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Thermo Scientific Applied Biosystems QuantStudio 7 Pro User Manual

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

Table of Contents

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Thermo Scientific Applied Biosystems QuantStudio 7 Pro Specifications

General IconGeneral
TypeReal-Time PCR System
Number of Channels6
Detection MethodFluorescence
Temperature Accuracy±0.25°C
Temperature Uniformity±0.5°C
Excitation SourceLED
Detection SystemCCD camera
Thermal Cycler TypePeltier-based
Temperature Range4°C to 100°C
Sample Capacity96-well or 384-well
ConnectivityEthernet, USB
SoftwareQuantStudio Design and Analysis Software
Supported DyeFAM, SYBR Green, VIC, ROX
Block Format96-well or 384-well
Reaction Volume Range5–20 μL (384-well)
ThroughputUp to 384 samples
Multiplexing CapabilityYes
WeightVaries by configuration
Power100–240 VAC
OpticsLED excitation, CCD detection
Detection Channels6
Data CollectionReal-time

Summary

CHAPTER 1 Product information

Network and password security requirements

Details requirements for network and password security settings, including configuration and policy.

Network configuration and security

Defines responsibilities for network configuration and security settings in a laboratory.

Password security

Provides recommendations for maintaining unique and secure passwords for instrument accounts.

Instrument hardware description

Overview of the instrument

Provides a general overview of the QuantStudio 6 Pro and 7 Pro Real-Time PCR Systems.

Features of each instrument

Compares features between QuantStudio 6 Pro and QuantStudio 7 Pro systems.

Instrument filters and supported dyes

Details system dyes, filter wavelengths, and supported custom dyes.

Overview of data collection

Explains how the instrument collects raw fluorescence data during PCR cycles.

VeriFlex™ Zones

Describes VeriFlex Zones for independent temperature control in PCR runs.

AutoDelta settings

Explains AutoDelta for incremental changes in temperature or time during PCR cycles.

Parts of the instrument

Identifies and labels the key physical components of the instrument.

Instrument status indicator

Details the indicator lights and their corresponding instrument statuses.

Hands-free features

Covers hands-free operation features like facial authentication and voice commands.

Facial authentication

Describes the hands-free facial authentication for user sign-in.

Voice commands

Explains the instrument's voice command recognition for hands-free operation.

Indicators for the hands-free features

Details the indicators for facial authentication and voice commands.

Software description

Parts of the home screen

Identifies and describes the elements on the instrument's home screen.

Connect and Cloud definitions

Defines terms like Connect, Cloud, and Thermo Fisher Connect used on the instrument.

Instrument, desktop software, and Connect platform features

Compares features available across the instrument, desktop, and Connect platforms.

Overview of file locations and files

Explains where different types of files are stored and their descriptions.

Components of the files

Details the components included in system templates and plate files.

Third-party software

Provides guidelines for installing third-party software on the desktop.

Network connection options

Outlines options for connecting the instrument to a network or computer.

Types of runs

Standard curve run

Describes the process for determining absolute target quantity using a standard curve.

Relative standard curve run

Explains determining relative target quantity using a reference sample.

Comparative Ct (ΔΔCt) run

Details determining relative target quantity by comparing samples to a reference.

Genotyping run

Describes detecting single nucleotide polymorphism (SNP) variants.

Presence/absence run

Explains determining the presence or absence of a target nucleic acid sequence.

Melt curve run

Describes determining the melting temperature (Tm) of PCR amplification products.

System template file names

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

Lists system template file names applicable to the 96-well 0.2-mL block.

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

Lists system template file names applicable to the 96-well 0.1-mL block.

System template file names for the 384-well block

Lists system template file names applicable to the 384-well block.

System template file names for the TaqMan™ Array Card block

Lists system template file names for the TaqMan Array Card block.

Workflow

CHAPTER 2 Get started

Precautions for use

Highlights safety precautions including physical injury, fire, and handling hazards.

Installation and instrument verification

Outlines tasks performed during instrument installation and verification.

Overview of guest access

Describes the limits and configuration of guest access to the instrument.

Power on the instrument

Details how to power on the instrument and its sleep mode functionality.

Sign in

Explains the process for signing into the instrument using a PIN or facial authentication.

Sign in with a PIN

Provides steps for signing into the instrument using a personal identification number.

Sign in with facial authentication

Describes how to sign in using facial recognition and its requirements.

Enable or disable the microphone

Explains how to enable or disable the microphone for voice command features.

Use voice commands

Details how to use voice commands for hands-free operation of the instrument.

