Thermo Fisher Scientific QuantStudio User Manual

QuantStudio™ 6 Pro Real-Time PCR System and QuantStudio™ 7 Pro Real-Time PCR System

USER GUIDE

Publication Number MAN0018045 Revision G.0

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

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

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 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.

•

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.

■

CHAPTER 1 Product information ................................................ 14

Network and password security requirements ..................................... 14

Network conﬁguration and security .......................................... 14

Password security ......................................................... 14

Instrument hardware description ................................................. 15

Overview of the instrument .................................................. 15

Features of each instrument ................................................. 16

Instrument ﬁlters and supported dyes ........................................ 16

Overview of data collection ................................................. 18

VeriFlex™ Zones ........................................................... 18

AutoDelta settings ......................................................... 19

Parts of the instrument ..................................................... 20

Instrument status indicator .................................................. 22

Hands-free features ............................................................ 22

Facial authentication ....................................................... 22

Voice commands .......................................................... 22

Indicators for the hands-free features ........................................ 23

Software description ........................................................... 24

Parts of the home screen ................................................... 24

Connect and Cloud deﬁnitions .............................................. 26

Instrument, desktop software, and Connect platform features ................... 26

Overview of ﬁle locations and ﬁles ........................................... 27

Components of the ﬁles .................................................... 30

Third-party software ....................................................... 31

Network connection options ................................................ 31

Types of runs .................................................................. 31

Standard curve run ........................................................ 31

Relative standard curve run ................................................. 32

Comparative Ct (DDCt) run .................................................. 32

Genotyping run ............................................................ 33

Presence/absence run ...................................................... 33

Melt curve run ............................................................. 33

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

Contents

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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

Enable or disable the microphone ................................................ 44

Use voice commands .......................................................... 45

Sign out ...................................................................... 46

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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

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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

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

Set up or remove VeriFlex™ Zones ........................................... 59

Set up or remove the Auto Delta feature ...................................... 61

Conﬁgure ramp rates ....................................................... 62

Add or remove a pause ..................................................... 62

Options to edit the well details of a plate ﬁle ....................................... 62

Options to view a plate layout ............................................... 63

Assign or edit a well for a plate .............................................. 65

Assign or edit a well for a TaqMan™ Array Card ................................ 66

Add or edit the reagent details for a plate ..................................... 66

Apply the reagents to a plate ................................................ 67

Delete the reagent details ................................................... 67

Add or edit the reagent details for a TaqMan™ Array Card ....................... 68

Apply the reagents to a TaqMan™ Array Card .................................. 68

Edit a passive reference dye ................................................ 68

Import an Assay Information File (AIF) ........................................ 69

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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

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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

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

Contents

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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

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

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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

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CHAPTER 9 Use the instrument with the Security, Auditing, and

E‑signature (SAE) v2.0 module ................................................. 136

Overview of the Security, Auditing, and E‑signature (SAE) v2.0 module components ... 137

Overview of the instrument features when the SAE module is enabled ............... 137

Security, Auditing, and E‑signature (SAE) v2.0 module functions .................... 138

Functions that are controlled ............................................... 138

Functions that can be audited ............................................. 139

Functions that can be signed ............................................... 139

Security, Auditing, and E‑signature (SAE) v2.0 module roles ........................ 139

Dialog boxes in the SAE module ................................................ 140

Proﬁles when the SAE module is enabled ........................................ 141

SAE-enabled system components .............................................. 141

Compatibility between SAE-enabled and SAE-disabled components ............ 142

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

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 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

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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

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CHAPTER 11 Conﬁgure the instrument settings .............................. 166

View the instrument details ..................................................... 166

View the license agreement .................................................... 167

View the privacy policy for the Connect cloud-based platform ...................... 167

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

Contents

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

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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

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

Contents

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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

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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

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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

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APPENDIX E Safety .............................................................. 213

Symbols on this instrument .................................................... 213

Standard safety symbols .................................................. 214

Additional safety symbols ................................................. 215

Location of safety labels .................................................. 215

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

Contents

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

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APPENDIX F Documentation and support ..................................... 232

Related documentation ........................................................ 232

Customer and technical support ................................................ 233

Limited product warranty ...................................................... 233

Index ..................................................................................... 234

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

Product information

Network and password security requirements ............................................ 14

■

Instrument hardware description ....................................................... 15

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Hands-free features ................................................................... 22

■

Software description .................................................................. 24

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Types of runs ........................................................................ 31

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System template ﬁle names ............................................................ 34

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Workﬂow ............................................................................ 40

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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.

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

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

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

Chapter 1 P

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 E‑signature (SAE) v2.0 module

[1]

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 E‑signature (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

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]

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]

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

Filters

Wavelength

(nm)

1 2

x1-m1 x2-m2

x3-m3

x4-m4

x5-m5 x6-m6

Emission Spectra

Chapter 1 P

Instrument hardware description

roduct information

x1-m1—FAM™ dye, S

x2-m2—VIC™ dye

x3-m3—ABY™ dye, NED™ dye, Cy®3, T

YBR GREEN™ dye

AMRA™ dye

x4-m4—JUN™ dye, RO

x5-m5—Cy® 5, MUS

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.

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

Chapter 1 Product information

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.

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

Chapter 1 P

Instrument hardware description

roduct information

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

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

Chapter 1 Product information

Instrument hardware description

Parts of the instrument

Figure 3 Front of the instrument

Cameras

Touchscreen

Microphones

USB port

Indicator light

Proximity sensor

Access door for block change

Speakers

Drawer

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

Chapter 1 P

Instrument hardware description

roduct information

Figure 4 Back of the instrument

USB ports

Wi-Fi dongle port

Ethernet port

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)

ON/OFF switch

Power inlet receptacle

Chapter 1 Product information

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.

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

Indicators for the hands-free features

Indicators for facial authentication

Chapter 1 Product information

Hands-free features

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)

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.

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

1 2

9 10

Chapter 1 Product information

Software description

Parts of the home screen

Figure 5 Home screen

Instrument name

Instrument calendar

Microphone

Help

Eject

Status dial

Table 1 Parts of the home screen

Element of the home

scr

een

Block installed

Current user

Connectivity icons

Buttons to access plate ﬁles

Instrument settings

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.

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

Table 1 Parts of the home screen (continued)

Chapter 1 P

roduct information

Software description

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]

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.

Chapter 1 Product information

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

—

— —

—

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 —

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.

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

Chapter 1 Product information

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

(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

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

Chapter 1 Product information

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

•

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

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

Third-party software

Before installing third-party software on the computer running the desktop software, conﬁrm that the third-party software will not do the following:

•

Restrict Ethernet communication.

•

Interfere with instrument or computer operation.

Network connection options

You can connect an instrument to a network or computer in the conﬁgurations listed below. For more information, see Appendix B, “Connect the instrument to a network”.

Chapter 1 P

roduct information

Types of runs

Direct connection

wired wired or wireless wired or wireless

Types of runs

Standard curve run

A standard curve run determines the absolute target quantity in samples.

The softwar

The software generates a standard curve using data from the standard dilution series.

The software uses the standard curve to interpolate the absolute quantity of target in the test samples.

e measures ampliﬁcation of the target in a standard dilution series and in test samples.

Local area network (LAN)

connection

Connect platform connection

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

Chapter 1 Product information

Types of runs

Relative standard curve run

A relative standard curve runs determines the relative target quantity in samples.

The software measures ampliﬁcation of the target of interest and of an endogenous control target in a standard dilution series, in a reference (calibrator) sample, and in test samples.

The endogenous control is a target that is expressed equally in all samples; examples of endogenous controls are β‐actin, GAPDH, and 18S ribosomal RNA. The software can algorithmically incorporate multiple endogenous control targets in relative quantiﬁcation calculations.

The reference sample is used as the basis for relative quantiﬁcation results (or 1× sample). For example, in a study of drug eects on gene expression, an untreated control is an appropriate reference sample.

The software generates standard curves for the target of interest and the endogenous control using data from the corresponding standard dilution series.

The software uses the standard curves to interpolate the quantities of the target of interest and the endogenous control in each sample. The target quantity in each sample is then normalized to the sample's endogenous control quantity.

To determine the relative quantity of the target in test samples, the software divides the normalized target quantity in the sample by the normalized target quantity in the reference sample.

Comparative Ct (DDCt) run

A comparative Ct (DDCt) run determines the relative target quantity in samples.

The software measures ampliﬁcation of the target of interest and of an endogenous control target in a reference (calibrator) sample and in test samples.

The measurements for the target of interest are normalized to the endogenous control.

To determine the relative quantity of the target in test samples, the software compares the normalized ΔCq (ΔCt or ΔCrt) for the sample to the normalized ΔCq (ΔCt or ΔCrt) for the reference sample.

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

Genotyping run

A genotyping runs detects the single nucleotide polymorphism (SNP) variants of a target nucleic acid sequence.

Genotyping runs use preformulated TaqMan™ SNP Genotyping Assays that include the following components:

•

Two sequence-speciﬁc primers for ampliﬁcation of sequences containing the SNP of interest

•

Two allele-speciﬁc TaqMan™ probes for Allele 1 and Allele 2

The software normalizes the ﬂuorescence of the reporter dyes to the ﬂuorescence of the passive reference dye in each well.

The software plots the normalized reporter dye signal of each sample well on an Allelic Discrimination Plot, which contrasts the reporter dye intensities of the allele-speciﬁc probes.

The software algorithmically clusters the sample data, and assigns a genotype call to the samples of each cluster according to its position on the plot.

Presence/absence run

Chapter 1 Product information

Types of runs

Presence/absence run determines the presence or absence of a target nucleic acid sequence in a sample.

The software calls the target present or absent based on an algorithmically determined call threshold. (The call threshold is dierent from the Ct threshold; the Ct threshold is not used to make calls.)

Melt curve run

Melt curve runs determines the melting temperature (Tm) of the ampliﬁcation products of a PCR that used intercalating dyes.

In the software, melt curve analysis is included in the default run method for any run type that uses intercalating dyes.

The software plots a melt curve based on the ﬂuorescence of the dye with respect to change in temperature.

Using the melt curve, the software calculates the melting temperature (Tm).

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

Chapter 1 Product information

System template ﬁle names

The ﬁrst part of the ﬁle name varies, based on the instrument (QuantStudio™ 6 Pro System or QuantStudio™ 7 Pro System).

The instrument will display the system templates applicable to the block that is installed.

