QuantStudio™ 3 and 5 Real‑Time PCR

Systems
INSTALLATION, USE, AND MAINTENANCE

Firmware v1.4
Publication Number MAN0010407
Revision D.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: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE
LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR
ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.
Revision Date Description
D.0 22 July 2021 Updates – describes new features in Firmware v1.4.x and other changes, including:
• Updated the name of the cloud-based platform to Thermo Fisher™ Connect.
• Added instructions for connecting to the Thermo Fisher™ Connect cloud-based
platform.
• Updated the firewall instrument-to-computer port number.
• Updated licensing information.
• Added Network and password security requirements section
• Added Perform internal validations before software upgrades section
• Added information for updating the firmware.
• Update operating system to Windows™ 10 (64‑bit).
• Added the MicroAmp™ Optical Film Compression Pad as an optional accessory
for the 96-well 0.2-mL block when using a MicroAmp™ Optical 96-Well Reaction
Plate, including instructions to load and unload the plate if using this accessory.
• Specified that an instrument profile is only for the instrument. It is not related to
any other account for the system or the software.
• Specified that if the connection between the instrument and the desktop software
is interrupted during a run, the instrument will complete the run. The EDS file must
be transferred manually to the desktop software with a USB drive or through a
network drive.
• Changed all references to Bleach, 10% solution to Na-hypochlorite (0.1% v/v)
solution
• Updated the calibration and verification schedule.
– Specified that Background and Dye calibrations must be performed after an
ROI/Uniformity calibration.
– Specified ROI/Uniformity calibration invalidates all other calibrations.
– Added that the Background calibration can be used to obtain the most
accurate data for the removal of background fluorescence.
– Specified that a Background calibration and a Dye calibration do not
invalidate all other calibrations.
– Added a recommendation that RNase P instrument verification be
performed after instrument calibrations.
• Added troubleshooting information for RNase P verification.
• Added troubleshooting information if the connection between the instrument and
the computer is not recognized.
• Added storage and transport conditions to the environmental requirements.
• Specified that restoring factory defaults can only be performed by an
administrator and specified that the most recent valid ROI/Uniformity,
Background, and System Dye calibrations are not deleted when factory defaults
are restored.

C.0 December 2015 Updates – describes new features in Firmware v1.2.x, including:
• Updated workflow to create an instrument profile
• Streamlined workflow for connectivity to Thermo Fisher™ Connect
• Improved display of VeriFlex™ Zones
• Plate insert reminder before starting run
• Support for 96-well Fast (0.1 mL) plates
(continued)

Revision Date Description

B.0 September 2015 Updates – describes new features in Firmware v1.1.x, including:
• Experiment runs: monitor real-time data, edit cycle number and lock screen
during a run, view end plot, and support for 384-well plates
• File management: access Network folders, navigate folder structures and save
templates on instrument, and perform batch actions for file management
• Instrument configuration: support for Security, Audit, and e-Signature (SAE),
smart monitoring, and choice of server region

Includes information on software feature comparison, definitions of terms, parts of

method, network connection options, experiment types, desktop software installation.
A.0 April 2015 New document. Describes installation, operation, and maintenance of the QuantStudio™
3 and 5 Real‑Time PCR Systems.

Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these
products, you accept the terms and conditions of all applicable Limited Use Label Licenses.
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 GLOBAL
LIFE SCIENCES SOLUTIONS GERMANY GMBH. Microsoft and Windows are trademarks of Microsoft Corporation. Pentium is a
trademark of Intel Corporation. Google and Chrome are trademarks of Google, Inc.
©2021 Thermo Fisher Scientific Inc. All rights reserved.
 Contents

About this guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

■ CHAPTER 1 Product information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Network and password security requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Network configuration and security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Password security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Perform internal validations before software upgrades . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Update the instrument firmware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Backup the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Instrument hardware description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Instrument overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Parts of the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Software description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Instrument, desktop, and cloud software features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Folders, templates, experiments, and projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Third-party software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Network connection options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Types of runs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

■ CHAPTER 2 Start, sign on, and configure the instrument . . . . . . . . . . . . . . . . . . . . . 21

Installation and instrument verification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Precautions for use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Power on the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Parts of the home screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Use the instrument without signing in . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Create a new instrument profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Sign in . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Sign out . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Configure instrument settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

4 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
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■ CHAPTER 3 Create and run experiments on the instrument . . . . . . . . . . . . . . . . . . 29

Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Options for running an experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Create and run an experiment from a template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Run an experiment from a saved file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Repeat the last instrument run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Edit an experiment before starting a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Enter or edit template properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Edit the run method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Define, assign, and view well details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Load and unload the plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Load and unload a plate in the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Load and unload a plate in the instrument with a compression pad . . . . . . . . . . . . . . 38
View, pause, or stop a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
View real-time data and plots on the instrument touchscreen . . . . . . . . . . . . . . . . . . . . 40
Pause or stop an instrument run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Adjust the display of real-time plots on the instrument touchscreen . . . . . . . . . . . . . . 41
Lock the touchscreen during a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Transfer, view, or manage files and results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Transfer EDS files from the instrument home screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
View run history and delete or transfer files from the instrument . . . . . . . . . . . . . . . . . 42
Manage templates (EDT files) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

■ CHAPTER 4 Calibrate and verify instrument performance . . . . . . . . . . . . . . . . . . . . . 43

Calibration and verification schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Calibration descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
View the calibration status and set reminders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
View calibration status and set reminders in the instrument . . . . . . . . . . . . . . . . . . . . . 45
™
View calibration status and set reminders in Thermo Fisher Connect . . . . . . . . . . . . 45
Perform ROI/uniformity, background, and dye calibrations . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Workflow: Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Prepare a calibration plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Perform calibrations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
View calibration images and transfer results to USB . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Troubleshoot calibration failure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Identify contamination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Create a background plate (optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Perform instrument verification using RNase P plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Instrument verification description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
RNase P instrument verification plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Performance specifications pass criteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Prepare an RNase P plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 5
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Perform RNase P verification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Troubleshoot verification failure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Calibrate custom dyes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Custom dyes overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Use a dilution series to determine an optimal custom dye concentration . . . . . . . . . . 59
Calibrate the custom dye . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Calibrate for a custom melt curve experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

■ CHAPTER 5 Maintain the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Backup or restore the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Decontaminate the sample block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Materials required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Clean the sample block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Detailed procedures for cleaning the sample block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Replace the instrument fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Materials required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Replace the fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Power on or off, store, and move . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Enable Sleep Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Power on the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Power off the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Prepare the instrument to store, move, or ship . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Move the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Return the instrument for service . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

■ CHAPTER 6 Configure the instrument and manage instrument profiles . . . . . 75

Initial start‑up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Manage profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Create an administrator instrument profile during initial start-up . . . . . . . . . . . . . . . . . 76
Manage all instrument profiles (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Edit an instrument profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
™
Link an instrument profile to Thermo Fisher Connect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Recommended order to set up profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
™
Overview of local instrument profiles and Thermo Fisher Connect profiles . . . . . . . 78
™
Thermo Fisher Connect instrument profile roles and functions . . . . . . . . . . . . . . . . . . 79
™
Test the connection to the Thermo Fisher Connect platform . . . . . . . . . . . . . . . . . . . . 79
™
Link the instrument to your Thermo Fisher Connect account . . . . . . . . . . . . . . . . . . . 80
™
Link a local profile to a Thermo Fisher Connect profile . . . . . . . . . . . . . . . . . . . . . . . . . 82
™
Unlink a Thermo Fisher Connect account . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
If you link when you are signed in to the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
™
Change the PIN for a Thermo Fisher Connect profile . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Enable SAE mode (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Require instrument profile sign-in (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

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Enable remote instrument monitoring (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

Update instrument software (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Restore factory defaults . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Configure the network . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Set up a wired connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Set up a wireless connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
™
Select a region for Thermo Fisher Connect (Administrator only) . . . . . . . . . . . . . . . . . . . . . 88
Manage the instrument name (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Set the date and time (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Manage the Sign Out Timer (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

■ APPENDIX A Install and connect the instrument to a network . . . . . . . . . . . . . . . . 90

Workflow: Install and connect to a network . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

Before you begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Unpack and install the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Power on and follow the startup wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Connect the computer to the instrument directly or to a LAN . . . . . . . . . . . . . . . . . . . . . . . . 92
Instrument and computer connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Download and install the desktop software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Computer requirements for the desktop software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Download the desktop software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Install the desktop software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Networking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Supported options for instrument and computer connections . . . . . . . . . . . . . . . . . . . 95
Control and monitor networked instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Ethernet port overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Firewall ports that must be open . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Networking guidelines and best practices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98

■ APPENDIX B Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99

■ APPENDIX C Parts and materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101

Kits, consumables, accessories, and reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101

Consumables (96‑well, 0.2‑mL format) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
384-well consumables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Consumables (96-well, 0.1-mL format) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
General-use materials and consumables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 7
Contents

■ APPENDIX D Instrument specification and layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105

Configured system dimensions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

Instrument clearances . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Electrical requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Environmental requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Network requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

■ APPENDIX E Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110

Symbols on this instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110

Conformity symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Safety alerts on this instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Location of safety labels on the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Safety information for instruments not manufactured by Thermo Fisher Scientific . . . . . 114
Instrument safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
General . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Physical injury . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Electrical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Cleaning and decontamination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Safety and electromagnetic compatibility (EMC) standards . . . . . . . . . . . . . . . . . . . . . . . . . 116
Safety compliance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
EMC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Environmental design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Chemical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Biological hazard safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120

■ APPENDIX F Documentation and support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121

Related documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121

Obtain information from the Help system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Customer and technical support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Limited product warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123

8 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 About this guide

Purpose
This guide provides information about installing, using, and maintaining the QuantStudio™ 3 and 5
Real‑Time PCR Systems.

