample information and target information must be added (saved as a separate plate file). The sample information and target information can be added on the desktop software or on the Connect platform after the run is complete.
emplate.
(Load plate file) and the T
emplates folder
Instrument Desktop Connect
Plate File
From
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(Load plate file)
QuantStudio™ 6 Pro Real-Time PCR System and QuantStudio™ 7 Pro Real-Time PCR System User Guide
A file that has been saved fr
Can be edited and saved.
Can be edited and saved as a separate plate file.
Contains the thermal protocol for the real-time PCR.
Can contain the sample information.
Can contain the target information.
Sample information and target information must be added if not present. The sample information and target information can be added on the desktop software or on the Connect platform after the run is complete.
om a system template.
Instrument Desktop Connect
Chapter 1 P
roduct information
Software description
(continued)
Item Description and function Supported in
Plate File
From (Run last)
The plate file associated with the last run for the profile.
Can be edited and saved.
Can be edited and saved as a separate plate file.
Contains the thermal protocol for the real-time PCR.
Contains the sample information. The sample information can be edited on the desktop software or on the Connect platform after the run is complete.
Contains the target information. The target information can be edited on the desktop software or on the Connect platform after the run is complete.
Sample information and target information can be edited on the instrument.
If the sample information and the target information for the last run were added on the desktop software or on Connect after the run was complete, they will not be included on the plate file that is on the instrument.
Instrument
1
Data file
Contains the r
Can be viewed on the instrument only immediately after the run is complete.
Transfer to Connect or to the desktop software to view and analyze data.
eal-time PCR data.
Compatibility of plate files
The plat
A plate file for a QuantStudio™ 6 Pro System can only be opened on this instrument. It cannot be opened on a QuantStudio™ 7 Pro System.
A plate file for a QuantStudio™ 7 Pro System can only be opened on this instrument. It cannot be opened on a QuantStudio™ 6 Pro System.
e files are specific to the instrument.
Instrument (limited) Desktop Connect
QuantStudio™ 6 Pro Real-Time PCR System and QuantStudio™ 7 Pro Real-Time PCR System User Guide
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Chapter 1 Product information
1
Software description
Components of the files
Component
Properties
Method Thermal cycling conditions
Instrument Desktop Connect
Data file name
Reagent information
Name
Type
Lot number
Barcode
Catalog number
Expiry date
Plate barcode or TaqMan Array Card barcode
Location to send data after the run is complete
T
emperature
Time
Cover temperature
Reaction volume
Data collection points
Ramp rates
VeriFlex™ Zones
Auto Delta settings
Experiment file name
Plate barcode or TaqMan™ Array Card barcode
User name
Instrument type
Block type
Analysis module
Chemistry (reagent information)
Run mode
Comments
(Connect platform only) Notifications
Thermal cycling conditions
Plate Sample names
Targets
SNP assays
Run Monitor a run in progress
View time remaining, temperature, method, and amplification plots
Pause, resume, or stop a run
Results Not applicable Review plots
Export Export results
Data files are transferred to the desktop software or the Connect platform for analysis
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QuantStudio™ 6 Pro Real-Time PCR System and QuantStudio™ 7 Pro Real-Time PCR System User Guide
Define and assign samples, targets or SNP assays, and tasks in the Plate setup screen.
Monitor a run in progress
View time remaining
Export results
Monitor a run in progress (link to Connect Instrument Details)
View time remaining, temperature, method, and amplification plots
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