System template ﬁle names for the 96-well 0.2-mL block

System template name

QS7Pro-96-Well-0-2ml_GT_Fast.edt

QS7Pro-96-Well-0-2ml_GT_Std.edt

QS7Pro-96-Well-0-2ml_Melt_Fast.edt

QS7Pro-96-Well-0-2ml_Melt_Std.edt

QS7Pro-96-Well-0-2ml_PA_Fast.edt

Run type

•

Genotyping run

•

96-well, 0.2-mL Standard plate

•

Fast cycling mode

•

Genotyping run

•

96-well, 0.2-mL Standard plate

•

Standard cycling mode

•

Melt curve run (no PCR stage)

•

96-well, 0.2-mL Standard plate

•

Fast cycling mode

•

Melt curve run (no PCR stage)

•

96-well, 0.2-mL Standard plate

•

Standard cycling mode

•

Presence/absence run

•

96-well, 0.2-mL Standard plate

•

Fast cycling mode

QS7Pro-96-Well-0-2ml_PA_Std.edt

QS7Pro-96-Well-0-2ml_PCR_Melt_Fast.edt

QS7Pro-96-Well-0-2ml_PCR_Melt_Std.edt

QS7Pro-96-Well-0-2ml_RQ_Fast.edt

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

•

Presence/absence run

•

96-well, 0.2-mL Standard plate

•

Standard cycling mode

•

Melt curve run (with PCR stage)

•

96-well, 0.2-mL Standard plate

•

Fast cycling mode

•

Melt cur

•

96-well, 0.2-mL Standard plate

•

Standard cycling mode

•

Comparative Ct run

•

96-well, 0.2-mL Standard plate

•

Fast cycling mode

ve run (with PCR stage)

(continued)

Chapter 1 Product information

System template ﬁle names

System template name

QS7Pro-96-Well-0-2ml_RQ_Std.edt

QS7Pro-96-Well-0-2ml_RSC_Fast.edt

QS7Pro-96-Well-0-2ml_RSC_Std.edt

QS7Pro-96-Well-0-2ml_SC_Fast.edt

QS7Pro-96-Well-0-2ml_SC_Std.edt

Run type

•

Comparative Ct run

•

96-well, 0.2-mL Standard plate

•

Standard cycling mode

•

Relative standard curve run

•

96-well, 0.2-mL Standard plate

•

Fast cycling mode

•

Relative standard curve run

•

96-well, 0.2-mL Standard plate

•

Standard cycling mode

•

Standard curve run

•

96-well, 0.2-mL Standard plate

•

Fast cycling mode

•

Standard curve run

•

96-well, 0.2-mL Standard plate

•

Standard cycling mode

System template ﬁle names for the 96-well 0.1-mL block

System template name

QS7Pro-96-Well-0-1ml_GT_Fast.edt

QS7Pro-96-Well-0-1ml_GT_Std.edt

QS7Pro-96-Well-0-1ml_Melt_Fast.edt

QS7Pro-96-Well-0-1ml_Melt_Std.edt

•

Genotyping run

•

96-well, 0.1-mL Standard plate

•

Fast cycling mode

•

Genotyping run

•

96-well, 0.1-mL Standard plate

•

Standard cycling mode

•

Melt curve run (no PCR stage)

•

96-well, 0.1-mL Standard plate

•

Fast cycling mode

•

Melt cur

•

96-well, 0.1-mL Standard plate

•

Standard cycling mode

ve run (no PCR stage)

Run type

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

Chapter 1 Product information

System template ﬁle names

(continued)

System template name

QS7Pro-96-Well-0-1ml_PA_Fast.edt

QS7Pro-96-Well-0-1ml_PA_Std.edt

QS7Pro-96-Well-0-1ml_PCR_Melt_Fast.edt

QS7Pro-96-Well-0-1ml_PCR_Melt_Std.edt

QS7Pro-96-Well-0-1ml_RQ_Fast.edt

Run type

•

Presence/absence run

•

96-well, 0.1-mL Standard plate

•

Fast cycling mode

•

Presence/absence run

•

96-well, 0.1-mL Standard plate

•

Standard cycling mode

•

Melt curve run (with PCR stage)

•

96-well, 0.1-mL Standard plate

•

Fast cycling mode

•

Melt curve run (with PCR stage)

•

96-well, 0.1-mL Standard plate

•

Standard cycling mode

•

Comparative Ct run

•

96-well, 0.1-mL Standard plate

•

Fast cycling mode

QS7Pro-96-Well-0-1ml_RQ_Std.edt

QS7Pro-96-Well-0-1ml_RSC_Fast.edt

QS7Pro-96-Well-0-1ml_RSC_Std.edt

QS7Pro-96-Well-0-1ml_SC_Fast.edt

QS7Pro-96-Well-0-1ml_SC_Std.edt

•

Comparative Ct run

•

96-well, 0.1-mL Standard plate

•

Standard cycling mode

•

Relative standard curve run

•

96-well, 0.1-mL Standard plate

•

Fast cycling mode

•

Relative standar

•

96-well, 0.1-mL Standard plate

•

Standard cycling mode

•

Standard curve run

•

96-well, 0.1-mL Standard plate

•

Fast cycling mode

•

Standard curve run

•

96-well, 0.1-mL Standard plate

•

Standard cycling mode

d curve run

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

System template ﬁle names for the 384-well block

Chapter 1 Product information

System template ﬁle names

System template name

QS7Pro-384-Well-GT-Fast.edt

QS7Pro-384-Well-GT-Std.edt

QS7Pro-384-Well-Melt-Fast.edt

QS7Pro-384-Well-Melt-Std.edt

QS7Pro-384-Well-PA-Fast.edt

Run type

•

Genotyping run

•

384-well plate

•

Fast cycling mode

•

Genotyping run

•

384-well plate

•

Standard cycling mode

•

Melt curve run (no PCR stage)

•

384-well plate

•

Fast cycling mode

•

Melt curve run (no PCR stage)

•

384-well plate

•

Standard cycling mode

•

Presence/absence run

•

384-well plate

•

Fast cycling mode

QS7Pro-384-Well-PA-Std.edt

QS7Pro-384-Well-PCR-Melt-Fast.edt

QS7Pro-384-Well-PCR-Melt-Std.edt

QS7Pro-384-Well-RQ-Fast.edt

QS7Pro-384-Well-RQ-Std.edt

•

Presence/absence run

•

384-well plate

•

Standard cycling mode

•

Melt curve run (with PCR stage)

•

384-well plate

•

Fast cycling mode

•

Melt cur

•

384-well plate

•

Standard cycling mode

•

Comparative Ct run

•

384-well plate

•

Fast cycling mode

•

Comparative Ct run

•

384-well plate

•

Standard cycling mode

ve run (with PCR stage)

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

Chapter 1 Product information

System template ﬁle names

(continued)

System template name

QS7Pro-384-Well-RSC-Fast.edt

QS7Pro-384-Well-RSC-Std.edt

QS7Pro-384-Well-SC-Fast.edt

QS7Pro-384-Well-SC-Std.edt

•

Relative standard curve run

•

384-well plate

•

Fast cycling mode

•

Relative standard curve run

•

384-well plate

•

Standard cycling mode

•

Standard curve run

•

384-well plate

•

Fast cycling mode

•

Standard curve run

•

384-well plate

•

Standard cycling mode

Run type

System template ﬁle names for the TaqMan™ Array Card block

Note: The TaqMan™ Array Card is only available for the QuantStudio™ 7 Pro System.

System template name Run type

QS7Pro-TAC-PA-Fast.edt

QS7Pro-TAC-PA-Std.edt

QS7Pro-TAC-RQ-Fast.edt

QS7Pro-TAC-RQ-Std.edt

QS7Pro-TAC-SC-Fast.edt

•

Presence/absence run

•

TaqMan™ Array Card

•

Fast cycling mode

•

Presence/absence run

•

TaqMan™ Array Card

•

Standard cycling mode

•

Comparative Ct run

•

TaqMan™ Array Card

•

Fast cycling mode

•

Comparative Ct run

•

TaqMan™ Array Card

•

Standard cycling mode

•

tandard curve run

•

TaqMan™ Array Card

•

Fast cycling mode

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

(continued)

System template name Run type

QS7Pro-TAC-SC-Std.edt

QS7Pro-TAC-RQ-Melt-Fast.edt

QS7Pro-TAC-RQ-Melt-Std.edt

QS7Pro-TAC-SC-Melt-Fast.edt

Chapter 1 Product information

System template ﬁle names

•

Standard curve run

•

TaqMan™ Array Card

•

Standard cycling mode

•

Comparative Ct run with melt curve

•

TaqMan™ Array Card

•

Fast cycling mode

•

Comparative Ct run with melt curve

•

TaqMan™ Array Card

•

Standard cycling mode

•

Standard curve run with melt curve

•

TaqMan™ Array Card

•

Fast cycling mode

QS7Pro-TAC-SC-Melt-Std.edt

•

Standard curve run with melt curve

•

TaqMan™ Array Card

•

Standard cycling mode

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

Chapter 1 Product information

Workﬂow

(PIN or facial authentication)

▼

Open a plate ﬁle

(System template or saved plate ﬁle)

▼

(Optional) Edit the plate ﬁle

▼

Load the plate into the instrument

▼

Start the run

▼

Unload the plate from the instrument

▼

(Optional) Transfer the data ﬁle

(A location to transfer the data ﬁle might have been selected before the run. The data ﬁle only

needs to be transferred manually after the run in order to transfer to a new location.)

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

Precautions for use ................................................................... 41

■

Installation and instrument veriﬁcation .................................................. 42

■

Overview of guest access ............................................................. 42

■

Power on the instrument .............................................................. 43

■

Enable or disable the microphone ...................................................... 44

■

Use voice commands ................................................................. 45

■

Sign out ............................................................................. 46

■

Precautions for use

Get started

CAUTION! PHYSICAL INJURY HAZARD. Do not remove the instrument cover. There are no

components inside the instrument that you can safely service yourself. If you suspect a problem, contact technical support.

CAUTION! FIRE HAZARD. F

listed and certiﬁed fuses of the same type and rating as those currently in the instrument.

CAUTION! PHY

temperature can reach 100°C. Allow it to cool to room temperature before handling.

CAUTION! Befor

Thermo Fisher Scientiﬁc, conﬁrm with Thermo Fisher Scientiﬁc that the proposed method will not damage the instrument.

CAUTION! Use ﬂat caps for tubes. Rounded caps can damage the heat

SICAL INJURY HAZARD. During instrument operation, the sample block

e using a cleaning or decontamination method other than those recommended by

or continued protection against the risk of ﬁre, replace fuses only with

ed cover.

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

Chapter 2 Get star

Installation and instrument veriﬁcation

ted

Installation and instrument veriﬁcation

The instrument is installed by a representative from Thermo Fisher Scientiﬁc. The following tasks will be performed during the installation process:

•

Unpack the instrument and the computer

•

Install the instrument and the computer

•

Install QuantStudio™ Design and Analysis Software v2 on the computer

•

Perform calibrations and RNase P veriﬁcation

There is a recommended order to create instrument proﬁles and link Connect accounts to the instrument (see “Recommended order to set up proﬁles” on page 123).

Overview of guest access

The instrument can be used without signing in. The following limits are in place if you do not sign in to the instrument:

•

All actions are recorded to the guest proﬁle.

•

You have access only to the public folder for selecting and storing experiments.

•

You cannot transfer data ﬁles to Connect.

•

Data ﬁles can only be transferred to a USB drive or a network drive.

The instrument can be conﬁgured so that guest access is not permitted (see “Require sign-in” on

page 122).