Sign out

Provides instructions on how to sign out of the instrument.

CHAPTER 3 Create and run plates on the instrument

Options to run a plate

Covers options for running a plate, including using templates or saved files.

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

Details creating and running a plate using pre-loaded or custom plate files.

Overview of customized data export

Explains how to perform primary and secondary analysis and export results.

(Optional) Scan a barcode using a barcode scanner

Describes using an optional barcode scanner for plate or card tracking.

Load a plate into the instrument

Provides instructions for loading a plate into the instrument drawer.

Load a TaqMan™ Array Card into the instrument

Details loading a TaqMan Array Card into the instrument drawer.

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

Provides instructions for safely unloading plates or cards from the instrument.

CHAPTER 4 Edit a plate before starting a run

Overview of a template file with restricted editing

Explains how template files with restricted editing are indicated and managed.

Options to edit the properties of a plate file

Covers editing properties like sample setup and export settings for plate files.

Import a sample setup

Describes importing a sample setup file to define sample positions on a plate.

Import an auto export setting

Explains importing custom export settings for data analysis.

Delete an auto export setting

Provides steps to delete previously imported auto export settings.

Options to edit the method of a plate file

Details editing method parameters like temperature, time, and cycles.

Method elements

Identifies and explains the components of a PCR method.

Edit the method

Provides instructions on how to edit method parameters like temperature and volume.

Add or remove steps

Explains adding or removing PCR steps within a method.

Add or remove stages

Details adding or removing stages (e.g., Hold, PCR, Melt Curve) in a method.

Add or remove data collection locations

Describes how to designate or remove data collection steps in a method.

Set up or remove VeriFlex™ Zones

Guides on configuring or removing VeriFlex Zones for temperature control.

Set up or remove the Auto Delta feature

Explains how to set up or remove the Auto Delta feature for PCR stages.

Configure ramp rates

Details how to adjust the ramp rate for temperature changes between stages/steps.

Add or remove a pause

Describes adding or removing pauses in the thermal cycling protocol.

Options to edit the well details of a plate file

Covers editing well details like sample names, targets, and reagents.

Options to view a plate layout

Explains the available views for a plate layout (Plate view, Well table view).

View a 384-well plate

Describes viewing and editing a 384-well plate, including zoom functionality.

View a TaqMan™ Array Card

Explains viewing the plate tab for a TaqMan Array Card.

Assign or edit a well for a plate

Details assigning or editing well information like sample name and target.

Add a target or an assay

Provides steps for adding or defining targets or assays for wells.

Assign or edit a well for a TaqMan™ Array Card

Describes assigning or editing well information for TaqMan Array Cards by port.

Add or edit the reagent details for a plate

Explains adding or editing reagent details for wells or multiple wells.

Apply the reagents to a plate

Details applying reagent details to wells or selected wells.

Delete the reagent details

Provides steps to delete reagent details from wells or the entire plate.

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

Explains adding or editing reagent details for ports on a TaqMan Array Card.

Apply the reagents to a TaqMan™ Array Card

Details applying reagent details to ports on a TaqMan Array Card.

Edit a passive reference dye

Describes selecting a passive reference dye for signal normalization.

Import an Assay Information File (AIF)

Explains how to import an Assay Information File for plate setup.

CHAPTER 5 Options for a run

Screens available during a run

Describes the different screens accessible while a run is in progress.

Edit a plate file during a run

Explains how to edit sample and target information during an active run.

Pause an instrument run

Details how to pause a run to add reagents or edit cycle counts.

Stop an instrument run

Provides instructions on how to stop an instrument run.

View the method during a run

Describes how to view the run's method details while it is active.

View real-time data and plots during a run

Explains how to view real-time amplification data and plots during a run.

View the time remaining during a run

Describes how to check the estimated time remaining for an active run.

Lock the touchscreen during a run

Explains how to lock the touchscreen to prevent interference during a run.

Unlock the touchscreen during a run

Provides instructions on how to unlock the touchscreen.

Instrument Schedule

Covers scheduling runs and managing the instrument's calendar.

CHAPTER 6 View and manage files

Manage plate files

Covers operations related to managing plate files, including copying and deleting.

Copy plate files

Details the process for copying plate files to different locations.

Delete plate files

Provides instructions on how to delete plate files from the instrument.

Manage data files

Covers managing data files, including viewing QC status and plots.

View QC Check status after a run

Explains how to view the QC Check status after a run is completed.

View an amplification plot after a run

Describes how to view amplification plots immediately after a run.

Transfer a data file immediately after a run

Details transferring data files immediately after a run is finished.