Note: For information and instructions on performing experiments on these systems, see QuantStudio™
Design and Analysis Desktop Software User Guide (Pub. No. MAN0010408).

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 9
 1 Product information

■ Network and password security requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

■ Perform internal validations before software upgrades . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
■ Update the instrument firmware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
■ Instrument hardware description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
■ Software description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
■ Network connection options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
■ Types of runs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

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.

Perform internal validations before software upgrades

IMPORTANT! If you have a validated workflow, you must perform all internal validations as required by
your organization's standard operating procedures before performing a software upgrade.

10 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 1 Product information
Update the instrument firmware 1

Update the instrument firmware

If your instrument is not on version 1.4 or later of the firmware you must update the firmware
to access the features and updates described in Revision D.0 of the revision history. For more
information, see “Revision history” on page 2. For information on updating your firmware, see https://
www.thermofisher.com/us/en/home/global/forms/life-science/quantstudio-3-5-software.html.
Prior to updating your firmware, we recommend you perform a backup. For information on performing a
backup, see “Backup the instrument” on page 11.

Backup the instrument

1. In the home screen, touch Settings4Maintenance and Service4Backup/Restore.

2. Touch Backup Instrument.

3. Select a location to store the backup settings for your instrument.

4. If backing up to a USB drive, insert a USB drive into the front-panel USB port.

5. Enter a backup file name, then touch Done.

6. Select the elements to backup, or leave them all selected.

7. Touch Backup.

Instrument hardware description

Instrument overview
The QuantStudio™ 3 and 5 Real‑Time PCR Systems use fluorescence-based polymerase chain reaction
(PCR) reagents to perform:
• Quantitative detection of target nucleic acid sequences (targets).
• Qualitative detection of targets (endpoint analysis, genotyping experiments, and presence/absence
experiments).
• Qualitative analysis of the PCR product (post-PCR melt curve analysis).

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 11
 Chapter 1 Product information
1 Instrument hardware description

The following fixed-block configurations are available:

QuantStudio™ 3 Real-Time PCR System QuantStudio™ 5 Real‑Time PCR System

• 96-Well VeriFlex™ 0.2-mL Block (4 Color) • 96-Well VeriFlex™ 0.2-mL Block

• 96-Well VeriFlex™ 0.1-mL Block (4 Color) (6 Color De‑coupled)
• 384-Well Block (5 Color)
• 96–Well VeriFlex™ 0.1-mL Block
(6 Color De‑coupled)

The instrument can be run directly from the touchscreen to create and start experiments. To design
experiments or to analyze data, the instrument can be integrated with the QuantStudio™ Design and
Analysis Software.
An optional barcode scanner and optional wireless adapter can be purchased separately.

Instrument filters and supported dyes

System dyes
The instruments use a coupled four-color, coupled five-color, or de-coupled six-color filter set that
supports the dyes shown in the following table and figure. For more information about available spectral
dye calibration kits, contact Support.

Filter wavelength (nm)[1] Factory-calibrated

Peak filter Color Example custom dyes
Excitation Emission dyes

FAM™ dye,
x1-m1 Blue 470 ± 15 520 ± 15 SYT09
SYBR™ Green

JOE™ dye,
x2-m2 Green 520 ± 10 558 ± 12 VIC™ dye
HEX™ dye, TET™ dye[2]

NED™ dye, TAMRA™

x3-m3 Yellow 550 ± 10 587 ± 10 Cy®3
dye, ABY™ dye

x4-m4 Orange 580 ± 10 623 ± 14 ROX™ dye, JUN™ dye Texas Red™ dye

MUSTANG PURPLE™
x5-m5 Red 640 ± 10 682 ± 14 LIZ™ dye
dye, Cy®5

x6-m6 Deep-Red 662 ± 10 711 ± 12 None [3] Cy® 5.5

[1] The central wavelengths are the optimized wavelengths.
[2] The HEX™ and TET™ dyes 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.

12 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 1 Product information
Instrument hardware description 1

Wavelength
(nm)

Emission
Spectra

x1-m1 x2-m2 x3-m3 x4-m4 x5-m5 x6-m6 Filters

1 2 3 4 5

1 x1-m1 — FAM™ dye, SYBR™ Green

2 x2-m2 — VIC™ dye
3 x3-m3 — ABY™ dye, NED™ dye, Cy®3, TAMRA™ dye
4 x4-m4 — JUN™ dye, ROX™ dye, Texas Red™ dye
5 x5-m5 — Cy®5, MUSTANG PURPLE™ dye

Custom dyes
The instrument can run assays designed with custom dyes.
Custom dyes include:
• 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 59).
• 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 the filter-
wavelength table in “System dyes” on page 12).
• The custom dye 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™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 13
 Chapter 1 Product information
1 Instrument hardware description

About data collection

The instrument collects raw fluorescence data at different points during the PCR cycle, depending on
the type of run performed.
When you create an experiment template (EDT file) in the software, 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, optionally, a different filter set for the melt curve stages.

Run type Experiment type Data collection point

Real-time • Standard curve During the thermal cycling protocol.

• Relative standard curve Typical timing is to collect data at each cycle of a PCR
• Comparative CT (ΔΔCT) stage or continuously during a melt stage.
• Melt curve

Post-PCR • Genotyping • After thermal cycling is completed.

(endpoint) • Presence/ Absence For Presence/Absence and Genotyping experiments,
data collection before the PCR cycle is optional, but
recommended.
• (Optional) Before thermal cycling starts.
Collecting data during the run can confirm
genotyping results by viewing traces in allelic
discrimination plots or viewing genotyping calls at
earlier cycles.

Blocks with VeriFlex™ Zones

Applied Biosystems™ VeriFlex™ technology provides independent temperature zones that offer
enhanced functionality and precise control over your real-time PCR runs.

QuantStudio™ 3 System QuantStudio™ 5 System

Three programmable VeriFlex™ Zones. Six programmable VeriFlex™ Zones.[1]

[1] Only applicable for 96-well 0.2-mL and 0.1-mL blocks.

14 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 1 Product information
Software description 1

These independent zones are ideal for real-time PCR optimization or the ability to run multiple
experiments in the same run. Unlike standard gradients which give a sigmoidal temperature curve
across the columns, blocks with VeriFlex™ Zones help deliver accurate temperatures across every zone.

Parts of the instrument

1 Touchscreen – Controls the instrument.

2 USB port – For connection to an external network drive or external data storage device.
3 Instrument drawer – Contains sample plate.

The instrument includes three additional USB ports on the back of the instrument.

Note: The instrument recognizes only one external storage device at a time for data transfer.

Software description
Instrument, desktop, and cloud software features
The instrument software and the QuantStudio™ Design and Analysis Software (desktop and Thermo
Fisher™ Connect) include the features described below.