Use the instrument as a guest

If the Guest button is not visible on the Sign In screen, guest access has been disabled. An administrator must enable guest access (see “Require sign-in” on page 122).

Guest button

In the Sign-In scr

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

een, tap Guest.

Power on the instrument

If left unattended, the instrument automatically enters sleep mode to conserve power. The default time that an instrument is inactive before going into sleep mode is 15 minutes.

Tap anywhere on the touchscreen to determine if the instrument is in sleep mode.

If the screen becomes active, the instrument is already powered on.

If the home screen does not display, power on the instrument by pressing the ON/OFF switch on the rear panel.

Chapter 2 Get star

Power on the instrument

ted

Figure 6 Location of the ON/OFF switch

ON/OFF switch

Note: The length of time that the instrument is inactive befor customized (see “Enable and edit sleep mode” on page 163).

e going into sleep mode can be

Sign in

Sign in with a PIN

Create an instrument pr proﬁle” on page 127 and “Link the instrument to your Connect account” on page 126).

In the Sign In screen, tap the PIN ﬁeld, then enter your PIN.

If your instrument proﬁle is not the default that is displayed, tap

oﬁle.

Enter your PIN, then tap Enter.

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

oﬁle before signing into the instrument (see “Create a new local instrument

, then select your instrument

Chapter 2 Get started

Enable or disable the microphone

You are signed in and the home screen is displayed.

See “Parts of the home screen” on page 24.

Sign in with facial authentication

For information on indicators for facial authentication, see “Indicators for facial authentication” on

page 23.

For lighting guidelines, see “Light guidelines” on page 191.

Create an instrument proﬁle before signing into the instrument (see “Create a new local instrument

proﬁle” on page 127 or “Link the instrument to your Connect account” on page 126). The instrument proﬁle must be set up with facial authentication (see “Add facial authentication to an existing instrument proﬁle” on page 132).

The instrument must accept facial authentication (see “Conﬁgure the instrument for the hands-free features” on page 185).

The instrument must have the sign-in screen displayed. Sign out the current user to return to the sign-in screen (see “Sign out” on page 46).

Stand in front of the instrument.

Center yourself in front of the instrument. The ideal position is approximately 27 inches (69 cm) from the camera.

Note: You do not need to position yourself as closely to the instrument to sign in as when you took the photos to set up facial authentication.

ait while the instrument searches for a match with the photos associated with proﬁles.

(Optional) Reposition yourself if the instrument indicates that the face is out of position.

Ensure that you are centered in front of the instrument. Move away from the instrument and towards the instrument to ﬁnd the correct position.

The user is signed into the instrument and the home screen is displayed.

Enable or disable the microphone

The microphone can be disabled if the voice command function is available. A blue microphone icon indicates that the voice command function is available.

The microphone cannot be manually disabled if the voice command function is already not available. A gray microphone icon indicates that the voice command function is unavailable. To enable or disable the voice command function for the instrument, see “Conﬁgure the instrument for the hands-free features” on page 185.

For a description of the indicators, see “Indicators for voice commands” on page 23.

Tap The micr

(Microphone).

ophone icon will change to red with a bar to indicate that it is disabled (

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

If the proximity sensor does not detect a person, the microphone icon will change to gray with a bar ( ). It will change back to red with a bar when the proximity sensor detects a person.

Use voice commands

The instrument must accept voice commands (see “Conﬁgure the instrument for the hands-free features” on page 185).

A Connect proﬁle must be used. For information about linking a local instrument proﬁle to a Connect proﬁle, see “Link a local proﬁle to a Connect proﬁle” on page 127.

Voice commands are not available when the instrument is used as a guest. Voice commands are not available with a local instrument proﬁle.

The instrument must display a screen where a voice command is supported.

For information on indicators for voice commands, see “Indicators for voice commands” on page 23.

Say "Alexa™, open pro instrument", wait for the instrument audio prompt and, then issue the voice command.

The instrument audio prompt depends on the voice command that was issued.

Chapter 2 Get star

Use voice commands

ted

Voice command Instrument audio output Instrument action

Home — The home screen is displayed.

Open door — Instrument drawer opens.

Shut door — Instrument drawer closes.

Begin Run

End run

Lock screen —

Change Block

Instrument scheduler

Help —

Smart support

[1]

"Are you sure you want to start the run? Yes or no."

"Are you sure you want to stop the run? Yes or no."

—

— The instrument schedule is displayed.

— The Smart Help screen is displayed.

If yes, the instrument starts the run. If no, the Plate properties screen is

displayed.

If yes, the instrument stops the run and displays the Plate properties screen.

If no, the run continues.

The instrument locks the screen. The status dial displays Locked.

If the instrument has a block installed, the Change Block screen is displayed.

If there is no block in the instrument, the Install Block screen is displayed.

The help topic associated with the current page on the screen is displayed.

Calibrations — The Calibration screen is displayed.

[1]

nsaved changes are discarded after the instrument action is completed.

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

Chapter 2 Get star

Sign out

In the home screen, tap (Proﬁle).

Tap Sign out, then tap Yes to conﬁrm.

You are signed out and the Sign In screen is displayed.

ted

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

Create and run plates on the

instrument

Options to run a plate ................................................................. 47

■

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

■

Options to run a plate

Create and run a plate from a system template or a saved plate ﬁle

A system template is a plate ﬁle that is pre-loaded on the instrument and not editable. It can be edited and saved as a new custom plate ﬁle.

Plate ﬁles can be edited in Connect or the desktop software.

The Run Queue folder contains plate ﬁles sent to the instrument from the desktop software.

In the home screen, tap one of the following options:

•

(Load plate ﬁle)

•

Set up run

Tap the location of the system template or the plate ﬁle in the left column.

•

Run Queue

•

Public

•

My Instrument

e: My instrument is not available if you are using the instrument as a guest. You must be

Not

signed in.

•

Templates

•

Connect

e: You must be signed in with a Connect proﬁle.

Not

•

Network Drive

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

Chapter 3 Cr

Options to run a plate

eate and run plates on the instrument

•

USB Drive

Tap the template ﬁle name in the right column. The Plate Properties screen is displayed.

(Optional) In the Plate Properties screen, edit the Data ﬁle name.

The default ﬁle name is the template name appended with the date and time. To edit the default ﬁle name, see “Manage the ﬁle name convention of the data ﬁle” on page 185.

(Optional) Use the barcode scanner.

See “(Optional) Scan a barcode using a barcode scanner” on page 51.

Tap the location to send the data ﬁle.

•

Connect platform

Not

e: You must be signed in with a Connect proﬁle.

•

USB drive

•

Network drive

•

This instrument

Not

e: This option is not available if you are using the instrument as a guest. You must be

signed in.

The connection status of each location is displayed.

If the connection between the instrument and the location that was select is interrupted, the instrument completes the run. The data ﬁle is saved on the instrument. The data ﬁle must be transferred to another location manually (see “Transfer data ﬁles at a later time” on

page 81).

(Optional) Select the Export run results with checkbox.

For more information about this setting, see “Overview of customized data export” on page 50. To import a dierent export setting, see “Import an auto export setting” on page 55.

(Optional) Edit the run method (see page 57).

(Optional) Edit the plate (see page 65).

10.

Load a plate into the instrument (see page 51).

11.

Tap Start run, then conﬁrm that a plate was loaded.

The conﬁrmation page can be disabled.

The status dial is displayed. The status dial contains the following information:

•

The block temperature

•

The elapsed time of the run

•

The status of the run

ed to save the data ﬁle

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

Chapter 3 Create and run plates on the instrument

Figure 7 Home screen during a run

or options during a run, see Chapter 5, “Options for a run”.

Options to run a plate

Repeat the last run

The last run is associated with the proﬁle. It is not the last run for the instrument.

In the home screen, tap The Plat

(Optional) In the Plate Properties screen, edit the Data ﬁle name.

The default ﬁle name is the template name appended with the current date and time. To edit the default ﬁle name, see “Manage the ﬁle name convention of the data ﬁle” on page 185.

(Optional) Use the barcode scanner.

See “(Optional) Scan a barcode using a barcode scanner” on page 51.

Tap the location to send the data.

•

e Properties screen is displayed.

Connect platform

Not

e: You must be signed in with a Connect proﬁle.

USB drive Network drive This instrument

(Run last).

Not

e: This option is not available if you are using the instrument as a guest. You must be

signed in.

The connection status of each location is displayed.

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

Chapter 3 Cr

Overview of customized data export

The status dial is displayed. The status dial contains the following information:

•

eate and run plates on the instrument

If the connection between the instrument and the location that was selected to save the data ﬁle is interrupted, the instrument completes the run. The data ﬁle is saved on the instrument. The data ﬁle must be transferred to another location manually (see “Transfer data ﬁles at a later time” on

page 81).

(Optional) Select the Export run results with checkbox.

For more information about this setting, see “Overview of customized data export” on page 50. To import a dierent export setting, see “Import an auto export setting” on page 55.

(Optional) Edit the run method (see page 57).

(Optional) Edit the plate (see page 65).

Load a plate into the instrument (see page 51).

Tap Start run, then conﬁrm that a plate was loaded.

The conﬁrmation page can be disabled.

The block temperature

The elapsed time of the run

The status of the run

See Figure 7 on page 49.

For options during a run, see Chapter 5, “Options for a run”.

Overview of customized data export

The instrument can perform the primary analysis and the secondary analysis of the data, then export the results.

The instrument has a default export setting.

The export settings can be customized. The instrument will perform the primary and secondary analysis according to the export setting ﬁle.

The export settings are customized in the QuantStudio™ Design and Analysis Software v2, then transferred to the instrument. The export settings are in a JSON ﬁle format.

The export settings cannot be created or edited on the instrument.

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

Chapter 3 Cr

(Optional) Scan a barcode using a barcode scanner

eate and run plates on the instrument

(Optional) Scan a barcode using a barcode scanner

The instrument is compatible with an optional Handheld Barcode Scanner (Cat. No. 4488442, purchased separately). The barcode scanner reads Code 128 (alphanumeric), which supports 128 ASCII character barcodes.

For safety information, see “Laser safety” on page 223.

Tap the Barcode ﬁeld.

Hold the scanner 20–30 cm away from a plate or container label and aim at the center of the barcode, then press the trigger.

Slowly move the scanning beam across the barcode until the scanner emits a high-pitched tone.

When the scanner scans a barcode, it automatically transmits the following information:

•

Transmits the alphanumeric equivalent of the barcode to the Barcode ﬁeld.

•

Transmits other reagent information.

For more information about the hand-held barcode scanner, see the user documentation provided with the barcode scanner.

Load a plate into the instrument

IMPORTANT! The instrument should be used by tr

moving parts hazard.

CAUTION! Use ﬂat caps for 0.2-mL tubes and 0.1-mL tubes. Rounded caps can damage the heat

cover.

Load the plate onto the block.

Tap

(Eject) to open the drawer.

•

Well A1 of the plate is in the top-left corner of the block.

•

If the plate has a barcode, the barcode faces the front of the instrument.

