ThermoFisher Scientific QuantStudio 6 Pro User manual

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

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: 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
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.
•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.

Revision Date Description
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.
©2020 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 Product information ................................................ 13
Network and password security requirements ..................................... 13
Network configuration and security .......................................... 13
Password security ......................................................... 13
Instrument hardware description ................................................. 14
Overview of the instrument .................................................. 14
Features of each instrument ................................................. 15
Instrument filters and supported dyes ........................................ 15
Overview of data collection ................................................. 17
VeriFlex™Zones ........................................................... 17
AutoDelta settings ......................................................... 18
Parts of the instrument ..................................................... 19
Instrument status indicator .................................................. 21
Hands-free features ............................................................ 21
Facial authentication ....................................................... 21
Voice activation ........................................................... 21
Indicators for the hands-free features ........................................ 22
Software description ........................................................... 23
Parts of the home screen ................................................... 23
Connect and Cloud definitions .............................................. 25
Instrument, desktop software, and Connect platform features ................... 25
Overview of file locations and files ........................................... 26
Components of the files .................................................... 29
Third-party software ....................................................... 30
Network connection options ................................................ 30
Types of runs .................................................................. 30
Standard curve run ........................................................ 30
Relative standard curve run ................................................. 31
Comparative Ct(DDCt) run .................................................. 31
Genotyping run ............................................................ 32
Presence/absence run ...................................................... 32
Melt curve run ............................................................. 32
4QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide

System template file names ..................................................... 33
System template file names for the 96-well 0.2-mL block ....................... 33
System template file names for the 96-well 0.1-mL block ....................... 34
System template file names for the 384-well block ............................. 36
Workflow ..................................................................... 38
■CHAPTER 2 Get started .......................................................... 39
Precautions for use ............................................................. 39
Installation and instrument verification ............................................ 40
Overview of guest access ....................................................... 40
Use the instrument as a guest ............................................... 41
Power on the instrument ........................................................ 42
Sign in ........................................................................ 43
Sign in with a PIN .......................................................... 43
Sign in with facial authentication ............................................. 43
Enable or disable the microphone ................................................ 44
Use voice commands .......................................................... 44
Sign out ...................................................................... 45
■CHAPTER 3 Create and run plates on the instrument ......................... 46
Options to run a plate .......................................................... 46
Create and run a plate from a system template or a saved plate file .............. 46
Repeat the last run ......................................................... 48
Overview of customized data export .............................................. 49
(Optional) Scan a barcode using a barcode scanner ................................ 50
Load a plate into the instrument .................................................. 50
Unload a plate from the instrument ............................................... 51
■CHAPTER 4 Edit a plate before starting a run .................................. 52
Overview of a template file with restricted editing .................................. 52
Options to edit the properties of a plate file ........................................ 53
Import a sample setup ..................................................... 53
Import an auto export setting ................................................ 53
Delete an auto export setting ................................................ 53
Options to edit the method of a plate file .......................................... 54
Method elements .......................................................... 55
Edit the method ........................................................... 55
Add or remove steps ....................................................... 56
Add or remove stages ...................................................... 56
Add or remove data collection locations ...................................... 56
Set up or remove VeriFlex™Zones ........................................... 57
Contents
QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide 5

Set up or remove the Auto Delta feature ...................................... 58
Configure ramp rates ....................................................... 59
Add or remove a pause ..................................................... 59
Options to edit the well details of a plate file ....................................... 60
Options to view a plate layout ............................................... 60
View a 384-well plate ....................................................... 61
Assign or edit a well ........................................................ 62
Add or edit the reagent details ............................................... 63
Apply the reagents to a plate ................................................ 63
Delete the reagent details ................................................... 63
Edit a passive reference dye ................................................ 64
Import an Assay Information File (AIF) ........................................ 64
■CHAPTER 5 Options for a run .................................................... 65
Screens available during a run ................................................... 65
Edit a plate file during a run ..................................................... 66
Pause an instrument run ........................................................ 67
Stop an instrument run ......................................................... 67
View the method during a run ................................................... 68
View real-time data and plots during a run ........................................ 68
Adjust the display of real-time plots during a run ............................... 69
View the time remaining during a run ............................................. 69
Lock the touchscreen during a run ............................................... 69
Unlock the touchscreen during a run ............................................. 70
Instrument Schedule ........................................................... 70
Overview of the instrument schedule ......................................... 70
Schedule a run ............................................................ 70
Cancel a scheduled run .................................................... 71
■CHAPTER 6 View and manage files ............................................. 72
Manage plate files .............................................................. 72
Copy plate files ............................................................ 72
Delete plate files ........................................................... 73
Manage data files .............................................................. 73
View QC Check status after a run ............................................ 73
View an amplification plot after a run ......................................... 75
Transfer a data file immediately after a run .................................... 76
Transfer data files at a later time ............................................. 76
View the list of data files on the instrument .................................... 77
Delete data files from the instrument ......................................... 77
Contents
6QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide

■CHAPTER 7 Calibrate and verify instrument performance ..................... 79
Instrument and block calibration ................................................. 79
Calibration and verification schedule ............................................. 80
Calibration descriptions ......................................................... 81
View the calibration status and set reminders ...................................... 81
View the calibration status on the instrument .................................. 81
Set calibration frequency and reminders on the instrument ...................... 82
View calibration status and set reminders on the Connect platform .............. 82
Export a calibration report ....................................................... 83
Perform ROI/uniformity, background, and dye calibrations .......................... 84
Calibration workflow ....................................................... 84
Prepare a calibration plate .................................................. 84
Perform calibrations ........................................................ 86
View the calibration images ................................................. 87
Transfer calibration results .................................................. 89
Transfer calibration data files ................................................ 89
Troubleshoot calibration failure .............................................. 89
Identify contamination ...................................................... 90
Create a background plate (optional) ......................................... 90
Perform verification using RNase P plates ......................................... 91
Instrument verification description ........................................... 91
RNase P instrument verification plate ........................................ 92
Performance specifications pass criteria ...................................... 93
Prepare an RNase P plate ................................................... 93
Perform RNase P verification ................................................ 94
Troubleshoot verification failure .............................................. 96
Calibrate custom dyes .......................................................... 98
Overview of custom dyes ................................................... 98
Use a dilution series to determine an optimal custom dye concentration .......... 98
Calibrate the custom dye .................................................. 101
Calibrate for a custom melt curve run ............................................ 104
■CHAPTER 8 Manage profiles ................................................... 107
Require sign-in ............................................................... 107
Recommended order to set up profiles .......................................... 108
Overview of local instrument profiles and Connect profiles ......................... 108
Connect instrument profile roles and functions ................................... 109
Test the connection to the Connect platform ..................................... 109
Link the instrument to your Connect account ..................................... 111
Create a new local instrument profile ............................................ 112
Link a local profile to a Connect profile .......................................... 113
Unlink a Connect account ...................................................... 114
Contents
QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide 7

If you link when you are signed in to the instrument ............................... 115
If you link when you are not signed in to the instrument ............................ 116
Manage individual instrument profiles ........................................... 117
Create an administrator instrument profile during initial start-up ................ 117
Set up facial authentication at the initial creation of an instrument profile ........ 117
Add facial authentication to an existing instrument profile ...................... 118
Change the PIN for an instrument profile .................................... 118
Change the PIN for a Connect profile ....................................... 119
Manage all instrument profiles as an administrator ................................ 119
View all instrument profiles ................................................. 119
Reset the PIN for a profile ................................................. 119
Add a profile ............................................................. 120
Enable or disable administrator privileges .................................... 120
Delete a profile ........................................................... 121
■CHAPTER 9 Use the instrument with the Security, Auditing, and
E‑signature (SAE) v2.0 module ................................................. 122
Overview of the Security, Auditing, and E‑signature (SAE) v2.0 module components ... 123
Overview of the instrument features when the SAE module is enabled ............... 123
Security, Auditing, and E‑signature (SAE) v2.0 module functions .................... 124
Functions that are controlled ............................................... 124
Functions that can be audited ............................................. 125
Functions that can be signed ............................................... 125
Security, Auditing, and E‑signature (SAE) v2.0 module roles ........................ 125
Dialog boxes in the SAE module ................................................ 126
Profiles when the SAE module is enabled ........................................ 127
SAE-enabled system components .............................................. 127
Compatibility between SAE-enabled and SAE-disabled components ............ 128
Enable SAE functions ......................................................... 129
Workflow: Enable SAE functions ............................................ 129
Configure SAE Administrator Console application profiles ..................... 129
Enable SAE on the instrument and specify the SAE server (administrator only) ... 130
Connect to the SAE server ................................................. 131
Enable SAE functions in QuantStudio™Design and Analysis Software v2 ........ 131
Disable SAE on the instrument (administrator only) ................................ 132
Sign in as a local administrator with SAE enabled ................................. 133
Sign in with SAE enabled ...................................................... 134
Sign out with SAE enabled ..................................................... 135
Change your SAE account password on the instrument ............................ 136
Sign a plate setup ............................................................. 137
Enter an audit reason .......................................................... 138
View signing records for a plate file .............................................. 139
Contents
8QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide

View audit records ............................................................ 140
Use the instrument when the SAE server is oine ................................. 141
E-signature requirements to start a run .......................................... 141
Signing in after automatic screen locking ........................................ 142
SAE error messages and actions ................................................ 142
■CHAPTER 10 Maintain the instrument ......................................... 143
Install a block ................................................................ 143
Change the block ............................................................. 144
Remove the block ............................................................. 145
Decontaminate the sample block ............................................... 146
Materials required ........................................................ 146
Clean the sample block ................................................... 147
Detailed procedures for cleaning the sample block ............................ 148
Replace the instrument fuses ................................................... 149
Materials required ........................................................ 149
Replace the fuses ........................................................ 149
Power on or o, store, and move ................................................ 150
Enable and edit sleep mode ............................................... 150
Power on the instrument ................................................... 151
Power o the instrument ................................................... 151
Prepare the instrument to store, move, or ship ............................... 152
Move the instrument ...................................................... 152
■CHAPTER 11 Configure the instrument settings .............................. 153
View the instrument details ..................................................... 153
View the license agreement .................................................... 154
View the privacy policy for the Connect cloud-based platform ...................... 154
Configure the instrument settings ............................................... 155
Enable or disable demonstration mode ...................................... 155
Edit the instrument name (administrator only) ................................ 155
Set the date and the time .................................................. 155
Configure the heated cover settings ......................................... 156
Adjust the speaker volume ................................................. 156
Configure the network ..................................................... 156
Select the region for the Connect platform ................................... 157
Select a disk storage management mode .................................... 158
Enable and edit automatic sign-out ......................................... 158
Set an access key for external software to connect to the instrument ............ 159
Reset the access key for external software to connect to the instrument ......... 159
Contents
QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide 9

Configure maintenance and service settings ...................................... 159
Request technical support with Smart Help .................................. 159
Request instrument service with Smart Help ................................. 160
Perform a self-verification test .............................................. 161
View the last self-verification test result ...................................... 161
View the instrument log ................................................... 161
Export the instrument log .................................................. 162
View the instrument statistics .............................................. 162
Enable or disable remote monitoring ........................................ 163
Update the software ...................................................... 163
Repair the software ....................................................... 164
Back up the instrument .................................................... 164
Restore a backup of the instrument ........................................ 165
Overview of an instrument reset (restore factory default) ....................... 165
Reset the instrument (restore factory default) ................................. 166
Configure the instrument for the hands-free features .............................. 166
Manage the run history ........................................................ 166
Manage the file name convention of the data file .................................. 167
View the notifications .......................................................... 167
Enable and disable home screen notifications .................................... 168
Set up email notifications ...................................................... 168
Clear the notifications ......................................................... 169
■APPENDIX A Instrument specifications and layout ........................... 170
Instrument dimensions ........................................................ 170
Instrument and computer clearances ........................................ 171
Configured system dimensions ............................................ 172
Light guidelines .......................................................... 173
Electrical requirements ........................................................ 173
Environmental requirements .................................................... 174
■APPENDIX B Connect the instrument to a network .......................... 175
Connect the computer to the instrument directly or to a LAN ....................... 175
Connect the instrument to a wired network ....................................... 176
Connect the instrument to a wireless network .................................... 177
Instrument and computer connections ........................................... 178
Contents
10 QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide

Download and install the desktop software ....................................... 179
Computer requirements for the desktop software ............................. 179
Download the desktop software ............................................ 179
Install the desktop software ................................................ 180
Networking ................................................................... 180
Supported options for instrument and computer connections .................. 180
Control and monitor networked instruments .................................. 182
Networking guidelines and best practices ................................... 182
Firewall ports that must be open ............................................ 182
Ethernet port overview .................................................... 183
Third-party software ...................................................... 183
■APPENDIX C Parts and materials .............................................. 184
Kits, consumables, accessories, and reagents .................................... 184
96-well 0.2 mL consumables ................................................... 184
384-well consumables ......................................................... 185
96-well 0.1 mL consumables ................................................... 185
Accessories ................................................................. 186
■APPENDIX D Safety ............................................................. 187
Symbols on this instrument .................................................... 187
Standard safety symbols .................................................. 188
Additional safety symbols ................................................. 189
Location of safety labels .................................................. 189
Control and connection symbols ........................................... 193
Conformity symbols ...................................................... 193
Safety information for instruments not manufactured by Thermo Fisher Scientific ..... 194
Instrument safety ............................................................. 194
General ................................................................. 194
Physical injury ............................................................ 195
Electrical safety .......................................................... 196
Laser safety .............................................................. 197
Cleaning and decontamination ............................................. 198
Instrument component and accessory disposal .............................. 198
Safety and electromagnetic compatibility (EMC) standards ......................... 198
Safety standards ......................................................... 199
EMC standards ........................................................... 199
Environmental design standards ............................................ 200
Radio compliance standards ............................................... 200
RF transceiver specifications ............................................... 202
Chemical safety .............................................................. 203
Biological hazard safety ....................................................... 205
Contents
QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide 11