Transfer data files at a later time

Explains how to transfer data files at any time after a run.

View the list of data files on the instrument

Provides steps to view the list of data files stored on the instrument.

Delete data files from the instrument

Details how to delete data files stored on the instrument.

CHAPTER 7 Calibrate and verify instrument performance

Instrument and block calibration

Explains the calibration process for interchangeable blocks and instruments.

Calibration and verification schedule

Outlines the recommended frequency for instrument calibrations and verifications.

Calibration descriptions

Describes the purpose and pass criteria for various calibration types.

View the calibration status and set reminders

Details how to view calibration status and set reminders on the instrument.

Export a calibration report

Provides steps for exporting a calibration report as a TXT file.

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

Guides on performing ROI, background, and dye calibrations for standard blocks.

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

Details specific calibration procedures for the TaqMan Array Card block.

Perform verification using RNase P plates

Outlines instrument verification procedures using RNase P plates.

Perform verification using RNase P with a TaqMan™ Array Card

Details instrument verification using RNase P with a TaqMan Array Card.

Calibrate custom dyes

Provides procedures for calibrating custom dyes for assays.

Calibrate for a custom melt curve run

Guides on calibrating for high-resolution melt analysis runs with custom dyes.

CHAPTER 8 Manage profiles

Require sign-in

Explains how to enable or disable the sign-in requirement for instrument access.

Recommended order to set up profiles

Suggests an order for setting up instrument and Connect profiles.

Overview of local instrument profiles and Connect profiles

Compares features and storage for local vs. Connect profiles.

Connect instrument profile roles and functions

Details roles and allowed functions for Standard and Administrator profiles.

Test the connection to the Connect platform

Provides steps to test the instrument's connection to the Connect platform.

Link the instrument to your Connect account

Guides on linking the instrument to a Connect account for the first time.

Create a new local instrument profile

Explains how to create a new local instrument profile without Connect features.

Link a local profile to a Connect profile

Details linking an existing local profile to a Connect profile.

Unlink a Connect account

Provides steps to unlink a Connect account from the instrument.

If you link when you are signed in to the instrument

Describes linking to Connect while signed into the instrument.

If you link when you are not signed in to the instrument

Explains linking to Connect when not signed into the instrument.

Manage individual instrument profiles

Covers creating, setting up facial authentication, and managing profiles.

Change the PIN for an instrument profile

Details changing the PIN for a local instrument profile.

Change the PIN for a Connect profile

Explains how to change the PIN for a Connect profile via browser.

Manage all instrument profiles as an administrator

Provides administrative tools for viewing, resetting, adding, and deleting profiles.

Enable or disable administrator privileges

Guides on enabling or disabling administrator privileges for profiles.

Delete a profile

Provides steps to delete an instrument profile.

CHAPTER 9 Use the instrument with the Security, Auditing, and E-signature (SAE) v2.0 module

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

Describes the three main components of the SAE module.

Overview of the instrument features when the SAE module is enabled

Lists instrument features unavailable when the SAE module is enabled.

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

Details functions controlled, audited, and signed based on user role.

Functions that can be audited

Lists instrument functions that can be audited based on administrator configuration.

Functions that can be signed

Identifies instrument functions that require an e-signature.

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

Defines roles (Administrator, Scientist, Technician) and their privileges.

Dialog boxes in the SAE module

Shows examples of dialog boxes and prompts that may appear in the SAE module.

Profiles when the SAE module is enabled

Explains profile availability and sign-in requirements when SAE is enabled.

SAE-enabled system components

Lists system components compatible with SAE functions.

Compatibility between SAE-enabled and SAE-disabled components

Details compatibility issues between SAE-enabled and disabled components.

Enable SAE functions

Guides on enabling SAE functions via Administrator Console and the instrument.

Disable SAE on the instrument (administrator only)

Provides steps for administrators to disable SAE mode on the instrument.

Sign in as a local administrator with SAE enabled

Explains signing in as a local administrator when SAE is enabled.

Sign in with SAE enabled

Details the process for signing in with an SAE account when SAE is enabled.

Sign out with SAE enabled

Provides instructions on how to sign out when using SAE mode.

Change your SAE account password on the instrument

Guides on changing the SAE account password on the instrument.

Sign a plate setup

Details the process of signing a plate setup for audit purposes.

Enter an audit reason

Explains when and how to enter an audit reason for changes made.

View signing records for a plate file

Provides steps to view signing records associated with a plate file.

View audit records

Explains where audit records can be viewed (Design and Analysis Software, Console).