Thermo Fisher™
Feature Instrument Desktop
Connect

Use as guest (no sign in) ✓ ✓ [1] —

Create templates (unlocked or locked) — ✓ ✓

Edit unlocked templates ✓ ✓ ✓

Edit locked templates (password assigned by — ✓ ✓

template creator required)

Load system or user-created templates (.edt file) ✓ ✓ —

to instrument

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 15
 Chapter 1 Product information
1 Software description

(continued)

Thermo Fisher™
Feature Instrument Desktop
Connect

Change experiment settings in template (.edt file) ✓ — —

loaded on the instrument
Settings that can be changed in a locked
template (no password required):
• Properties: All settings
• Method: No changes allowed
• Plate: Sample names

Settings that can be changed in an unlocked

template:
• Properties: All settings
• Method: All settings
• Plate: Sample names

Load plate in instrument ✓ — —

Start run ✓ ✓ —

View real-time data during a run ✓ ✓ ✓

View instrument status (running, calibration ✓ — ✓

needed, and so on)

Analyze results — ✓ ✓

Set calibration reminders ✓ — ✓

Review exported calibration or RNase P — ✓ ✓

verification results
(only RNase P)
[1] Login required if the Security, Audit, and e-Signature (SAE) module is enabled (QuantStudio™ 5 System only)

16 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 1 Product information
Software description 1

Folders, templates, experiments, and projects

Term Definition Supported in

Folders in Load Location in which you can store templates (EDT files) on the Instrument
Experiment instrument:
• My Instrument – Displayed if you are signed in
• Public – Location in which all experiments run by guest
users are stored
• USB – USB for manual transfer to and from a computer
• Post Read – If you run an endpoint experiment, the pre-
read experiment is automatically saved in this folder for
post-read analysis

Experiment Template Default settings for an instrument run, can be modified before Instrument
File (EDT) instrument run.
Desktop
Two types:
Thermo Fisher™
• Factory-provided, accessed from Open Template Connect
(instrument) or Create Experiment (desktop or Thermo
Fisher™ Connect)
• User-created, accessed from Load Experiment

Experiment Run File Settings and data for a completed instrument run. Instrument
(EDS)
Desktop
Thermo Fisher™
Connect

Template and
experiment Instrument Desktop Thermo Fisher™ Connect
components

Properties • Experiment file name • Experiment file name

• Reagent information (Reagent • Plate barcode
barcode, Lot#) • User name
• Plate barcode • Instrument type
• Data destination (location for • Block type
auto-transfer of data)
• Experiment type
• Comments (Tags are not used
• Chemistry (reagent information)
at this time)
• Run mode
• Comments
• (Thermo Fisher™ Connect only) Notifications

Method Thermal cycling conditions Thermal cycling conditions

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 17
 Chapter 1 Product information
1 Network connection options

(continued)

Template and
experiment Instrument Desktop Thermo Fisher™ Connect
components

Plate Sample names Define and assign samples, targets or SNP assays, and
tasks in the Quick Setup and Advanced Setup panes of the
You cannot edit targets/SNP
Plate tab.
assays or tasks on the instrument.

Run Start and monitor a run in progress Start and monitor a run in Monitor a run in progress
progress (link to Thermo Fisher™
View: time remaining and
Connect Instrument Details)
temperature, method, plots View: time remaining and
temperature, method, plots View: time remaining and
Pause, resume, stop a run
temperature, method, plots

Results Not applicable Review plots

Export Not applicable Export results

Third-party software
Before installing third-party software on the computer running QuantStudio™ Design and Analysis
Software, confirm that the third-party software will not do the following:
• Restrict Ethernet communication.
• Interfere with instrument or computer operation.

Network connection options LAN

You can connect an instrument to a network or computer in the configurations listed below. For specific
information on networking, see “Networking” on page 95.

Local area network (LAN) Thermo Fisher™ Connect

Direct connection
connection connection

wired wired or wireless wired or wireless

LAN

LAN

18 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 1 Product information
Types of runs 1

Types of runs
Purpose Description

Standard curve run

Determines absolute 1. The software measures amplification of the target in a standard dilution series and in
target quantity in test samples.
samples. 2. The software generates a standard curve using data from the standard dilution series.
3. The software uses the standard curve to interpolate the absolute quantity of target in
the test samples.

Relative standard curve run

Determines relative 1. The software measures amplification of the target of interest and of an endogenous
target quantity in control target in a standard dilution series, in a reference (calibrator) sample, and in test
samples. 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 effects on gene expression, an untreated
control is an appropriate reference sample.
2. The software generates standard curves for the target of interest and the endogenous
control using data from the corresponding standard dilution series.
3. 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.
4. 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 (ΔΔCt) run

Determines relative 1. The software measures amplification of the target of interest and of an endogenous
target quantity in control target in a reference (calibrator) sample and in test samples.
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 effects on gene expression, an untreated
control is an appropriate reference sample.
2. The measurements for the target of interest are normalized to the endogenous control.
3. 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™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 19
 Chapter 1 Product information
1 Types of runs

Purpose Description

Genotyping run
Detects single Genotyping runs use preformulated TaqMan™ SNP Genotyping Assays that include the
nucleotide following components:
polymorphism (SNP)
variants of a • Two sequence-specific primers for amplification of sequences containing the SNP of
target nucleic acid interest
sequence. • Two allele-specific TaqMan™ probes for Allele 1 and Allele 2

1. The software normalizes the fluorescence of the reporter dyes to the fluorescence of
the passive reference dye in each well.
2. 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.
3. 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
Determines the The software calls the target present or absent based on an algorithmically determined call
presence or absence threshold. (The call threshold is different from the Ct threshold; the Ct threshold is not used
of a target nucleic
to make calls.)
acid sequence in a
sample.

Melt curve run

Determines the In the software, melt curve analysis is included in the default run method for any run type
melting temperature that uses intercalating dyes.
(Tm) of
the amplification 1. The software plots a melt curve based on the fluorescence of the dye with respect to
products of a change in temperature.
PCR that used 2. Using the melt curve, the software calculates the melting temperature (Tm).
intercalating dyes.

20 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 2 Start, sign on, and configure the
instrument

■ Installation and instrument verification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

■ Precautions for use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
■ Power on the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
■ Parts of the home screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
■ Use the instrument without signing in . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
■ Create a new instrument profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
■ Sign in . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
■ Sign out . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
■ Configure instrument settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Installation and instrument verification

Before the first use of the instrument, complete the following tasks:
• Install the instrument (see “Unpack and install the instrument” on page 91).
• Verify instrument performance (see “Perform instrument verification using RNase P plates” on
page 53).

Note:
· Instruments are factory calibrated, so no calibration is necessary at installation. However, we
recommend that you verify instrument performance before using the instrument.
· Regular calibration and verification should be performed according to the calibration and
verification schedule (see “Calibration and verification schedule” on page 43).

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 21
 Chapter 2 Start, sign on, and configure the instrument
2 Precautions for use

Precautions for use

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. For continued protection against the risk of fire, replace fuses only with
listed and certified fuses of the same type and rating as those currently in the instrument.

CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the sample block
temperature can reach 100°C. Allow it to cool to room temperature before handling.

CAUTION! Before using a cleaning or decontamination method other than those recommended by
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 heated cover.

Power on the instrument

1. Touch anywhere on the touchscreen to determine if the instrument is in sleep mode. If the home
screen is displayed, the instrument is already powered on.

2. If the home screen does not display, power on the

instrument by pressing the switch on the rear panel.

If left unattended, the instrument automatically enters sleep

mode (enabled by default) to conserve power.

Note: To customize the sleep mode setting, touch

Settings4Instrument Settings4Sleep Mode.

22 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 2 Start, sign on, and configure the instrument
Parts of the home screen 2

Parts of the home screen

1 2

9 6

8 7

1 Avatar and Instrument name

2 Eject icon
3 Help icon
4 Status dial
5 Current user name; instrument block type
6 Settings button
7 Buttons for accessing .edt files
8 Connectivity icons
9 Sign In (or My Profile) button

Table 1 Parts of the home screen

Element of the
Function For more information, see...
home screen

Avatar and Set by the administrator to uniquely identify instrument. “Manage the instrument name
Instrument name (Administrator only)” on page 88.

Eject icon Touch to open or close the instrument drawer. —

Help icon Touch to launch the touchscreen Help system to access —

step-by-step instructions.

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 23
 Chapter 2 Start, sign on, and configure the instrument
2 Parts of the home screen

Table 1 Parts of the home screen (continued)

Element of the
Function For more information, see...
home screen

Status dial • When the instrument is in use – Displays the sample —

block temperature, the elapsed run time, and the
run status.
You can swipe the dial to the left or touch to
access real-time views of the run.
• When the instrument is not in use – Displays Set up
run. You can start a run by touching the status dial.
• When the instrument is locked – Displays a lock
icon ( ) within the status dial.

Current user Displays the user name of the current signed-in user and —
name and block the instrument block type.
type
Note: If no user is signed-in, the instrument defaults to
the Guest profile.

Settings button Touch Settings to configure, calibrate, or learn about “Configure instrument settings” on
the instrument. page 26.

Buttons for Load Experiment – Touch to open a user-created .edt “Run an experiment from a saved
accessing file from a Thermo Fisher™ Connect account, USB, file” on page 30.
experiment and instrument folder, or network drive.
template files
Open Template – Touch to open a system .edt template “Create and run an experiment from
file. a template” on page 30.

Run Last – Touch to open the last .edt file run on the “Repeat the last instrument run” on
instrument. page 31.
• If you are signed-in, the file opened will be the last
file you ran when signed-in.
• If you are not signed-in, the file opened will be the
last file the guest profile ran.