(Eject) t

o close the drawer.

ained operators who have been warned of the

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

Chapter 3 Cr

Load a TaqMan™ Array Card into the instrument

eate and run plates on the instrument

Load a TaqMan™ Array Card into the instrument

IMPORTANT! The instrument should be used by trained operators who have been warned of the

moving parts hazard.

Load the plate onto the block.

The block has guides for the position of the array card.

(Eject) t

•

Well A1 of the array card is in the top-left corner of the block.

•

If the array card has a barcode, the barcode faces the front of the instrument.

o open the drawer.

The circles indicate the guides for the position of the array card.

(Eject) t

o close the drawer.

Unload a plate or a TaqMan™ Array Card from the instrument

CAUTION! PHY

reach 100°C. Allow it to cool to room temperature before handling.

CAUTION! PHY

temperature can reach 100°C. Allow it to cool to room temperature before handling.

SICAL INJURY HAZARD. During instrument operation, the plate temperature can

SICAL INJURY HAZARD. During instrument operation, the TaqMan™ Array Card

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

Chapter 3 Cr

Unload a plate or a TaqMan™ Array Card from the instrument

The status dial displays Run complete when the run is ﬁnished. If the automatic sign-out feature is enabled and the set time has elapsed, the instrument will display the Sign In screen.

Tap (Eject) to open the instrument drawer, then remove the plate.

eate and run plates on the instrument

Tap (Eject) t

For information on plate disposal, see “Chemical safety” on page 229 and “Biological hazard safety” on

page 231.

o close the instrument drawer.

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

Edit a plate before starting a run

Overview of a template ﬁle with restricted editing ........................................ 54

■

Options to edit the properties of a plate ﬁle .............................................. 55

■

Options to edit the method of a plate ﬁle ................................................ 56

■

Options to edit the well details of a plate ﬁle ............................................. 62

■

Overview of a template ﬁle with restricted editing

A template ﬁle can be set up with restricted editing in the QuantStudio™ Design and Analysis Software v2. If a template ﬁle is set up with restricted editing, only certain parts of the template ﬁle can be edited. The parts of the template ﬁle that cannot be edited are deﬁned by the user in QuantStudio™ Design and Analysis Software v2.

A user cannot set up the restricted editing properties on the instrument.

If a template ﬁle has restricted editing, it is noted in the following locations:

•

The top of the screen

•

Under the Data ﬁle properties heading

•

In the Data ﬁle name ﬁeld

The top of the screen

Under the Data ﬁle properties heading

In the Data ﬁle name ﬁeld

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

Chapter 4 Edit a plat

Options to edit the properties of a plate ﬁle

The following ﬁles can be edited:

•

A system template (see “Create and run a plate from a system template or a saved plate ﬁle” on

page 47)

A system template that is edited must be saved as a plate ﬁle. A system template cannot be overwritten.

•

A saved plate ﬁle (see “Create and run a plate from a system template or a saved plate ﬁle” on

page 47)

•

The plate ﬁle associated with the last run (see “Repeat the last run” on page 49)

The following items can be edited in the Properties tab:

•

Import the sample setup (see page 55)

Import a sample setup

This feature allows you to import a sample setup ﬁle. A sample setup ﬁle shows the position of each sample on the plate. The sample setup ﬁle is a TXT ﬁle or a CSV ﬁle.

e before starting a run

In the Properties tab, tap Actions, then tap Import sample setup.

In the Import Sample Setup screen, tap the appropriate folder, then tap the appropriate ﬁle.

Import an auto export setting

The export settings can be customized. For more information about the export settings, see “Overview of cust

The export settings ﬁle is in a JSON ﬁle format.

The export settings must be customized in the QuantStudio™ Design and Analysis Software v2, then they are imported onto the instrument.

omized data export” on page 50.

In the Properties tab, tap the Export run results with ﬁeld. The Auto Export Settings screen is displayed.

Tap Import.

Tap the location of the ﬁle in the left pane, then tap the ﬁle in the right pane.

Delete an auto export setting

In the P The Auto Export Settings screen is displayed.

roperties tab, tap the Export run results with ﬁeld.

Tap Delete.

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

Chapter 4 Edit a plate before starting a run

Options to edit the method of a plate ﬁle

The following ﬁles can be edited:

•

A system template (see “Create and run a plate from a system template or a saved plate ﬁle” on

page 47)

A system template that is edited must be saved as a plate ﬁle. A system template cannot be overwritten.

•

A saved plate ﬁle (see “Create and run a plate from a system template or a saved plate ﬁle” on

page 47)

•

The plate ﬁle associated with the last run (see “Repeat the last run” on page 49)

The following items can be edited in the Methods tab:

•

Time and temperature for each PCR step (see page 57)

•

Cover temperature and volume (see page 57)

•

Number of cycles (see page 57)

•

Steps (see page 58)

•

Stages (see page 58)

•

Data collection points (see page 58)

•

VeriFlex™ Zones (see page 59)

•

Auto Delta (see page 61)

•

Ramp rates (see page 62)

•

Pauses (see page 62)

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

Method elements

Chapter 4 Edit a plat

Options to edit the method of a plate ﬁle

e before starting a run

Method tab

Heated cover temperature

Reaction volume

Stage of thermal protocol

Step within a stage

Number of cycles for the stage

Temperature for the step

Hold time for the step

Data collection point

Edit the method

In the Method tab, tap Edit.

ap a ﬁeld, then enter the changes.

•

Cover temperature

•

Volume

•

Temperature for any steps

•

Time for any steps

•

Number of PCR cycles

Tap Save.

Enter a name for the plate ﬁle, then tap Done.

In the Save Template screen, select a storage location for the plate ﬁle, then tap Done. A conﬁrmation is displayed.

Tap Close.

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

Chapter 4 Edit a plate before starting a run

Options to edit the method of a plate ﬁle

Add or remove steps

Add a PCR step or remove a PCR step.

In the Method tab, tap Edit4Advanced4Manage steps.

Note: Use or to navigate through the method if it is not all displayed.

ap Add step, then tap

Enter the temperature and time, then tap Enter.

(Add) in the location of the st

ep to be added.

Tap Remove step, then tap

Tap Done.

The Method tab is displayed with the updated method.

Add or remove stages

Add a PCR stage or remove a PCR stage.

In the Method tab, tap Edit4Advanced4Manage stages.

e: Use

Not

ap Add Stage, then tap

Tap the type of stage.

•

Hold

•

Pre-Read

•

Post-Read

•

Inﬁnite

•

PCR

•

Melt Curve

or to navigate through the method if it is not all displayed.

(Remove) in the appr

(Add) in the location of the stage t

opriate step.

o be added.

The new stage is added. The time and temperature must be edited as part of the method (see “Edit the method” on page 57).

Tap Remove stage, then tap

ap Done.

(Remove).

Add or remove data collection locations

In the Method tab, tap Edit4Advanced4Data collection location.

or to navigate through the method if it is not all displayed.

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

Not

e: Use

Tap (Data collection location) to designate a step as a data collection location or to remove data collection from the step.

The (Data collection location) button functions as an on-o switch.

Data collection is o

Data collection is on

ap Done.

Set up or remove VeriFlex™ Zones

Chapter 4 Edit a plate before starting a run

Options to edit the method of a plate ﬁle

VeriFlex™ Zones are only available for 96-well blocks.

•

The QuantStudio™ 6 Pro System has three VeriFlex™ Zones.

•

The QuantStudio™ 7 Pro System has six VeriFlex™ Zones.

Note: For more information about compatibility of plate ﬁles with VeriFlex™ Zones between the two instruments, see “VeriFlex™ Zones” on page 18.

In the Method tab, tap Edit4Advanced4 V

Note: Use

Note: The PCR stage pr

or to navigate through the method if it is not all displayed.

ovides the option of VeriFlex™ Zones or the Auto Delta feature. Ensure that

eriFlex™ Zones / Auto Delta.

the VeriFlex™ Zones option is selected.

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

Chapter 4 Edit a plat

Options to edit the method of a plate ﬁle

e before starting a run

Figure 8 VeriFlex™ Z

VeriFlex™ Z

ap the temperature ﬁeld in the appropriate VeriFlex™ Zone.

Enter a temperature, then tap Enter.

ones is selected

ones and Auto Delta settings

The temperatures in adjacent zones must have a dierence of ≤5°C.

Tap Done. A stage with VeriFlex™ Zones is denoted with a

In the Method tab, tap

4Remove4Done t

icon.

o remove the VeriFlex™ Zones.

Note: The VeriFlex™ Zones setting is removed from the Method tab.

Indicates that this is the Method tab wher

Indicates that VeriFlex™ Z

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

ones are assigned. Tap to remove the VeriFlex™ Zones.

e the VeriFlex™ Zones settings can be removed

Set up or remove the Auto Delta feature

Note: The Auto Delta feature is only available in the PCR stage.

In the Method tab, tap Edit4Advanced4VeriFlex™ Zones / Auto Delta.

Note: Use or to navigate through the method if it is not all displayed.

See Figure 8 on page 60.

Enter the starting cycle to apply Auto Delta settings.

(Edit) in one of the PCR stages.

ap Auto Delta settings.

Chapter 4 Edit a plate before starting a run

Options to edit the method of a plate ﬁle

Set the Delta temperature slider to the value for the dier

Set the Delta time slider to the the dier

Tap Done.

ence in the time.

ence in the temperature.

position or the position, then enter the numerical value for

position or the position, then enter the numerical

A PCR step with an Auto Delta setting applied to it is denoted with an

In the Method tab, tap

4Remove4Done t

o remove the Auto Delta setting.

Note: The Auto Delta setting is removed from the Method tab.

Indicates that this is the Method tab wher

Indicates that Auto Delta is assigned. Tap to remove the Auto Delta settings.

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

e Auto Delta settings can be removed.

Chapter 4 Edit a plate before starting a run

Options to edit the well details of a plate ﬁle

Conﬁgure ramp rates

The ramp rate is how quickly the temperature changes from one stage or step to another stage or step. The maximum ramp rate for the instrument is 6.5°C/second.

In the Method tab, tap Edit4Advanced4Ramp rates.

Note: Use or to navigate through the method if it is not all displayed.

ap a ramp rate, then edit the value.

Tap Done.

Add or remove a pause

A pause allows you to open the drawer to add additional reagents to the plate.

In the Method tab, tap Edit4Advanced4Add pause.

e: Use

Not

Ent A pause in the thermal cycling protocol is denoted with a

Tap

Tap Done.

(Pause).

er a temperature and the cycle.

emperature of the pause are also denoted.

(Pause) to remove the pause.

or to navigate through the method if it is not all displayed.

. The cycle of the pause and the

Options to edit the well details of a plate ﬁle

The following ﬁles can be edited:

•

A system template (see page 47) A system template that is edited must be saved as a plate ﬁle. A system template cannot be

overwritten.