Use the instrument when the SAE server is offline

Describes instrument usage limitations when the SAE server is offline.

E-signature requirements to start a run

Explains e-signature requirements that may be needed to start a run.

Signing in after automatic screen locking

Details signing in after the instrument touchscreen automatically locks.

SAE error messages and actions

Provides a guide to SAE error messages and recommended actions.

CHAPTER 10 Maintain the instrument

Install a block

Guides on installing a block into the instrument when no block is present.

Change the block

Provides instructions for changing the instrument's block and heated cover.

Remove the block

Details how to remove the block and heated cover from the instrument.

Decontaminate the sample block

Explains procedures to eliminate fluorescent contaminants from the sample block.

Replace the instrument fuses

Provides instructions and materials needed to replace instrument fuses.

Power on or off, store, and move

Covers enabling sleep mode, powering the instrument, and storage/moving.

Enable and edit sleep mode

Details how to customize the instrument's sleep mode settings.

Power on the instrument

Provides instructions on how to power on the instrument.

Power off the instrument

Details how to safely power off the instrument.

Prepare the instrument to store, move, or ship

Explains steps to prepare the instrument for storage, moving, or shipping.

Move the instrument

Provides safety guidelines and techniques for moving the instrument.

CHAPTER 11 Configure the instrument settings

View the instrument details

Shows how to view instrument details like model, serial numbers, and software version.

View the license agreement

Provides access to the End User License Agreement (EULA) for the software.

View the privacy policy for the Connect cloud-based platform

Details the privacy policy for the Connect cloud-based platform.

Configure the instrument settings

Covers general instrument settings like demo mode, name, date, and time.

Enable or disable demonstration mode

Explains how to enable or disable demonstration mode on the instrument.

Edit the instrument name (administrator only)

Provides steps for administrators to edit the instrument name.

Set the date and the time

Details setting the instrument's date, time, time zone, and format.

Configure the heated cover settings

Explains how to configure the heated cover settings for idle periods.

Adjust the speaker volume

Provides instructions for adjusting the speaker volume for user feedback.

Configure the network

Guides on configuring wired or wireless network connections.

Configure a proxy server

Details connecting the instrument to a proxy server.

Select the region for the Connect platform

Explains how to select the region for the Connect platform.

Select a disk storage management mode

Describes managing disk space by selecting automatic or manual deletion.

Enable and edit automatic sign-out

Details configuring the automatic sign-out feature after inactivity.

Set an access key for external software to connect to the instrument

Guides on setting an access key for external software connection.

Reset the access key for external software to connect to the instrument

Provides steps to reset the access key for external software.

Configure maintenance and service settings

Covers requesting support, self-verification tests, and instrument logs.

Request technical support with Smart Help

Details requesting technical support using the Smart Help feature.

Request instrument service with Smart Help

Explains how to request instrument service through Smart Help.

Perform and view self-verification tests

Guides on performing and viewing results of self-verification tests.

Perform a hardware test

Details performing a hardware test to check instrument components.

View the last hardware test result

Explains how to view the results of the most recent hardware test.

Perform a peripheral test

Describes performing a peripheral test for touchscreen, speaker, camera, etc.

View the instrument log

Guides on viewing the instrument's event log with timestamps.

Export the instrument log

Provides steps to export the instrument log files to various destinations.

View the instrument statistics

Details how to view instrument statistics like disk space and cycle counts.

Enable or disable remote monitoring

Explains how to enable or disable remote monitoring of instrument progress.

Update the software

Guides on updating the instrument's software when updates are available.

Repair the software

Provides steps to repair the software if an update fails.

Back up the instrument

Details how to back up instrument settings and profiles to USB or Connect.

Restore a backup of the instrument

Explains how administrators can restore a backup of the instrument.

Upload a certificate for a TaqMan™ Array Plate with RFID

Guides on uploading a certificate for TaqMan Array Plates with RFID.

Overview of an instrument reset (restore factory default)

Describes information deleted and retained during an instrument reset.

Reset the instrument (restore factory default)

Provides steps to reset the instrument to factory default settings.

Request remote support

Explains how to grant remote access to a support representative.

Configure the instrument for the hands-free features

Guides on enabling facial authentication and voice commands.

Manage the run history

Directs users to view, export, or delete run history.

Manage the file name convention of the data file

Details how to customize data file naming conventions.

View the notifications

Explains how to view notifications on the instrument.

Enable and disable home screen notifications

Guides on enabling or disabling notifications displayed on the home screen.

Set up email notifications

Details configuring email notifications for specific event types.