Connectivity • —The instrument is connected to a wired —

icons network.
• —The instrument is wirelessly connected.
• —A USB drive is plugged into the instrument.
• —The instrument is linked to a Thermo Fisher™
Connect account.

Sign In button • Touch Sign In to sign into an instrument profile “Sign in” on page 25.
and link to a Thermo Fisher™ Connect account.
(My Profile button
when a user is • Touch My Profile to change instrument profile
signed in) settings, link to a Thermo Fisher™ Connect account,
or lock the instrument during a run.

24 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 2 Start, sign on, and configure the instrument
Use the instrument without signing in 2

Use the instrument without signing in

If the instrument is configured by an Administrator to allow guest access ( Settings4Manage
Users4Sign In Required set to off), you can use the instrument without signing in.
The following limits are in place if you do not sign in to the instrument:
• All actions are recorded to Guest user profile.
• You have access only to the Public folder for selecting and storing experiments.
• You cannot transfer data to Thermo Fisher™ Connect (only to USB or network drive).

Create a new instrument profile

1. In the home screen, touch Sign In, then touch Get Started.

2. Touch Name, enter a username, then touch Done.

3. Touch PIN Code, enter a four-digit numerical password, then touch Enter.

Note: Touch the Show PIN checkbox to switch PIN display on or off.

4. Touch Confirm PIN, then repeat step 2.

5. Touch Create profile.

6. Sign in to the profile you just created.

See “Sign in” on page 25.

Note: To enable access to Thermo Fisher™ Connect, see “Link an instrument profile to Thermo Fisher™
Connect” on page 77.

Sign in
Create an instrument profile before signing into the instrument. See “Create a new instrument profile”
on page 25.

Note: An instrument profile is a user account specifically for the instrument. It is not related to any
other user account for the system or software.

1. In the home screen, touch Sign In.

2. Touch Sign In, then select your username.

3. Enter your PIN, then touch Enter.

Note: To enable access to Thermo Fisher™ Connect, see “Link an instrument profile to Thermo Fisher™
Connect” on page 77.

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 25
 Chapter 2 Start, sign on, and configure the instrument
2 Sign out

Sign out
1. In the home screen, touch My Profile.

2. Touch Sign Out.

Configure instrument settings

Touch Settings in the home screen to configure settings as needed.

Touch for step-by-step instructions on configuring settings.

Options Description

Instrument Settings

Instrument Name Instrument name. If connected to a network, the instrument name must be unique.
(Administrator only) (Optional) Add an avatar image for the instrument (.jpg, .png, or .gif) from a USB.

Sleep Mode Enable the instrument to enter a standby mode after a set length of inactivity.

Heated Cover Temperature Set the temperature of the heated cover for instrument operation and standby mode.
Enable heated cover to automatically turn off during standby mode.

Network Drive Specify a default network location for the signed-in user.

Insert Plate Reminder Enable a reminder to insert a plate before starting a run from the instrument.

OEM Connection Only Required for API access to the instrument. When enabled, the desktop cannot
connect to the instrument.
(Administrator only)
API access to the instrument is exclusive to authorized OEM partners.

Cloud Region Specify the regional server location to access Thermo Fisher™ Connect.
(Administrator only) Note: Once you set a region for the cloud platform, restore factory defaults to change
the region.

26 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 2 Start, sign on, and configure the instrument
Configure instrument settings 2

Options Description

Date/Time Set time zone and date and time formats.

Network Connection Set wired or wireless network connection for the instrument.

Restore Factory Defaults Restore the instrument to the factory settings.

IMPORTANT! Back up the instrument before restoring factory defaults (see “Backup
or restore the instrument” on page 67).

Note: When you restore an instrument to its factory defaults:

· User profiles and files stored on the instrument are deleted, including all user-
created .edt and .eds files and any custom dye and custom melt calibrations.
· System templates and factory calibrations remain on the instrument.

SAE Mode When enabled the following items apply:

(Administrator only) • The home screen displays SAE mode.

(QuantStudio™ 5 Instrument • Runs must be started from the desktop software. The instrument locks out
only) access to load experiments, open templates, repeat the last run, start a run,
change the instrument name, and change the date/time.
• Only an administrator can perform calibrations.
• A user can monitor a run and view the method from the instrument touchscreen.

About Instrument

About Instrument Displays the instrument Model Name, Block Serial Number, and Firmware Version.

License Agreement Displays the End User Software License Agreement and the Limited Product Warranty.
You can export the License Agreement to a USB drive.

Notifications

— Enable home screen notifications of instrument errors and software updates. This
function is not related to the Notifications function in the cloud software.
The number of new, unviewed notifications displays over Settings in the home screen.

Maintenance and Service

Software Update Update the instrument software.

(Administrator only)

Monitoring Enable:
(Administrator only) • Remote Monitoring Service to automatically send critical device statistics to
Thermo Fisher Scientific (does not monitor or send data).
• Thermo Fisher Scientific Cloud Monitor to allow real-time monitoring of
instrument runs from a Cloud account.

Instrument Statistics Displays instrument usage information: Block Cycle Count and LED Life.

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 27
 Chapter 2 Start, sign on, and configure the instrument
2 Configure instrument settings

Options Description

Calibrations • Perform calibrations

– ROI and Uniformity
– Dye
– Custom (including Background calibration)
• View calibration history and set calibration reminders in History and Reminders

RNase P Verification Perform instrument verification using an RNase P plate.

Self Verification Test Check the instrument hardware functions.

Log View and export Instrument Log.

Backup / Restore • Backup Instrument

• Restore a Backup (Administrator only)

Ship Prep Mode Place the instrument in a safe state for shipping, moving, or long-term storage.

Run History

— Displays the experiments run on the instrument and whether the data was transferred.
Note: Experiments run while a user is signed-in can only be viewed or transferred by
that user or an administrator.
Touch an experiment to view experiment run details and to transfer or delete .eds file.

Manage Users

Sign In Required Enable the restriction of instrument use to only signed-in users (disables Guest profile
use).
(Administrator only)

Sign Out Timer Set the duration of inactivity before a user is automatically signed out.
(Administrator only)

Manage Profiles • Instrument

(Administrator only) • Cloud

• All Profiles

Displays the profile information for the instrument and the associated Thermo Fisher™
Connect cloud-based account.

28 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 3 Create and run experiments on the
instrument

■ Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
■ Options for running an experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
■ Edit an experiment before starting a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
■ Load and unload the plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
■ View, pause, or stop a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
■ Transfer, view, or manage files and results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Workflow
Start the instrument

(Optional) Sign in to your instrument profile

(Optional) Link to your Thermo Fisher™ Connect account

Load an existing experiment template (EDT file) or

Create an experiment template (EDT file)

Modify experiment settings as needed

Load the plate in the instrument

Start the run from the instrument or the desktop software

(Optional) Monitor the run from Thermo Fisher™ Connect

Transfer results (EDS file) to the desktop software or Thermo Fisher™ Connect, then analyze

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 29
 Chapter 3 Create and run experiments on the instrument
3 Options for running an experiment

Options for running an experiment

Create and run an experiment from a template
In the home screen:

1. Touch Open Template.

2. (Optional) Touch a category in the left column.

3. Touch the file name.

4. (Optional) Enter or edit template properties, including Run File Name (EDS file name), Plate
Barcode, Reagent Information, and Data Destination (see “Enter or edit template properties”).

5. (Optional) Edit the run method (see “Edit the run method” on page 33).
• Add, remove, or edit a step, stage, melt curve, or data collection point.
• Adjust the heated cover temperature, sample volume, or number of cycles.
• Configure VeriFlex™ Zones, ramp rate, and pause settings.

6. (Optional) Define plate wells with sample names and view Well ID, Targets, or Dyes (see “Define,
assign, and view well details”).

7. Load a plate into the instrument (see “Load and unload the plate” on page 37).

8. Touch Start Run.

When prompted, confirm that you inserted a plate.

Note: To disable this reminder, select Do not show again or select Settings4Insert Plate
Reminder in the home screen.

Run an experiment from a saved file

In the home screen:

1. Touch Load Experiment.

2. Touch the appropriate icon to navigate to your file location.

• For files saved to the guest profile, touch My Instrument4Public.
• For pre and post read files, touch My Instrument4Post Read.

3. Touch the file name.

4. (Optional) “Manage templates (EDT files)” in either USB or My Instrument.

5. (Optional) Enter or edit template properties, including Run File Name (EDS file name), Plate
Barcode, Reagent Information, and Data Destination (see “Enter or edit template properties”).