•

A saved plate ﬁle (see “Create and run a plate from a system template or a saved plate ﬁle” on

page 47)

•

The plate ﬁle associated with the last run (see “Repeat the last run” on page 49)

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

The following items can be edited in the Plate tab:

•

Sample name and sample type (see “Assign or edit a well for a plate” on page 65 and “Assign or edit a well for a TaqMan™ Array Card” on page 66)

•

Target name, reporter dye, and quencher dye (see page 66)

•

Reagents (see “Add or edit the reagent details for a plate” on page 66 and “Add or edit the reagent details for a TaqMan™ Array Card” on page 68)

•

Passive reference dye (see page 68)

•

Import an assay information ﬁle (AIF; see page 69)

A plate layout ﬁle for preplated assays will already be populated with the target name, reporter dye, and quencher dye.

Options to view a plate layout

The following views are available for a plate layout:

•

Plate view

–

Shows each well on the plate

–

Tap to provide information about the sample name, sample type, target name, reporter dye, or quencher dye

–

An individual well

–

Multiple wells (tap each individual well)

–

A row (tap the letter)

–

A column (tap the number)

–

Tap (Select all) to select all of the wells in the plate

•

Well table view

–

Shows the well ID, the sample, the target, the reporter, the quencher, the type, and the reagents

Chapter 4 Edit a plate before starting a run

Options to edit the well details of a plate ﬁle

The plate view and the well table view can show the sample color or the target color with the Color By dropdown list.

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

Chapter 4 Edit a plat

Options to edit the well details of a plate ﬁle

Select all button

Plate view button

Well table view button

Color by dropdown list

e before starting a run

View a 384-well plate

The Plat 384-well view. You can zoom in to a 96-well section of the 384-well plate in order to edit the plate.

e tab displays a 384-well plate if the 384-well block is installed. The plate can be edited in the

In the r

egion of the 384-well plate that you want to zoom in on, pinch outwards with two ﬁngers.

(Optional) To change the region that you are zoomed in on, use two ﬁngers to drag the plate in the appropriate direction.

The 384-well plate can zoom in on any 96-well section. It is not limited to speciﬁc 96-well quadrants.

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

Chapter 4 Edit a plat

Options to edit the well details of a plate ﬁle

If you selected a full row or column in the 96-well view, only the set of wells that was visible in the 96-well view is selected. The full row or column of the 384-well plate is not selected.

To return to the full 384-well view from the 96-well section, pinch inwards with two ﬁngers.

e before starting a run

View a TaqMan™ Array Card

The Plate tab displays a TaqMan™ Array Card if the TaqMan™ Array Card block is installed.

The samples and reagents are edited by port. The samples and reagents are not edited by well.

The targets are added by an assay information ﬁle. The targets cannot be edited on the instrument touchscreen.

Figure 9 Plate tab for a TaqMan™ Arr

Port

ay Card

Assign or edit a well for a plate

A target or an assay must be deﬁned (see “

A sample setup ﬁle can be imported instead of assigning or editing a well manually (see “Import a sample setup” on page 55).

In the Plate tab, tap a well or multiple wells.

Tap the Sample Information pane, then tap Samples.

Note: If no wells are selected, the pane is labeled Legend.

er a sample name.

Ent

Select a sample type from the dropdown list.

Add a target or an assay” on page 66).

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

Chapter 4 Edit a plate before starting a run

Options to edit the well details of a plate ﬁle

Tap Target/SNP, then select Target or Assay from the dropdown list.

Tap a row in the table, then tap Done.

Add a target or an assay

In the Plate tab, tap a well or multiple wells.

Tap the Sample Information pane, then tap Target/SNP.

Tap a row in the table, then tap Add New.

Enter the target, then select the reporter dye and the quencher dye from the respective dropdown lists.

Tap Add Target, then tap Close.

Assign the target or the assay to a well (see “Assign or edit a well for a plate” on page 65).

Assign or edit a well for a TaqMan™ Arr

An assay information ﬁle must be imported to assign targets (see “Import an Assay Information File (AIF)” on page 69). Targets cannot be assigned on the instrument touchscreen.

A sample can only be edited by port. It cannot be edited by individual well.

A sample setup ﬁle can be imported instead of assigning or editing a well manually (see “Import a sample setup” on page 55).

In the Plate tab, tap a port.

See Figure 9 on page 65.

Tap the Legend pane, then tap Samples.

Enter a sample name.

Select a sample type from the dropdown list.

Tap Done.

ay Card

Add or edit the reagent details for a plate

In the Plat

e tab, tap one of the following items.

•

A single well

•

Multiple wells

•

(Select all)

ap the Sample Information pane, then tap Reagents.

Note: If no wells are selected, the pane is labeled Legend.

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

Tap a row in the table, then enter the information.

•

Reagent name

•

Reagent type

•

Lot number

ap Save reagent.

Tap Done.

Apply the reagents to a plate

Add the reagents before they are applied to a plate (see “Add or edit the reagent details for a plate” on

page 66).

Chapter 4 Edit a plat

Options to edit the well details of a plate ﬁle

•

SKU (Part number)

•

Expiration date

e before starting a run

In the Plat

•

ap the Sample Information pane, then tap Reagents.

Note: If no wells are selected, the pane is labeled Legend.

ap a row in the table to apply it to the plate.

Tap Done.

e tab, tap one of the following items.

A single well

Multiple wells

(Select all)

Delete the reagent details

In the Plat

•

Tap the Sample Information pane, then tap Reagents.

e tab, tap one of the following items.

A single well

Multiple wells

(Select all)

Note: If no wells are selected, the pane is labeled Legend.

(Optional) T

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

ap Clear all.

Chapter 4 Edit a plat

Options to edit the well details of a plate ﬁle

Tap a row in the table, then delete the information in each ﬁeld.

•

Reagent name

•

Reagent type

•

Lot number

ap Save reagent.

Tap Done.

e before starting a run

•

SKU (Part number)

•

Expiration date

•

Quencher dye

Add or edit the reagent details for a TaqMan™ Arr

In the Plate tab, tap a port.

See Figure 9 on page 65.

Tap the Legend pane, then tap Reagents.

Tap a row in the table.

Tap Add new, then enter the information.

•

Reagent name

•

Reagent type

•

ot number

ap Save reagent, then tap Done.

•

SKU (Part number)

•

Expiration date

Apply the reagents to a TaqMan™ Array Card

Add the reagents before they are applied to a plate (see “Add or edit the reagent details for a TaqMan Array Card” on page 68).

A reagent can only be applied by port. It cannot be applied by individual well.

ay Card

™

In the Plate tab, tap a port.

See Figure 9 on page 65.

Tap the Legend pane, then tap Reagents.

Tap a row in the table to apply it to the port.

Tap Done.

Edit a passive reference dye

A passive reference dye normalizes the ﬂuor

In the Plate tab, tap Actions4Edit passive reference dye. The Passive Reference Dye screen is displayed.

Select the passive reference dye.

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

escent reporter signal in real-time PCR.

The passive reference dye is displayed under the plate diagram.

Import an Assay Information File (AIF)

The Assay Information File is provided in TXT format and/or XML and HTML format, depending on the product line and order date. The HTML format is a reference for users. The XML or the TXT format is imported.

For a detailed description of the AIF, see Understanding Your Shipment (Pub. No. MAN0017153)

In the Plate tab, tap Actions4Import AIF ﬁle.

In the Import AIF ﬁle screen, tap the appropriate folder, then tap the appropriate ﬁle.

Chapter 4 Edit a plate before starting a run

Options to edit the well details of a plate ﬁle

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

Options for a run

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

■

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

■

Screens available during a run

From the home screen, you can swipe or tap the arrows to navigate to dierent screens. The following screens are available:

•

A screen displaying the method (swipe left once or tap the right arrow ( ) once)

•

The real-time ampliﬁcation plot (swipe left twice or tap the arrow right ( ) twice)

•

The time remaining in the run (swipe left three times or tap the right arrow ( ) three times)

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

Figure 10 Home screen during a run

Arrow

Actions menu

Chapter 5 Options for a run

Edit a plat

e ﬁle during a run

Edit a plate ﬁle during a run

The tar after a run has started.

gets and samples can be added or edited after a run has started. The method cannot be edited

In the home screen during a run, tap

See Figur

Tap Set up.

In the Plate tab, tap a well or multiple wells.

Note: Use the plate view to edit or assign a well (see “Options to view a plate layout” on page 63).

ap the Sample Information pane, then tap Samples.

Note: If no wells are selected, the pane is labeled Legend.

Ent

•

e 10 on page 71.

er a sample name, then select a sample type from the dropdown list.

Unknown

Standard

No template control (NTC)

(Actions).

Tap Target/SNP, then select Target or Assay from the dropdown list.

Tap a row in the table, then tap Close4Done.

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

Chapter 5 Options for a run

ause an instrument run

Pause an instrument run

Pause a run to add reagents to the plate or to edit the number of cycles.

In the home screen during a run, tap (Actions).

See Figure 10 on page 71.

Tap Pause run, then enter a pause temperature.

(Optional) Tap Edit to change the number of cycles.

(Optional) Tap

CAUTION! PHY

can reach 100°C. If you want to access the plate during a run pause, enter room temperature as the pause temperature and allow the plate to cool to room temperature before handling.

(Eject) t

SICAL INJURY HAZARD. During instrument operation, the plate temperature

o open the drawer, then tap

Stop an instrument run

CAUTION! PHY

reach 100°C. If you want to access the plate during a run pause, enter room temperature as the pause temperature and allow the plate to cool to room temperature before handling.

In the home scr

See Figur

Tap Stop run.

Unload the plate (see “Unload a plate or a TaqMan™ Array Card from the instrument” on page 52).

SICAL INJURY HAZARD. During instrument operation, the plate temperature can

een during a run, tap

e 10 on page 71.

(Actions).

(Eject) t

o close the drawer.

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

View the method during a run

In the home screen during a run, swipe left once or tap the right arrow ( ) once.

Chapter 5 Options for a run

View the method during a run

Start time

Method, including the current stage

End time

Time remaining

Swipe right once or tap the left arr

iew real-time data and plots during a run

In the home screen during a run, swipe left twice or tap the right arrow (

ow (

) once to return to the home screen.

) twice.

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

Chapter 5 Options for a run

iew the time remaining during a run

(Optional) Tap the dropdown list then select the view for the plot.

•

Linear

•

Log 10

(Optional) Tap Actions4Analyze amp plots.

(Optional) Tap Actions4View well details to see the ampliﬁcation for a speciﬁc well.

Swipe right twice or tap the left arrow (

) twice to return to the home screen.

Adjust the display of real-time plots during a run

In the r

eal-time ampliﬁcation plot, tap

ap the arrows to pan left or right, or swipe left or right within the ampliﬁcation plot.

(Zoom) or pinch.

View the time remaining during a run

In the home screen during a run, swipe left three times or tap the right arrow ( The time r

Swipe right three times or tap the left arrow (

ock the touchscreen during a run

After you have started a run, you can lock the touchscreen so that other users cannot interfere with instrument operation.

emaining in the run is displayed.

) three times to return to the home screen.

) three times.