■APPENDIX E Documentation and support.................................... 206
Related documentation ........................................................ 206
Customer and technical support ................................................ 207
Limited product warranty ...................................................... 207
Index ..................................................................................... 208
Contents
12 QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide

Product information
■Network and password security requirements ........................... 13
■Instrument hardware description ....................................... 14
■Hands-free features .................................................. 21
■Software description ................................................. 23
■Types of runs ........................................................ 30
■System template file names ........................................... 33
■Workflow ........................................................... 38
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.
1
QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide 13

Instrument hardware description
Overview of the instrument
The Applied Biosystems™QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems
use fluorescent-based 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
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
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 activation
•Speakers for feedback from voice activation and for instructional videos
Chapter 1 Product information
Instrument hardware description
1
14 QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide

•Smart Help to request technical support or instrument service directly from the
instrument
•Barcode scanner for tracking plates
Features of each instrument
Feature QuantStudio™6 Pro System QuantStudio™7 Pro System
Filter set[1] Coupled five-color filter set Decoupled six-by-six color filter
set
VeriFlex™Zones[2] Three VeriFlex™Zones Six VeriFlex™Zones
Security, Auditing,
and E‑signature
(SAE) v2.0 module
— Available[3]
[1] See “System dyes” on page 15.
[2] See “VeriFlex™Zones” on page 17.
[3] See Chapter 9, “Use the instrument with the Security, Auditing, and E‑signature (SAE) v2.0 module”.
Instrument filters and supported dyes
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.
Peak
filter Color Filter wavelength (nm)[1]
System dyes Example
custom dyes
Excitation Emission
x1-m1 Blue 470 ± 15 520 ± 15 FAM™dye, SYBR
GREEN™dye SYT09
x2-m2 Green 520 ± 10 558 ± 11 VIC™dye
JOE™dye,
HEX™dye, TET™
dye[2]
x3-m3 Yellow 550 ± 11 586 ± 10
NED™dye,
TAMRA™dye,
ABY™dye
Cy®3 dye
x4-m4 Orange 580 ± 10 623 ± 14 ROX™dye, JUN™
dye Texas Red™dye
Chapter 1 Product information
Instrument hardware description 1
QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide 15

(continued)
Peak
filter Color Filter wavelength (nm)[1]
System dyes Example
custom dyes
Excitation Emission
x5-m5 Red 640 ± 10 682 ± 14
MUSTANG
PURPLE™dye,
Cy®5
LIZ™dye
x6-m6 Deep-
Red 662 ± 10 711 ± 12 None[3] Cy®5.5 dye
[1] The 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.
Filters
Wavelength
(nm)
1 2 345
x1-m1 x2-m2 x3-m3 x4-m4 x5-m5 x6-m6
Emission
Spectra
1x1-m1—FAM™dye, SYBR GREEN™dye
2x2-m2—VIC™dye
3x3-m3—ABY™dye, NED™dye, Cy®3,
TAMRA™dye
4x4-m4—JUN™dye, ROX™dye, Texas Red™
dye
5x5-m5—Cy®5, MUSTANG 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 98).
•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 15).
•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.
Chapter 1 Product information
Instrument hardware description
1
16 QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide

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)
•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.
VeriFlex™Zones
VeriFlex™Zones provide independent temperature zones that oer enhanced
functionality and precise 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). The
QuantStudio™7 Pro System has six VeriFlex™Zones (Figure 2).
Note: VeriFlex™Zones are only applicable for the 96-well 0.2-mL block and the 96-
well 0.1-mL block.
Chapter 1 Product information
Instrument hardware description 1
QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide 17

Figure 1 Three VeriFlex™Zones
Figure 2 Six VeriFlex™Zones
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 28.
AutoDelta settings
AutoDelta enables an incremental increase or decrease in the temperature or time in
a PCR cycle.
To use AutoDelta, specify a dierence in the time and the temperature. Specify the
PCR cycle for this change to be applied.
Chapter 1 Product information
Instrument hardware description
1
18 QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide

Parts of the instrument
1
2
3
4
5
6
8
9
7
Figure 3 Front of the instrument
1Cameras
2Touchscreen
3Microphones
4USB port
5Indicator light
6Proximity sensor
7Access door for block change
8Speakers
9Drawer
Chapter 1 Product information
Instrument hardware description 1
QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide 19

2
3
4
6
5
1
Figure 4 Back of the instrument
1USB ports
2Wi-Fi dongle port
3Ethernet port
4RS-232 port (service use only)
5ON/OFF switch
6Power inlet receptacle
Note: The instrument recognizes only one external storage device at a time for data
transfer.
The USB ports at the rear of the instrument can be used for external devices, for
example, a mouse or a keyboard.
Chapter 1 Product information
Instrument hardware description
1
20 QuantStudio™6 Pro and 7 Pro Real-Time PCR Systems User Guide