30 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 3 Create and run experiments on the instrument
Options for running an experiment 3

6. (Optional) Edit the run method (see “Edit the run method” on page 33).
• Add, remove, or edit a step, stage, melt curve, or data collection point.
• Adjust the heated cover temperature, sample volume, or number of cycles.
• Configure VeriFlex™ Zones, ramp rate, and pause settings.

7. (Optional) Define plate wells with sample names and view Well ID, Targets, or Dyes (see “Define,
assign, and view well details”).

8. Load a plate into the instrument (see “Load and unload the plate” on page 37).

9. Touch Start Run.

When prompted, confirm that you inserted a plate.

Note: To disable this reminder, select Do not show again or select Settings4Insert Plate
Reminder in the home screen.

Repeat the last instrument run

This feature applies only to runs started from the instrument and is not available for runs started from
the desktop software. If you are signed-in, this feature applies to the last run from your instrument
profile.
In the home screen:

1. Touch Run Last.

2. (Optional) Enter or edit template properties, including Run File Name (EDS file name), Plate
Barcode, Reagent Information, and Data Destination (see “Enter or edit template properties”).

3. (Optional) Edit the run method (see “Edit the run method” on page 33).
• Add, remove, or edit a step, stage, melt curve, or data collection point.
• Adjust the heated cover temperature, sample volume, or number of cycles.
• Configure VeriFlex™ Zones, ramp rate, and pause settings.

4. (Optional) Define plate wells with sample names and view Well ID, Targets, or Dyes (see “Define,
assign, and view well details”).

5. Load a plate into the instrument (see “Load and unload the plate” on page 37).

6. Touch Start Run.

When prompted, confirm that you inserted a plate.

Note: To disable this reminder, select Do not show again or select Settings4Insert Plate
Reminder in the home screen.

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 31
 Chapter 3 Create and run experiments on the instrument
3 Edit an experiment before starting a run

Edit an experiment before starting a run

Enter or edit template properties
Access a template (EDT file). For more information, see the following sections:
• “Create and run an experiment from a template” on page 30.
• “Run an experiment from a saved file” on page 30.
• “Repeat the last instrument run” on page 31.

In the Properties screen, touch Edit to enter or edit template properties.

• Edit the file name for the EDS file for the run.
a. Touch the Run File Name field.

b. Enter the name for the EDS file, then touch Done.

• Enter a plate barcode.

a. Touch the Plate Barcode field.

b. Enter or scan the plate barcode, then touch Done.

• Record reagents and their expiration dates.

a. Touch Reagent Information.

b. Touch Add, or touch an existing reagent, then touch Edit or Delete.

c. Touch the Name, Type, Lot #, Reagent Barcode, Part #, or Expiration Date field to enter
individual reagent information.

d. Touch Done.

• Automatically transfer run data (EDS file) when an instrument run ends.
a. Touch Data Destination.

b. Touch the appropriate icon to select a data destination.

c. Under the desired data destination, select Automatically transfer experiment.

d. Touch Done.

• Enter a comment.
a. Touch Comments.

b. Enter text, then touch Done.

32 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 3 Create and run experiments on the instrument
Edit an experiment before starting a run 3

Scan a barcode using the optional 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.

1. Click the Barcode field.

2. 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.

3. 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 (Lot #, Part #, Expiration Date, etc.)

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

Edit the run method

Access a template (EDT file):
• “Create and run an experiment from a template” on page 30.
• “Run an experiment from a saved file” on page 30.
• “Repeat the last instrument run” on page 31.

For an overview of the method as it is graphically represented on the touchscreen, see “Method
elements” on page 34.
In the Method screen:

1. Touch Edit.

2. Touch a field, enter changes, then touch Enter.

Note: Touch–drag to quickly increase or decrease a step temperature.

3. Touch Manage Steps to add or remove a step, stage, melt curve, or data collection point.

Note: The Manage Steps screen also provides access to configuring VeriFlex™ Zones, Ramp
Rates, and Add Pause settings (see “Configure VeriFlex™ Zones, ramp rates, and pause settings”
on page 35).

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 33
 Chapter 3 Create and run experiments on the instrument
3 Edit an experiment before starting a run

Method elements

2 3

1 Method tab 6 Number of cycles for the stage

2 Heated cover temperature 7 Temperature for the step
3 Reaction volume 8 Hold time for the step
4 Stage of thermal protocol 9 Data collection point
5 Step within a stage

Manage steps, stages, melt curves, and data collection points

Add or remove a step, stage, melt curve, or data collection point using the Manage Steps option.
You can also configure ramp rates and pause settings from the Manage Steps screen (see “Configure
VeriFlex™ Zones, ramp rates, and pause settings” on page 35).

• In the Method screen, touch Edit4Manage Steps.

Option Procedure
1. Touch Add/Remove steps4Add steps.
2. Touch on the left or right border of a step to add a step before or
Add a step after the step, respectively.
3. Enter parameters for the new step, then touch Enter.
4. Touch Done.

1. Touch Add/Remove steps4Remove steps.

Remove a step
2. Touch on the step to be removed, then touch Done.

34 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 3 Create and run experiments on the instrument
Edit an experiment before starting a run 3

(continued)
Option Procedure
1. Touch Add/Remove stages4Add stages.
2. Touch on the left or right border of a stage to add a stage before or
after the stage, respectively.
Add a stage
3. Edit parameters of the new stage in the Method screen. See “Edit the
run method” on page 33.
4. Touch Done.

1. Touch Add/Remove stages4Remove stages.

Remove a stage
2. Touch on the stage to be removed, then touch Done.

1. Touch Melt curves4Add melt curve.

2. Touch on the left or right border of a step to add a melt curve before
or after the step, respectively.
3. Select Continuous or Step and hold.
Add a melt curve 4. Touch melt curve parameters to edit, then touch Done.
5. Touch Done.

Note: Depending on the experiment type, there can be restrictions on the

addition or placement of melt curves.

1. Touch Remove melt curve.

Remove a melt curve
2. Touch on the melt curve to be removed, then touch Done.

Add or remove data 1. Touch Data collection location.

collection points 2. Touch to switch data collection on or off.

Configure VeriFlex™ Zones, ramp rates, and pause settings

In the Method screen, touch Edit4Manage Steps4Advanced Options.

• To use VeriFlex™ Zones (96‑well blocks only):

a. Touch VeriFlex™ Zones.

b. Touch on the step to apply VeriFlex™ Zones.

c. Touch each zone to edit the temperature, then touch Enter.

The background colors of the VeriFlex™ Zones change with the temperature edit. Zones with
higher temperatures display a background brighter than those with lower temperatures.

d. (Optional) Apply additional VeriFlex™ Zones.

e. Touch Done.

• To edit Ramp Rates:

a. Touch Ramp Rates.

b. Touch the ramp rates fields.

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 35
 Chapter 3 Create and run experiments on the instrument
3 Edit an experiment before starting a run

c. Touch Enter.

d. (Optional) Edit additional steps, then touch Done.

• To add a pause into the method:

a. Touch Add Pause.

b. Touch in a stage.

c. Enter the pause temperature, and the cycle after which the pause will occur.

d. Touch Enter.
The pause is represented by a P in the corner of the stage.

e. Touch Done.

Define, assign, and view well details

1. Access a template (EDT file). For more information, see the following sections.
• “Create and run an experiment from a template” on page 30.
• “Run an experiment from a saved file” on page 30.
• “Repeat the last instrument run” on page 31.

2. In the Plate screen, define, assign, and view well details.

Option Procedure
Define and assign samples in the 1. Touch .
plate layout view
2. Touch Manage or touch an individual well.
3. Touch the Samples subtab.
4. Select one or more wells, then touch Edit.
5. Enter sample names for the selected wells, then touch Done.

Define and assign samples in the 1. Touch .

well table view
2. Touch Edit to edit sample names for individual wells.
3. Touch a sample name field, enter a new name, then touch
Done.

View target information 1. Touch .

2. Touch Manage or touch an individual well.
3. Touch the Targets subtab.
4. Touch Details to view target information, then touch Done.

3. Touch Done to return to the Plate tab.

36 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 3 Create and run experiments on the instrument
Load and unload the plate 3

Load and unload the plate

If a compression pad is not used, see “Load and unload a plate in the instrument” on page 37.
A compression pad is needed for some applications with a 96-well 0.2-mL MicroAmp plate.
See your product documentation to confirm if the use of a compression pad is required.
To load and unload the plate, see “Load and unload a plate in the instrument with a compression pad”
on page 38.

Load and unload a plate in the instrument

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

1. Load the plate.

a. Touch to eject the instrument drawer.

b. Load the plate onto the plate adaptor so that the following criteria are met.
• Position well A1 of the plate in the top-left corner of the plate adapter.
• Ensure that the barcode faces the front of the instrument.