Note: You must be signed in.

In the home scr

Tap Lock screen4Lock. The status dial displays Locked.

The touchscreen automatically unlocks when the run is complete.

The touchscreen can be unlocked during the run (see “Unlock the touchscreen during a run” on

page 75).

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

een during a run, tap

roﬁle).

Unlock the touchscreen during a run

The touchscreen can be unlocked by the user who locked it or an administrator. The touchscreen automatically unlocks when the run is complete.

Tap anywhere on the touchscreen.

Tap the PIN Code ﬁeld, then enter your PIN. The status dial is displayed without Locked.

Instrument Schedule

Overview of the instrument schedule

The instrument schedule allows a user to reserve the instrument at a particular date and time.

Chapter 5 Options for a run

Unlock the t

ouchscreen during a run

A Connect pr

The instrument is not locked to prevent any other users at the time.

Schedule a run

In the home screen, tap

Select a view

•

Day

•

Week

•

Month

Tap a time.

The day on the calendar can be selected in the month view. The day view and the week view show the schedule in 30-minute increments.

Edit the start date, end date, start time, and end time.

(Optional) Add notes.

Tap Save, then tap Done to exit the schedule.

oﬁle is required.

(Calendar).

Cancel a scheduled run

In the home scr

Select a view

•

Day

•

Week

•

Month

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

een, tap

(Calendar).

Chapter 5 Options for a run

Instrument Schedule

Tap the reservation. The Edit Reservation screen is displayed.

Tap Cancel Reservation, then tap Yes.

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

Manage plate ﬁles .................................................................... 77

■

Manage data ﬁles .................................................................... 78

■

Manage plate ﬁles

Copy plate ﬁles

In the home screen, tap Load plate ﬁle or Set up run.

Tap the appropriate folder.

•

Run Queue

•

Public

•

Connect

•

Network Drive

•

USB Drive

View and manage ﬁles

ap Manage.

Tap the ﬁle, then tap Copy ﬁles.

Multiple ﬁles can be selected.

Select the destination folder.

•

Public

•

Connect

•

Network Drive

•

USB Drive

ap Paste.

Tap

(Back) t

o return to the home screen.

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

Chapter 6 View and manage ﬁles

Manage data ﬁles

Delete plate ﬁles

System templates cannot be deleted. A plate ﬁle that was saved from a system template can be deleted.

For descriptions of ﬁles, see “Files” on page 28.

In the home screen, tap Load plate ﬁle or Set up run.

Tap the appropriate folder.

•

Run Queue

•

Public

•

Connect

•

Network Drive

•

USB Drive

ap Manage.

Tap the ﬁle, then tap Delete ﬁles.

Multiple ﬁles can be selected.

Tap Yes to conﬁrm.

Tap

(Back) to return to the home screen.

Manage data ﬁles

View QC Check status after a run

The status dial displays Run complete when a run is complete. After Done is tapped, the ampliﬁcation plot can no longer be viewed on the instrument.

In the home screen after a run is complete, see the status of the QC Check.

The status of the QC Check is displayed under the status dial.

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

Figure 11 QC Check passed

QC Check

Chapter 6 V

iew and manage ﬁles

Manage data ﬁles

Figure 12 Review required for QC Check

QC Check

See the QC data in the QuantS

tudio™ Design and Analysis Software v2 or the QuantStudio

Design and Analysis v2.

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

™

Chapter 6 V

Manage data ﬁles

iew and manage ﬁles

View an ampliﬁcation plot after a run

The status dial displays Run complete when a run is complete. The ampliﬁcation plot can only be viewed immediately after a run. After Done is tapped, the ampliﬁcation plot can no longer be viewed on the instrument.

If the automatic sign-out feature is enabled and the set time has elapsed, the instrument will display the Sign In scr

een. The ampliﬁcation plot cannot be viewed on the instrument after the run.

In the home screen after a run is complete, tap Details. The ampliﬁcation plot is displayed. The display can be adjusted (see “Adjust the display of real-

time plots during a run” on page 74).

(Optional) On the Details screen, tap the Plot Types dropdown list, then select a plot type.

•

Rn vs. Cycle

•

dRn vs. Cycle

(Optional) On the Details screen, tap the Y-Scales dropdown list, then select the view for the plot.

•

Linear

•

Log 10

(Optional) Tap Well details, then tap Samples or Targets.

Select an ampliﬁcation plot preview, then tap View amp plot.

(Optional) Tap a speciﬁc well on the right side of the ampliﬁcation plot to see the details for the single well.

Tap Close to return to the home screen.

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

Transfer a data ﬁle immediately after a run

This section describes the transfer of a data ﬁle immediately after a run. To transfer a data ﬁle or a set of data ﬁles at a later time, see “Transfer data ﬁles at a later time” on page 81.

In the home screen, the status dial displays Run complete when a run is complete. The home screen also shows the location that the data ﬁle was transferred to. The location for transfer was selected before the run was started (see “Create and run a plate from a system template or a saved plate ﬁle” on

page 47 and “Repeat the last run” on page 49).

If the automatic sign-out feature is enabled and the set time has elapsed, the instrument with display the Sign In screen. Data ﬁles cannot be transferred from the home screen. They can be transferred at a later time (see “Transfer data ﬁles at a later time” on page 81).

Data ﬁles will be transferred to the location that was selected before the run was started, even if the user was automatically signed out.

In the home screen after a run is complete, tap Transfer ﬁle.

Select the destination for the data ﬁle.

•

Public

•

Connect

Chapter 6 V

iew and manage ﬁles

Manage data ﬁles

e: You must be signed in with a Connect proﬁle.

Not

•

Network Drive

•

USB Drive

•

My Instrument

e: This option is not available if you are using the instrument as a guest. You must be

Not

signed in.

ap OK, then tap Transfer.

Transfer data ﬁles at a later time

This section describes the transfer of a data ﬁle or a set of data ﬁles at any time. To transfer a data ﬁle immediately after a run, see “Transfer a data ﬁle immediately after a run” on page 81.

•

Guests can only transfer guest data ﬁles.

•

A user that is signed in can transfer their own data ﬁles.

•

Administrators can transfer all data ﬁles.

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

Chapter 6 V

Manage data ﬁles

iew and manage ﬁles

Tap (Settings)4Run history. The Run History screen is displayed. It contains a list of the runs performed on the instrument

associated with the proﬁle. Administrators can view all of the runs performed.

(Optional) Tap the table header to sort by that parameter.

•

Run name

•

Date

•

Transferred

•

User (Administrator only)

Tap the data ﬁles to be transferred or tap Select all.

Multiple data ﬁles can be selected.

Tap Transfer, then tap the storage location.

Tap Done.

View the list of data ﬁles on the instrument

•

Guests can only view the list of guest data ﬁles.

•

A user that is signed in can view the list of their own data ﬁles.

•

Administr

In the home screen, tap The Run History screen is displayed.

Tap an individual run record, then tap View. The following details are displayed:

•

(Optional) T

(Optional) Tap Delete to delete the data ﬁle from the instrument.

Tap Cancel to return to the Run History screen.

ators can view all data ﬁles.

The ﬁle name

The run status

The user name

The star

ap Transfer to transfer the data ﬁle.

Delete data ﬁles fr

(Settings)4Run hist

t time and the end time

om the instrument

ory.

•

The duration of the run

•

The reaction volume

•

The cover temperature

•

Guests cannot delete any data ﬁles.

•

A user that is signed in can delete their own data ﬁles.

•

Administrators can delete all the data ﬁles.

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

Chapter 6 V

In the home screen, tap (Settings)4Run history. The Run History screen is displayed. It contains a list of the runs performed on the instrument

associated with the proﬁle. Administrators can view all of the runs performed.

(Optional) Tap the table header to sort by that parameter.

•

Run name

•

Date

•

Transferred

•

User (Administrator only)

Tap the data ﬁles to be deleted or tap Select all.

Multiple data ﬁles can be selected.

Tap Delete, then tap Yes to conﬁrm.

iew and manage ﬁles

Manage data ﬁles

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

Calibrate and verify instrument

performance

Instrument and block calibration ........................................................ 84

■

Calibration and veriﬁcation schedule .................................................... 85

■

Calibration descriptions ............................................................... 86

■

View the calibration status and set reminders ............................................ 87

■

Export a calibration report ............................................................. 89

■

Perform ROI/uniformity, background, and dye calibrations for plate blocks .................. 89

■

Perform ROI/uniformity, background, dye, and normalization calibrations for the

■

TaqMan™ Array Card block ............................................................ 97

Perform veriﬁcation using RNase P plates .............................................. 103

■

Perform veriﬁcation using RNase P with a TaqMan™ Array Card ........................... 108

■

Calibrate custom dyes ............................................................... 113

■

Calibrate for a custom melt curve run .................................................. 120

■

Instrument and block calibration

The QuantStudio™ 6 Pro System and the QuantStudio™ 7 Pro System have interchangeable blocks. The calibration status applies to the combination of the instrument and the block.

If a block is moved to an instrument that it has not been calibrated on, that combination of block and instrument needs to be calibrated. This applies even if the block has previously been calibrated on a dierent instrument.

If a block is moved back to an instrument that is has previously been calibrated on, it does not need to be calibrated again. It needs to be calibrated again if the calibration is expired.

A run can still be started if a calibration of the block on the instrument is expired. A run cannot be started if a block has never been calibrated on the instrument.

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

Chapter 7 Calibrate and verify instrument performance

Calibration and veriﬁcation schedule

The instrument and block will be calibrated during the installation. To ensure optimal performance, perform calibrations at the recommended frequency.

Note: After instrument calibration, we recommend performing instrument veriﬁcation using the provided RNase P plate.

Calibration and veriﬁcation schedule

IMPORTANT! P

erform calibrations and instrument runs under the speciﬁed environmental conditions (see “Environmental requirements” on page 192). Exposure to extreme temperatures can adversely aect the instrument performance and shorten the life span of the instrument components.

To set calibration frequencies and reminders, see one of the following sections:

•

iew the calibration status on the instrument (see page 87)

•

View calibration status and set reminders on the Connect platform (see page 88)

Calibration Recommended frequency

•

ROI/Uniformity

Background

very two years (recommended).

•

Always perform new Background and Dye calibrations after an ROI/Uniformity calibration.

You will be prompted to run a Background calibration after the ROI/Uniformity calibration is complete.

The ROI/Uniformity calibration and the Background calibration must pass in order to accept the results. It is recommended to transfer the ﬁles if the calibration fails in order to troubleshoot.

Note: Performing an ROI/Uniformity calibration invalidates all other calibrations.

•

Every month (recommended).

•

Background calibration can also be performed, as needed:

–

To check for contamination (depends on usage and laboratory conditions).

–

To obtain the most accurate data for the removal of background

ﬂuorescence.

Note: Performing a Background calibration does not invalidate any other calibration.

•

Dye

Normalization

(TaqMan™ Array Card block only)

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

Every two years (recommended).

•

During a Dye calibration, only the dyes on the given spectral calibration plate are calibrated.