Clear the notifications

Provides steps to clear notifications from the instrument.

APPENDIX A Instrument specifications and layout

Instrument dimensions

Provides physical dimensions and weight of the instrument.

Instrument and computer clearances

Specifies required clearances around the instrument and computer for access.

Configured system dimensions

Illustrates clearances needed for the instrument with a computer.

Light guidelines

Offers guidelines for optimal lighting for facial authentication.

Electrical requirements

Details voltage, power, and receptacle requirements for instrument operation.

Environmental requirements

APPENDIX B Connect the instrument to a network

Connect the computer to the instrument directly or to a LAN

Describes direct wired connection of computer to instrument or LAN.

Connect the instrument to a wired network

Guides on connecting the instrument to a wired network.

Connect the instrument to a wireless network

Details connecting the instrument to a wireless network.

Instrument and computer connections

Illustrates the physical back panel ports for instrument and computer connections.

Download and install the desktop software

Covers computer requirements and steps to download/install desktop software.

Install the desktop software

Provides instructions for installing the QuantStudio desktop software.

Networking

Offers general networking information and best practices for instrument integration.

Control and monitor networked instruments

Explains how to control and monitor instruments connected to a network.

Networking guidelines and best practices

Provides recommendations for optimal network configuration and usage.

Firewall ports that must be open

Lists necessary firewall ports for instrument discovery and connection.

Ethernet port overview

Describes the capabilities and services supported by the instrument's Ethernet port.

Third-party software

Provides warnings regarding third-party software interference.

APPENDIX C Detailed procedures for preparation of a TaqMan™ Array Card

Guidelines for preparation of a card

Offers guidelines for handling and preparing TaqMan Array Cards.

TaqMan™ Array Card diagram

Illustrates the components and layout of a TaqMan Array Card.

Load the PCR reaction mix

Provides steps for loading the PCR reaction mix into the Array Card.

Centrifuge the card

Details the procedure for centrifuging the loaded TaqMan Array Card.

Seal the card

Explains how to seal the TaqMan Array Card using the sealer.

APPENDIX D Parts and materials

Kits, consumables, accessories, and reagents

Lists kits, consumables, accessories, and reagents with catalog numbers.

96-well 0.2 mL consumables

Details consumables for 96-well, 0.2 mL plates and calibration kits.

96-well 0.1 mL consumables

Lists consumables for 96-well, 0.1 mL plates and calibration kits.

384-well consumables

Details consumables for 384-well plates and calibration kits.

TaqMan™ Array Card consumables

Lists calibration and verification kits for TaqMan Array Cards.

Accessories

Lists required accessories for TaqMan Array Cards and general items.

APPENDIX E Safety

Symbols on this instrument

Explains safety symbols used on the instrument and in the manual.

Standard safety symbols

Details standard safety symbols like Caution, Warning, and Danger.

Additional safety symbols

Lists additional safety symbols such as moving parts.

Location of safety labels

Shows the locations of safety labels on the instrument's back panel and drawer.

Safety information for instruments not manufactured by Thermo Fisher Scientific

Provides safety guidance for non-Thermo Fisher Scientific accessories.

Instrument safety

Covers general safety, physical injury, electrical, laser, and cleaning hazards.

General

Provides general safety warnings regarding instrument covers and hazards.

Physical injury

Highlights risks of moving/lifting injury and cautions about moving parts.

Electrical safety

Details warnings and precautions related to fuse installation and electrical supply.

Laser safety

Warns about laser hazards associated with optional barcode scanners.

Cleaning and decontamination

Provides guidelines for safe cleaning and decontamination procedures.

Instrument component and accessory disposal

Offers guidance on proper disposal of electronic waste and accessories.

Safety and electromagnetic compatibility (EMC) standards

Lists standards and requirements for safety and EMC compliance.

Safety standards

References various safety standards for electrical equipment.

EMC standards

Lists relevant EMC standards for electromagnetic compatibility.

Environmental design standards

References environmental standards like WEEE and RoHS.

Radio compliance standards

Details radio compliance standards like EU RE Directive and FCC Part 15.

RF transceiver specifications

Provides specifications for the RFID reader transceiver.

Chemical safety

Offers general guidelines for chemical handling, storage, and waste disposal.

Biological hazard safety

Provides safety guidelines for handling potentially biohazardous materials.

APPENDIX F Documentation and support

Related documentation

Lists related documents and their publication numbers for further information.

Customer and technical support

Provides contact information for service and support resources.

Limited product warranty

Outlines the warranty terms and conditions for the product.

Related product manuals