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

Note: (For 96-well 0.2-mL blocks only) Do not remove the black plate adapter before loading
a plate or tube strips. If used, tube strips can fit loosely in the adapter, but the heated cover
will apply the appropriate pressure to seat the tube strips securely in the adapter.

Note: The 384-well and 96-well Fast (0.1-mL) block configurations do not require a plate
adapter.

c. Touch to close the instrument drawer.

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 37
 Chapter 3 Create and run experiments on the instrument
3 Load and unload the plate

2. When the run ends, unload the plate.

a. Touch to eject the instrument drawer.

b. Remove the plate.

c. Touch to close the instrument drawer.

CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the plate temperature
can reach 100°C. Allow it to cool to room temperature before handling.

Note: If the instrument does not eject the plate, contact Support.

Load and unload a plate in the instrument with a compression pad

Some applications use a compression pad for a 96-well 0.2-mL MicroAmp plate.

1. Load the plate.

a. Touch to eject the instrument drawer.

b. Load the plate onto the plate adaptor so that the following criteria are met.
• Position well A1 of the plate in the top-left corner of the plate adapter.
• Ensure that the barcode faces the front of the instrument.

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

Note: (For 96-well 0.2-mL blocks only) Do not remove the black plate adapter before loading
a plate or tube strips. If used, tube strips can fit loosely in the adapter, but the heated cover
will apply the appropriate pressure to seat the tube strips securely in the adapter.

38 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 3 Create and run experiments on the instrument
Load and unload the plate 3

c. Before loading the plate in the drawer, place the MicroAmp™ Optical Film Compression Pad
with the gray side down on the surface of the plate to ensure a proper seal between the
instrument and the adhesive film.

IMPORTANT! Be careful to place the compression pad with the brown side up and the
gray side down, centered on top of the plate. Ensure that the compression pad is free from
wrinkles and signs of deterioration prior to use.

d. Touch to close the instrument drawer.

2. When the run ends, unload the plate.

a. Touch to eject the instrument drawer.

b. Remove the plate.

c. Touch to close the instrument drawer.

d. Remove the MicroAmp™ Optical Film Compression Pad from the plate and store it inside the
pack.
IMPORTANT!
· If the compression pad becomes stuck inside the instrument, call service to clean the
heated cover.
· Between each use, place the pad back in the pouch so that it does not dry out.
· Each compression pad may be used up to 20 times before discarding. Do not use more
than 20 times.

CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the plate temperature
can reach 100°C. Allow it to cool to room temperature before handling.

Note: If the instrument does not eject the plate, contact Support.

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 39
 Chapter 3 Create and run experiments on the instrument
3 View, pause, or stop a run

View, pause, or stop a run

Do any of the following actions during an instrument run.
• View real-time data and plots (see “View real-time data and plots on the instrument touchscreen”
on page 40).
• Adjust the display of real-time plots (see “Adjust the display of real-time plots on the instrument
touchscreen” on page 41).
– Touch or swipe left once to view real‑time run method information or to edit the number of
cycles.
– Touch or swipe left twice to view real‑time data and plots.
• Pause or stop an instrument run (see “Pause or stop an instrument run” on page 40).

View real-time data and plots on the instrument touchscreen

1. In the instrument home screen, during an instrument run, touch or swipe left twice.

2. Touch Well details.

3. Touch Samples, Targets, or Tasks to select a graphical representation of each selection.

4. Touch Close to return to the home screen.

Pause or stop an instrument run

In the home screen, during an instrument run:

1. Touch or swipe left once to view real‑time run method information.

2. Stop or pause the run.

• Touch Stop Run.
• Touch Pause, then enter a pause temperature.

CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the plate temperature
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.

3. (Optional) After pausing a run, touch Edit to change the number of cycles.

40 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 3 Create and run experiments on the instrument
Transfer, view, or manage files and results 3

Adjust the display of real-time plots on the instrument touchscreen

1. In the instrument home screen, during an instrument run, touch or swipe left twice to view
real-time data and plots.

2. Touch Zoom.

3. Touch or to zoom in or out.

4. Touch the arrows to pan left, right, up, or down on the graph.

5. Touch Close to return to the default view.

Lock 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.

Note: You must be signed-in to use this feature.

1. Lock the touchscreen.

a. In the home screen, touch My Profile.

b. Touch Lock Screen, then touch Lock.

2. Unlock the touchscreen.

a. Touch anywhere on the touchscreen.

b. Touch the PIN Code field, then enter your PIN.

Note: The touchscreen automatically unlocks when the run is complete.

Transfer, view, or manage files and results

Transfer EDS files from the instrument home screen
1. In the home screen, when a run ends, touch Transfer File.

2. Select the data destination for the EDS file.

3. Navigate to and select a folder.

4. Touch OK.

5. Touch Transfer.

Note: Touch Settings4Run History to transfer EDS files at any time.

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 Chapter 3 Create and run experiments on the instrument
3 Transfer, view, or manage files and results

View run history and delete or transfer files from the instrument
In the home screen, touch Settings4Run History.

• Touch an individual run record to view its details, then complete one of the following actions:
– Touch Delete to delete the run record.
– Touch Transfer to export the run data.
• Touch Manage to select multiple run records for simultaneous viewing, deletion, or transfer.

Note:
· Guests (users not signed-in) can only view guest run records.
· Users signed into their instrument profiles can also view their own run records.
· Administrators can view all run records.

Note: If the connection between the instrument and the desktop software is interrupted during the run,
the instrument still completes the run. However, the run data (EDS file) must be transferred from the
instrument to the desktop software using a USB drive or a network drive.

Manage templates (EDT files)

This feature applies to templates (EDT files) on a USB or in My Instrument. To manage run
results files (EDS files), see “Transfer EDS files from the instrument home screen” on page 41.

1. In the home screen, touch Load Experiment.

2. Touch USB or My Instrument.

3. Touch Manage Files.

4. (Optional) Navigate through the My Instrument, Public, USB, and Post Read folders to access an
EDT file. Folder availability depends on your sign-in status.

5. Touch one or more files to select for managing.

6. Delete or copy the files.

• Touch Delete Files, then confirm deletion.
• Touch Copy Files, select a file destination, then touch Paste Files.

7. Touch Done.

42 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 4 Calibrate and verify instrument
performance

■ Calibration and verification schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

■ Calibration descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
■ View the calibration status and set reminders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
■ Perform ROI/uniformity, background, and dye calibrations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
■ Perform instrument verification using RNase P plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
■ Calibrate custom dyes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
■ Calibrate for a custom melt curve experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Calibration and verification schedule

The instrument is factory-calibrated and does not require calibration at installation. To ensure optimal
performance, perform calibrations at the recommended frequency.

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

IMPORTANT! Perform calibrations and instrument runs under the environmental conditions that
are specified in “Environmental requirements” on page 108. Exposure to extreme temperatures can
adversely affect the instrument performance and shorten the life span of the instrument components.

To set the calibration frequency for the instrument, touch Settings4Maintenance and
Service4Calibrations4History and Reminders4Edit4Exp interval field.

Calibration Recommended frequency

ROI/Uniformity • Every two years (recommended)

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

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

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 43
 Chapter 4 Calibrate and verify instrument performance
4 Calibration descriptions

(continued)

Calibration Recommended frequency

Background • Every two years (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 • 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.

RNase P instrument • After installing or moving the instrument

verification • After performing instrument calibrations (recommended)
• As needed to confirm instrument performance

Note: To prepare custom dye plates and to perform custom calibrations, see “Calibrate custom dyes”
on page 59.

Calibration descriptions
Calibration description and purpose Pass Criteria

ROI/Uniformity

• The software captures images for each optical filter. The image for each filter
• The software uses calibration data to map the increase in fluorescence distinguishes all wells of the plate.
to the plate wells during subsequent runs and to evaluate well-to-well Each well in the image is distinct.
consistency of the signals.

Background

• The software captures background images for each optical filter in the The plate images for all filters are free
absence of sample and reagent, and it checks that the fluorescence of abnormal 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.

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View the calibration status and set reminders 4

(continued)
Calibration description and purpose Pass Criteria

Dye

• The software extracts a spectral profile for each dye standard, then Dye spectra peak within the same
produces a set of spectral profiles plotted as fluorescence vs filter. filter as their group.
• The software uses calibration data to characterize and distinguish the
individual contribution of each dye in the total fluorescence signals
collected by the instrument.

View the calibration status and set reminders

View calibration status and set reminders in the instrument
1. In the home screen, touch Settings4Maintenance and Service4Calibrations4History and
Reminders.

2. In the Calibration Reminders screen, view the status of each calibration type.

3. (Optional) Touch a calibration row to view the history of that specific calibration type, then touch
Done.

4. Touch Edit to set the calibration reminder settings. For each calibration type:
a. Slide the control On to enable the calibration reminder.

b. Edit the Exp interval and Remind me fields.

c. Touch Save.