Note: Performing a Dye calibration for a given dye plate does not invalidate any other calibration.

Every two years (recommended).

Chapter 7 Calibrate and verify instrument performance

Calibration descriptions

(continued)

Calibration Recommended frequency

•

RNase P instrument

veriﬁcation

After installing or moving the instrument.

•

After performing any of the calibrations.

•

As needed to conﬁrm instrument performance.

Note: To prepare custom dye plates and to perform custom calibrations, see “Calibrate custom dyes”

on page 113.

Calibration descriptions

The combination of the instrument and the block is calibrated (see “Instrument and block calibration”

on page 84).

Calibration description and purpose Pass criteria

ROI/Uniformity

•

The software captures images for each optical ﬁlter.

•

The software uses calibration data to map the increase in ﬂuorescence to the plate wells during subsequent runs and to evaluate well‑to‑well consistency of the signals.

Background

•

The software captures background images for each optical ﬁlter in the absence of sample and reagent, and it checks that the ﬂuorescence from each well is below a ﬂuorescence threshold.

•

The software uses calibration data to remove background ﬂuorescence during a run.

Note: You can also run this calibration to determine if contamination is related to the sample block or the plate.

Dye

•

The software extracts a spectral proﬁle for each dye standard, then produces a set of spectral proﬁles plotted as ﬂuorescence vs ﬁlter.

•

The software uses calibration data to characterize and distinguish the individual contribution of each dye in the total ﬂuorescence signals collected by the instrument.

The image for each ﬁlter distinguishes all wells of the plate.

Each well in the image is distinct.

The plate images for all ﬁlters are free of abnormal ﬂuorescence.

Dye spectra peak within the same ﬁlter as their group.

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

Chapter 7 C

(continued)

Calibration description and purpose Pass criteria

Normalization (TaqMan™ Array Card block only)

•

The software extracts a spectral proﬁle for each normalization standard.

•

The software uses the normalization standards to obtain a correction factor for the speciﬁc dyes, for example, FAM™ dye or VIC™ dye.

•

The correction factor is used to generate comparable component signal levels across instruments.

alibrate and verify instrument performance

View the calibration status and set reminders

Normalization standards have sucient signals to generate a correction factor.

View the calibration status and set reminders

View the calibration status on the instrument

The Status and Reminders screen also allows you to perform the following functions:

•

Transfer the calibration results (see page 94)

•

Transfer the calibration data ﬁles (see page 94)

•

View the calibration images (see page 93)

In the home screen, tap (Settings)4Maintenance and service4Calibration4Status and reminders.

The Status and Reminders screen is displayed. It shows the following information:

•

Type of calibration

Note:

For dye calibration, the type of calibration is listed as the dye that was calibrated, for

example, FAM. Normalization calibration is required for a TaqMan™ Array Card block. The type of calibration

is listed as FAM/ROX or VIC/ROX.

•

Status of the calibration

•

Last calibration

•

Date that the calibration expires

•

If a reminder is set

Tap a calibration row, then tap View to view the history of that speciﬁc calibration type.

•

e performed

Dat

•

Result of the calibration

ap Cancel to return to the Status and Reminders screen.

•

Whether the calibration is current

•

Operator

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

Chapter 7 Calibrate and verify instrument performance

View the calibration status and set reminders

Set calibration frequency and reminders on the instrument

In the home screen, tap (Settings)4Maintenance and service4Calibration4Status and reminders.

The Status and Reminders screen is displayed.

Tap a calibration row, then tap Edit.

Tap on the Expiration Interval ﬁeld, then enter the number of days.

The default is 730 days (2 years).

Tap on the Reminder ﬁeld, then enter the number of days The Next Reminder ﬁeld will be populated.

Set the On/O slider to the On position to enable a reminder about calibration.

Tap Save.

The calibration reminder can be set as a home screen notiﬁcation (see “Enable and disable home screen notiﬁcations” on page 186).

View calibration status and set reminders on the Connect platform

Note: The calibr

network.

Tap

Select any of your registered instruments.

In the Summary tab:

•

Tap

•

(Optional) Tap the notiﬁcation email address or addresses.

Note: More than one email address can receive the calibration reminders.

Note: The settings ar

•

(Optional) In the Downloads section, tap Maint calibration status report.

ation reminders feature requires a connection between the instrument and a computer

o Connect on a browser.

(Instrument) t

alibrations to view the status of each calibration type.

o open InstrumentConnect.

alibration Reminders to set the calibration reminder time table and enter

e automatically saved.

enance Summary.pdf to download the

In the Calibrations History tab:

•

View the history of each calibration type.

•

(Optional) Tap

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

to download the calibration history report.

Review calibration status

The calibration status can be reviewed in the QuantStudio™ Design and Analysis Software v2. The instrument must be added to the Manage Instruments list.

In the home screen, click Manage Instruments. To access instruments from a dierent screen, click System4Instruments.

In the Summary tab for the instrument, the calibration status is displayed in the Calibration Status column.

Export a calibration report

The calibration report is exported as a TXT ﬁle.

Chapter 7 C

alibrate and verify instrument performance

Export a calibration report

In the home screen, tap (Settings)4Maint reminders.

Tap Export, then select a destination.

•

Connect

•

Network Drive

•

USB Drive

The connectivity status of each location is displayed.

ap Done.

enance and service4Calibration4Status and

Perform ROI/uniformity, background, and dye calibrations for plate blocks

To calibrate the TaqMan™ Array Card block, see “Perform ROI/uniformity, background, dye, and normalization calibrations for the TaqMan™ Array Card block” on page 97.

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

Chapter 7 Calibrate and verify instrument performance

Perform ROI/uniformity, background, and dye calibrations for plate blocks

Calibration workﬂow

You are automatically prompted to perform background calibration.

Perform any time that ROI/uniformity and background calibrations are current.

(Optional ) Perform custom dye calibrations (see “Calibrate custom dyes” on page 113)

Perform any time that ROI/uniformity and background calibrations are current.

Perform an ROI/uniformity calibration

▼

Perform a background calibration

Perform any time that ROI/uniformity calibrations are current.

▼

Perform system dye calibrations

▼

Prepare a calibration plate

Required materials to prepare calibration plates

Note: We recommend calibrating with all Spectral Dye Calibrations Plates available for your block

conﬁguration even if you are not using all the dyes in the plates. This is recommended for optimal system performance.

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

Calibration plates

ROI/Uniformity plate

Background calibration plate

Dye calibration plates

Equipment and consumables

Centrifuge with plate adapter; buckets cleaned before use MLS

Powder‑free gloves MLS

Item Source

Safety glasses MLS

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

Chapter 7 Calibrate and verify instrument performance

Perform ROI/uniformity, background, and dye calibrations for plate blocks

Thaw, vortex, and centrifuge a calibration plate

IMPORTANT! Keep calibration plates protected from light until you perform the calibration. Do not

remove the plate from its packaging until you are ready to use it. Prolonged exposure to light can diminish the ﬂuorescence of the dyes in the wells of calibration plates.

Remove the calibr

ation plate from the freezer, then thaw the plate in its packaging for 30 minutes.

IMPORTANT! Use each plate within 2 hours of thawing.

While wearing powder‐fr the optical ﬁlm.

Note: Do not discard the packaging for the calibration plate. Each calibration plate can be used up to three time if the following conditions are met:

The plate is stored in its packing sleeve at –25°C to –15°C.

The plate is used within 6 months after opening.

The plate is used before the plate expiry date.

ortex the plate for 5 seconds, then centrifuge at 750–1,000 × g for 2 minutes.

Conﬁrm that the liquid in each well is at the bottom of the well and free of bubbles. If it is not, centrifuge the plate again.

ee gloves, remove the calibration plate from its packaging. Do not remove

IMPORTANT! K

of the plate can contaminate the sample block and cause an abnormally high background signal.

eep the bottom of the plate clean. Fluids and other contaminants on the bottom

Perform calibrations

In the home scr The Calibration screen is displayed.

In the Calibration screen, select a calibration type.

ROI/uniformity ROI and uniformity

Background Background

Dye System dye

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

een tap

Calibration type Tap

(Settings)4Maint

enance and service4Calibration.

Chapter 7 Calibrate and verify instrument performance

Perform ROI/uniformity, background, and dye calibrations for plate blocks

Note: You will be prompted to perform a background calibration after a ROI/Uniformity calibration.

ystem dye calibration only) Select the calibration plate.

Follow the instructions on the screen to start the calibration.

Load the plate into the instrument.

CAUTION! The instrument should be used by tr

moving parts hazard.

ap Start.

T When the ROI/Uniformity run is complete, you will be prompted to perform a background

calibration. When the Background calibration is complete, the Calibration Status will display. It will indicate

whether the calibration passed or failed.

(For calibrations that pass) Select an option.

Option Description

Details View the calibration images.

Transfer EDS Transfer the calibration ﬁle t

Reject results The calibration ﬁle is deleted.

Accept results The calibration ﬁle is saved.

If the results are accepted and the calibration ﬁle is saved, pr the combination of the instrument and the block will no longer be used.

(For calibrations that fail) Select an option.

ained operators who have been warned of the

o Connect, a USB drive, or a network drive.

evious calibration ﬁles associated with

Option Description

Details View the calibration images.

Transfer EDS Transfer the calibration ﬁle t

for troubleshooting).

Close The calibration ﬁle is deleted.

See “Troubleshoot calibration failure” on page 95.

Unload the plat

CAUTION! PHY

can reach 100°C. Allow it to cool to room temperature before handling.

Note: Use Smar with Smart Help” on page 172).

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

e from the instrument.

SICAL INJURY HAZARD. During instrument operation, the plate temperature

t Help if the instrument does not eject the plate (see “Request technical support

o Connect, a USB drive, or a network drive (recommended

10.

Return the plate to its original packaging.

Note: Do not discard the packaging for the calibration plate. Each calibration plate can be used up to three time if the following conditions are met:

The plate is stored in its packing sleeve at –25°C to –15°C.

The plate is used within 6 months after opening.

The plate is used before the plate expiration date.

View the calibration images

The instrument performs the ROI, uniformity, and background calibrations in sequence. You can view the calibration images after the background calibration is complete.

In the home screen, tap (Settings)4Maintenance and service4Calibration4Status and reminders.

The Status and Reminders screen is displayed.

Tap a calibration type in the table, then tap View.

Chapter 7 Calibrate and verify instrument performance

Perform ROI/uniformity, background, and dye calibrations for plate blocks

Tap a calibration date in the table, then tap View. The following details are displayed:

•

alibration name

•

Result

•

Date

•

Whether this calibration is current

ap Detail.

Calibration Example results indicating successful calibration

ROI

e: Select the desired ﬁlter

Not

combination from the Filter Set dropdown list.

Green circles around all wells and bright well centers.

•

The operator

•

Reagent name, part number, lot number, and expiration date

•

Comments.

Uniformity Signals from each well following a uniform trend.