5. (Optional) To transfer the calibration report, touch Export then follow the directions on the screen.

6. Touch Done.

View calibration status and set reminders in Thermo Fisher™ Connect

Note: The calibration reminders feature requires a connection between the instrument and a computer
network.

1. In Thermo Fisher™ Connect, click for the Instrument Connect page.

2. Select any of your registered instruments.

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 Chapter 4 Calibrate and verify instrument performance
4 Perform ROI/uniformity, background, and dye calibrations

3. In the Summary tab:

• Click Calibrations to view the status of each calibration type.
• (Optional) Click Calibration Reminders to set the calibration reminder time table and enter
the notification email address(es).

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

Note: The settings are automatically saved.

• (Optional) In the Downloads section, click Maintenance Summary.pdf to download the
calibration status report.

4. In the Calibrations History tab:

• View the history of each calibration type.
• (Optional) Click to download the calibration history report.

Perform ROI/uniformity, background, and dye calibrations

Workflow: Calibration
Note: The ROI and uniformity calibrations use the same calibration plate.

Perform an ROI calibration

Perform a uniformity calibration

You are automatically prompted to perform background calibration.

Perform a background calibration

Perform any time that ROI calibrations are current.

Perform system dye calibrations

Perform any time that ROI and background calibrations are current.

(Optional ) Perform custom dye calibrations (“Calibrate custom dyes” on page 59)
Perform any time that ROI and background calibrations are current.

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Prepare a calibration plate

Materials required for calibration plate preparation
• Plate(s) for the calibration that you are performing:
– ROI plate (the same plate is used for ROI and uniformity calibrations)
– Background calibration plate
– Dye 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.

Note: Do not discard the packaging for the calibration plates. Each calibration plate can be used
up to 3 times if the following conditions are met:
· The plate is stored in its packing sleeve at –15 to –25°C.
· The plate is used within 6 months after opening.
· The plate is used before the plate expiry date

• Centrifuge with plate adapter; buckets cleaned before use

• Powder‐free gloves
• Safety glasses

Thaw, vortex, and centrifuge a calibration plate

1. Remove the calibration plate from the freezer, then thaw the plate in its packaging. Keep plates
protected from light until you perform the calibration.
• Thaw each plate for 30 minutes.
• Use each plate within 2 hours of thawing.

IMPORTANT! Do not remove the plate from its packaging until you are ready to use it. The
fluorescent dyes in the wells of calibration plates are photosensitive. Prolonged exposure to light
can diminish the fluorescence of the dyes.

2. While wearing powder‐free gloves, remove the calibration plate from its packaging and retain the
packaging. Do not remove the optical film.

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

4. 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.

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IMPORTANT! Keep the bottom of the plate clean. Fluids and other contaminants on the bottom
of the plate can contaminate the sample block and cause an abnormally high background signal.

Perform calibrations
1. In the instrument home screen:

Calibration Touch
ROI/Uniformity[1] Settings4Maintenance and Service4Calibrations4ROI and Uniformity
Background[2] Settings4Maintenance and
Service4Calibrations4Custom4Background
Dye Settings4Maintenance and Service4Calibrations4Dye
[1] Automatically followed by Background calibration.
[2] Initiate via this route if performing Background calibration only.

2. Follow the instructions on the screen to start the calibration.

Note: Dye calibration only: Select the Dye Plate to run, then touch Next.

3. Load the plate.

a. Touch to eject the instrument drawer.

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b. Load the plate onto the plate adaptor so that the following criteria are met.
• Position well A1 of the plate in the top-left corner of the plate adapter.
• Ensure that the barcode faces the front of the instrument.

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

Note: (For 96-well 0.2-mL blocks only) Do not remove the black plate adapter before loading
a plate or tube strips. If used, tube strips can fit loosely in the adapter, but the heated cover
will apply the appropriate pressure to seat the tube strips securely in the adapter.

Note: The 384-well and 96-well Fast (0.1-mL) block configurations do not require a plate
adapter.

c. Touch to close the instrument drawer.

4. Touch Start.

5. When the run is complete and the screen displays Calibration Complete, touch View Results to
check the calibration status.

Calibration status Action

Passed Touch Next to proceed to the next required calibration.
Failed See “Troubleshoot calibration failure” on page 51.

Note: You can view the calibration images only after the ROI/Uniformity and Background
calibrations pass.

6. When the run ends, unload the plate.

a. Touch to eject the instrument drawer.

b. Remove the plate.

c. Touch to close the instrument drawer.

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CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the plate temperature
can reach 100°C. Allow it to cool to room temperature before handling.

Note: If the instrument does not eject the plate, contact Support.

7. Return the plate to its original packaging.

Note: Each calibration plate can be used up to 3 times if the following conditions are met:
· The plate is stored in its packing sleeve at –15 to –25°C.
· The plate is used within 6 months after opening.
· The plate is used before the plate expiry date

View calibration images and transfer results to USB

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

1. In the Calibration Status screen, touch Details.

2. In the Details screen, touch a calibration type to view its images and plots.

Calibration Example results indicating successful calibration

ROI Green circles around all wells and bright well centers.
Note: Select the desired filter
combination from the Filter Set
dropdown list.

Uniformity Signals from each well following a uniform trend.

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(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 correct filter.

3. In the Calibration Status screen, touch Accept Results or Reject Results.

Accepting the results saves the calibration data to the instrument and overwrites existing data.

4. (Optional) Touch Transfer EDS to transfer the calibration data to a USB.

Troubleshoot calibration failure

Observation Possible cause Recommended action

Calibration failed The plate was improperly Ensure the following:
prepared. • The correct plate was used for the
calibration performed.
• The plate was properly thawed.
• The plate was properly centrifuged.
• The plate was properly sealed.
The plate is damaged or Check for damage, improper plate seal, or
contaminated. contamination.
Order a replacement plate. If the replacement
plate fails, contact Support.
High fluorescence signal in Signals that exceed the See “Identify contamination” on page 52.
individual wells limit of normal fluorescence
may indicate fluorescent
contaminants on the plate or
the sample block.
Calibration failed but plate is The incorrect plate was used Use the plate that matches the calibration
undamaged for calibration performed. performed.

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Observation Possible cause Recommended action

Calibration failed but plate is The plate was improperly Repeat the calibration with the plate properly
undamaged prepared. prepared.
(continued)
If the calibration fails again, order a
replacement plate. If the replacement plate
fails, contact Support.

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.

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

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

3. 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 68).
Reversed The plate is contaminated.
Discard the plate, then perform the calibration using a new
calibration plate.

4. If the calibration fails after you decontaminate the sample block and replace the plate, contact
Support.

Create a background plate (optional)

Whenever possible, use a background plate listed in Appendix C, “Parts and materials”. These plates
contain a buffer 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! Wear powder-free gloves while creating the background plate.

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1. Remove a reaction plate from its box and place it on a clean, dry surface.

2. Aliquot deionized water to each well of the reaction plate.

The recommended volume for a 96-well plate is 10-20 µL.
The recommended volume for 384-well plate is 5 µL.

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

4. Use the plate for background calibration.

Perform instrument verification using RNase P plates

Instruments are factory-calibrated, so calibration is not necessary for initial installation. However,
perform instrument verification:
• After installation and before first use of the instrument.
• After performing instrument calibrations. (recommended)
• As needed to confirm instrument performance after calibrations, repair, preventative maintenance,
or change to the system.

The instrument requires valid ROI/uniformity, background, and dye calibrations to perform instrument
verification.

Instrument verification description

Purpose Description Pass criteria

Confirms the Quantifies the number of copies of The instrument passes performance specifications
performance of the the human RNase P gene in samples if the following inequality is true and the
instrument. with known concentrations of the instrument successfully distinguishes between
corresponding DNA template. unknown populations A and B.
[(CtA) – 3(σCtA)] > [(CtB) + 3(σCtB)]
where:
• CtA = Average Ct of unknown population A
• σCtA = Standard deviation of unknown
population A
• CtB = Average Ct of unknown population B
• σCtB = Standard deviation of unknown
population B

RNase P instrument verification plate

The RNase P plate contains the reagents necessary for the detection and quantitation of genomic
copies of the human RNase P gene (a single-copy gene encoding the RNase moiety of the RNase P
enzyme). Each well contains: PCR master mix, RNase P primers, FAM™ dye-labeled probe, and a
known concentration of human genomic DNA template.