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

Chapter 7 C

Perform ROI/uniformity, background, and dye calibrations for plate blocks

alibrate and verify instrument performance

(continued)

Calibration Example results indicating successful calibration

Background Few, if any, signals with abnormally high ﬂuorescence.

Dye Signals from each well following a uniform trend, and each dye

peaks at the corr

ect ﬁlter.

(Optional) F right side to see the results for a single well.

or Uniformity, Background, and Dye calibration images, tap on an individual well on the

Transfer calibration results

In the home screen, tap reminders.

The Status and Reminders screen is displayed.

Tap a calibration type in the table.

Tap Export.

(Settings)4Maint

Transfer calibration data ﬁles

This section describes transferring calibration ﬁles if the calibr

If the calibration fails, the calibration data ﬁle is not saved. The data ﬁle can only be transferred immediately after the calibration (see “Perform calibrations” on page 91).

In the home screen, tap reminders.

The Status and Reminders screen is displayed.

(Settings)4Maint

enance and service4Calibration4Status and

ation passed.

enance and service4Calibration4Status and

Tap a calibration type in the table, then tap View.

Tap a calibration date in the table, then tap View.

Tap Transfer EDS.

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

Troubleshoot calibration failure

Observation Possible cause Recommended action

Chapter 7 Calibrate and verify instrument performance

Perform ROI/uniformity, background, and dye calibrations for plate blocks

Calibration failed

High ﬂuorescence signal in individual wells

Calibration failed but plate is undamaged

The plate was improperly prepared.

The plate is damaged or contaminated.

Signals that exceed the limit of normal ﬂuorescence may indicate ﬂuorescent contaminants on the plate or the sample block.

The incorrect plate was used for calibration performed.

The plate was improperly prepared.

Ensure the following:

•

The correct plate was used for the calibration performed.

•

The plate was properly thawed.

•

The plate was properly centrifuged.

•

The plate was properly sealed.

Check for damage, improper plate seal, or contamination.

Order a replacement plate. Use Smart Help if the replacement plate fails (see “Request technical support with Smart Help” on

page 172).

See “Identify contamination” on page 95.

Use the plate that matches the calibration performed.

Repeat the calibration with the plate properly prepared.

If the calibration fails again, order a replacement plate. Use Smart Help if the replacement plate fails (see “Request technical support with Smart Help” on page 172).

Identify contamination

Signals that exceed the limit of normal ﬂuorescence may indicate ﬂuorescent contaminants on the calibration plate or the sample block. Common contaminants include ink residue from permanent pens, powder from disposable gloves, and dust.

View the calibration data and note the wells that failed the calibration.

Remove the plate from the instrument, rotate the plate 180°, then perform the calibration again.

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

Chapter 7 C

Perform ROI/uniformity, background, and dye calibrations for plate blocks

alibrate and verify instrument performance

Determine the location of the failed wells again as in step 1.

Position of failed wells Action

Identical The sample block is contaminated.

Decontaminate the sample block (see page 159).

Reversed The plate is contaminated.

Discard the plate, then perform the calibration using a new calibration plate.

Use Smar plate (see “Request technical support with Smart Help” on page 172).

t Help if the calibration fails after you decontaminate the sample block and replace the

Create a background plate (optional)

Whenever possible, use a background plate listed in “Required materials to prepare calibration plates”

on page 90. These plates contain a buer that accurately simulates the reagents used for PCR, and,

therefore, produces high-quality calibration data.

If a background plate is not available, you can create one as described below.

Required materials:

•

MicroAmp™ optical 96-well reaction plate

•

Optical adhesive cover or optical ﬂat caps

•

Pipettor, 200‐µL (with pipette tips)

•

Powder‐free gloves

•

Safety glasses

•

Deionized water

IMPORTANT! W

Remove a r

ear powder-free gloves while creating the background plate.

eaction plate from its box and place it on a clean, dry surface.

Aliquot 50 µL of deionized water to each well of the reaction plate.

Seal the plate using an optical adhesive cover or optical ﬂat caps.

Use the plate for background calibration.

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

Chapter 7 Calibrate and verify instrument performance

Perform ROI/uniformity, background, dye, and normalization calibrations for the TaqMan™ Array Card block

To calibrate the plate blocks, see “Perform ROI/uniformity, background, and dye calibrations for plate blocks” on page 89.

This section covers procedures speciﬁc to the TaqMan™ Array Card block. See the following sections for additional information:

•

Transfer calibration results (page 94)

•

Transfer data ﬁles from calibrations (page 94)

•

Troubleshoot calibration failure (page 95) To troubleshoot normalization calibration, see “Troubleshoot normalization calibration failure” on

page 102.

•

Identify contamination (page 95)

Calibration workﬂow

Perform an ROI/uniformity calibration

You are automatically prompted to perform background calibration.

▼

Perform a background calibration

Perform any time that ROI/uniformity calibrations are current.

▼

Perform system dye calibrations

Perform any time that ROI/uniformity and background calibrations are current.

▼

Perform normalization calibration

Perform after a dye calibration.

▼

(Optional) Perform custom dye calibrations (see “Calibrate custom dyes” on page 113)

Perform any time that ROI/uniformity and background calibrations are current.

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

Chapter 7 Calibrate and verify instrument performance

Perform ROI/uniformity, background, dye, and normalization calibrations for the TaqMan™ Array Card block

Prepare a calibration TaqMan™ Array Card

Required materials to prepare calibration TaqMan™ Array Card

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

Item Source

Calibration kit

ViiA™ 7 Array Card Spectral Calibration Kit, includes the following components:

•

Empty TaqMan™ Array Cards

•

FAM™ dye

•

VIC™ dye

•

ROX™ dye

•

ROI dye mix

•

Background buer

•

FAM™/ROX™ dye

•

VIC™/ROX™ dye

4432314

Equipment and consumables

Centrifuge with custom buckets and card holders, one of the following:

•

Sorvall™ centrifuge

•

Multifuge™ centrifuge

•

Megafuge™ centrifuge

TaqMan™ Array Card Sealer Contact your local sales oce

Blank balance TaqMan™ Array Cards Contact your local sales oce

Pipette, 200 µL with tips MLS

Permanent marker or pen MLS

Powder‑free gloves MLS

Safety glasses MLS

Fill the calibration TaqMan™ Arr

ay Cards

Contact your local sales oce

For detailed instructions to prepare a TaqMan™ Array Card, see Appendix C, “Detailed procedures for preparation of a TaqMan™ Array Card”.

IMPORTANT! W

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

ear powder-free gloves while creating the calibration array cards.

Chapter 7 Calibrate and verify instrument performance

Perform ROI/uniformity, background, dye, and normalization calibrations for the TaqMan™ Array Card block

This procedure explains how to create all of the array cards required to calibrate the block, but not all of them are required for at each calibration. Before preparing array cards for calibration, determine which calibrations are required (see “Calibration and veriﬁcation schedule” on page 85).

Note: For more information on the array card loading procedure, contact Technical Support.

Remove the tubes of calibration solutions from the freezer, allow them to thaw, then vortex the tubes to mix the contents well.

Remove the TaqMan™ Array Cards from their box and place them on a clean, dry surface.

Mark the side of the empty array cards with the following items:

•

Backgr

™

FAM

ROI

™

ROX

ound

•

™

VIC

FAM™/ROX

VIC™/ROX

™

Location to mark each TaqMan™ Arr

or each array card, pipet 100 µL of the appropriate calibration solution into each of the eight

ay Card

reservoirs in the array card.

See “Load the PCR reaction mix” on page 204.

Centrifuge the array cards, then check each array card for the correct ﬁll. See “Centrifuge the card” on page 204.

Seal the array cards.

See “Seal the card” on page 206.

IMPORTANT! If an arr

ay card is sealed improperly, it can leak and contaminate the sample block

and/or it can cause the associated calibration or RNase P test to fail.

IMPORTANT! Aft

er the array cards are sealed, store them in a dark place. Do not expose the array cards to light until you are ready to use them. The dyes in the array cards are photosensitive. Prolonged exposure to light can diminish the ﬂuorescence of the dye.

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

Chapter 7 C

Perform ROI/uniformity, background, dye, and normalization calibrations for the TaqMan™ Array Card block

alibrate and verify instrument performance

Perform calibrations

In the home screen tap (Settings)4Maintenance and service4Calibration. The Calibration screen is displayed.

In the Calibration screen, select a calibration type.

Calibration type Tap

ROI/uniformity ROI and uniformity

Background Background

Dye System dye

Normalization Instrument normalization

Note: Y

(Normalization only) Select the reporter dye and passive reference to calibrate.

Follow the instructions on the screen to start the calibration.

Load the TaqMan™ Array Card into the instrument.

See “Load a TaqMan™ Array Card into the instrument” on page 52.

CAUTION! The instrument should be used by tr

moving parts hazard.

ap Start.

T When the ROI/Uniformity run is complete, you will be prompted to perform a background

calibration. When the Background calibration is complete, the Calibration Status will display. It will indicate

whether the calibration passed or failed.

ou will be prompted to perform a background calibration after a ROI/Uniformity calibration.

ystem dye calibration only) Select the dye to calibrate.

•

FAM

•

VIC

•

ROX

•

FAM/ROX

•

VIC/ROX

ained operators who have been warned of the

100

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

Thermo Fisher Scientific QuantStudio User Manual

Specifications and Main Features

Frequently Asked Questions

User Manual

Contents

Product information

Network and password security requirements

Password security

Instrument hardware description

Overview of the instrument

Features of each instrument

System dyes

Custom dyes

Overview of data collection

VeriFlex™ Zones

AutoDelta settings

Parts of the instrument

Hands-free features

Instrument status indicator

Facial authentication

Voice commands

Indicators for the hands-free features

Indicators for facial authentication

Indicators for voice commands

Software description

Parts of the home screen

Instrument, desktop software, and Connect platform features

File locations

Files

Third-party software

Network connection options

Types of runs

Standard curve run

Relative standard curve run

Genotyping run

Melt curve run

Precautions for use

Get started

Overview of guest access

Use the instrument as a guest

Power on the instrument

Sign in

Sign in with a PIN

Enable or disable the microphone

Sign in with facial authentication

Use voice commands

Sign out

Options to run a plate

Repeat the last run

Overview of customized data export

(Optional) Scan a barcode using a barcode scanner

Load a plate into the instrument

Load a TaqMan™ Array Card into the instrument

Unload a plate or a TaqMan™ Array Card from the instrument

Edit a plate before starting a run

Import a sample setup

Import an auto export setting

Delete an auto export setting

Method elements

Edit the method

Add or remove steps

Add or remove stages

Add or remove data collection locations

Set up or remove VeriFlex™ Zones

Set up or remove the Auto Delta feature

Add or remove a pause

Options to view a plate layout

View a 384-well plate

View a TaqMan™ Array Card

Assign or edit a well for a plate

Add a target or an assay

Add or edit the reagent details for a plate

Apply the reagents to a plate

Delete the reagent details

Apply the reagents to a TaqMan™ Array Card

Edit a passive reference dye

Import an Assay Information File (AIF)

Options for a run

Screens available during a run

Pause an instrument run