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 Chapter 4 Calibrate and verify instrument performance
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2 3 4

5 6 7

Figure 1 96-well RNase P plate

1 Unknown A (5,000) 5 STD 5,000 copies
2 NTC (no template control) 6 STD 10,000 copies
3 STD 1,250 copies 7 STD 20,000 copies
4 STD 2,500 copies 8 Unknown B (10,000)

1 3 5

7 8

2 4 6

Figure 2 384-well RNase P plate

1 NTC (no template control) 5 STD 10,000 copies
2 STD 1,250 copies 6 STD 10,000 copies
3 STD 2,500 copies 7 Unknown A (5,000)
4 STD 5,000 copies 8 Unknown B (10,000)

54 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
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Performance specifications pass criteria

After the run, the software calculates average copy number values and standard deviation values.
The instrument passes performance specifications if the following inequality is true and the instrument
successfully distinguishes between unknown populations A and B.
[(CtA) – 3(σCtA)] > [(CtB) + 3(σCtB)]
• CtA = Average Ct of unknown population A
• σCtA = Standard deviation of unknown population A
• CtB = Average Ct of unknown population B
• σCtB = Standard deviation of unknown population B

The software automatically adjusts the threshold and omits a defined number of wells from the
unknown populations to meet the performance specifications. To view any omitted wells, open the
EDS file for the verification in the desktop software.

Prepare an RNase P plate

Materials required for RNase P plate preparation
• RNase P instrument verification plate
• Centrifuge with plate adapter; buckets cleaned before use
• Powder‐free gloves
• Safety glasses

Thaw, vortex, and centrifuge an RNase P plate

IMPORTANT! Expose the RNase P plate to room temperature for no more than 45 minutes, inclusive
of thawing and preparation time.
After thawing, the RNase P plate cannot be refrozen.

1. Remove the RNase P plate from the freezer, then thaw the plate in its packaging.
• Thaw the plate for approximately 5 minutes.
• Use the plate within 30 minutes of thawing.

2. Confirm that the bench, vortex, and centrifuge are clean. Before use, wipe the vortex and
centrifuge using a lint‑free tissue.

3. While wearing powder‐free gloves, remove the plate from its packaging.

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

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5. 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.

IMPORTANT! Keep the bottom of the plate clean. Fluids and other contaminants on the bottom
of the plate can contaminate the sample block and cause an abnormally high background signal.

Perform RNase P verification

1. In the home screen, touch Settings4Maintenance and Service4RNase P Verification.

2. Load the plate.

a. Touch to eject the instrument drawer.

b. Load the plate onto the plate adaptor so that the following criteria are met.
• Position well A1 of the plate in the top-left corner of the plate adapter.
• Ensure that the barcode faces the front of the instrument.

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

Note: (For 96-well 0.2-mL blocks only) Do not remove the black plate adapter before loading
a plate or tube strips. If used, tube strips can fit loosely in the adapter, but the heated cover
will apply the appropriate pressure to seat the tube strips securely in the adapter.

Note: The 384-well and 96-well Fast (0.1-mL) block configurations do not require a plate
adapter.

c. Touch to close the instrument drawer.

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3. Touch Start.

4. When the run is complete and the screen displays Verification Complete, touch View Results to
confirm the status of the run.

Calibration status Action

Passed Instrument is ready for use.
Failed See “Troubleshoot verification failure” on page 57.

5. In the RNase P Verification Status screen, touch:

• Accept Results to save the results to the instrument
• Reject Results to delete the RNase P verification results
• Export Results to export the calibration results to a USB

6. When the run ends, unload the plate.

a. Touch to eject the instrument drawer.

b. Remove the plate.

c. Touch to close the instrument drawer.

CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the plate temperature
can reach 100°C. Allow it to cool to room temperature before handling.

Note: If the instrument does not eject the plate, contact Support.

Troubleshoot verification failure

Observation Possible cause Recommended action

Verification failed The plate was improperly Ensure the following:
prepared. • The correct plate was used for the
verification performed.
• The plate was properly thawed.
• The plate was properly centrifuged.
• The plate was properly sealed.
Open the data file for the verification in the
desktop software or Thermo Fisher™ Connect
to view the flags and troubleshooting details
for failed wells.
The plate is damaged or Check for damage, improper plate seal, or
contaminated. contamination.
Order a replacement plate. If the replacement
plate fails, contact Support.

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Observation Possible cause Recommended action

High fluorescence signal The reaction volume is not Ensure that reaction volumes in the plate are
correct. correct and match the volume that is entered
in the Method tab.
Signals that exceed the Examine the bottom of the reaction plate. If
limit of normal fluorescence there is contamination, prepare a new plate
may indicate fluorescent and run the experiment again.
contaminants on the plate or Identify the location of contamination on the
the sample block. plate or sample block.
1. Obtain a background plate.
2. Follow the procedures that are described
in “Identify contamination” on page 52.
Verification failed but plate is The incorrect plate was used Use the correct RNase P plate for verification.
undamaged for verification.
The plate was improperly Repeat the verification with a new properly
prepared. prepared plate.
Note: The verification procedure is an
experiment run, so each RNase P plate can
only be used once.
Open the data file for the verification in the
desktop software or Thermo Fisher™ Connect
to view the flags and troubleshooting details
for failed wells.
If the verification fails again, order a
replacement plate. If the replacement plate
fails, contact Support.

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Calibrate custom dyes 4

Calibrate custom dyes

Custom dyes overview
The instrument can run assays designed with custom dyes. Custom dyes include:
• Dyes that are not manufactured by Thermo Fisher Scientific.
• Dyes or formulations of dyes that are not system dyes for the instrument.
• For custom dye requirements, see “Custom dyes” on page 13.

Workflow: Custom dye calibration

For each custom dye, determine the optimal dye concentration. Use this concentration to prepare all
subsequent dye calibration plates.

Use a dilution series to determine an optimal custom dye concentration

Prepare a custom dye dilution plate

Run the dilution plate as an experiment

Determine the optimal dye concentration

Calibrate the custom dye using the optimal concentration

Create a custom dye calibration plate

Add a custom dye to the instrument

Perform a custom dye calibration

Use a dilution series to determine an optimal custom dye concentration

Custom dye dilution guidelines
Prepare a dilution series for each custom dye.
• Target several dye concentrations within a range of 100–2,000 nM.
• Choose a 2‑ or 3‑fold difference in dilution points.
• Dispense 10–20 µL per well for 96‑well plates or 5 µL per well for 384‑well plates.
• Dilute the dye in buffer compatible with your master mix.
• (Intercalating dyes only) Add the appropriate amount of amplified PCR product to generate
fluorescence.

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Prepare a custom dye dilution plate

IMPORTANT! Wear powder-free gloves throughout the procedure.

1. Prepare a 2- or 3-fold dilution series of the custom dye.

2. Dispense aliquots of each dilution into the center of a reaction plate, then seal the plate.
A full plate is not needed. See the following figures for suggested replicates.
100 nM

200 nM

400 nM

800 nM

1600 nM
100 nM
200 nM
400 nM
800 nM
1600 nM

100 nM
200 nM
400 nM
800 nM
1600 nM

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

4. 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.

IMPORTANT! Keep the bottom of the plate clean. Fluids and other contaminants on the bottom
of the plate can contaminate the sample block and cause an abnormally high background signal.

60 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 4 Calibrate and verify instrument performance
Calibrate custom dyes 4

Run the dilution plate as an experiment

1. Load the plate into the instrument.

CAUTION! The instrument should be used by trained operators who have been warned of the
moving parts hazard.

2. Set up a genotyping experiment on the instrument.

• Load an experiment created in the desktop or cloud software.
a. In the home screen, touch Load Experiment.
b. Select the experiment location, then the experiment file.
• Create a new experiment on the instrument touchscreen.
a. In the home screen, touch Open Template4Genotyping4Genotyping Post.
b. (Optional) In the Properties tab, edit the experiment properties.
c. In the Method tab, set the hold temperature to 60°C with a 2 minute hold and enter the
appropriate reaction volume.
d. In the Plate tab, enter the dilution series information for the appropriate wells.

3. Touch Start Run.

4. When the run is complete, download the results for analysis.

5. Unload the plate from the instrument.

CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the plate temperature
can reach 100°C. Allow it to cool to room temperature before handling.

Note: If the instrument does not eject the plate, contact Support.

Determine the optimal dye concentration

Review the dye signal data and select the dilution to use for dye calibration.

1. In the Results tab of the desktop or cloud software, select Raw Data Plot.
This plot displays the raw fluorescence signal of each optical filter, for individual wells.

Note: The Raw Data Plot cannot be viewed on the instrument touchscreen.

2. For each replicate population of dilutions, select the wells in the Plate Layout to view in the plot.

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 Chapter 4 Calibrate and verify instrument performance
4 Calibrate custom dyes

3. Examine the raw data to identify the wells yielding signals according to the ranges shown in the
following table.

Plate type Acceptable signal range[1]

96-well 800,000 to 3,200,000
384-well 400,000 to 2,000,000
[1] Signal range for the optical filter where the dye is brightest.

4. (Optional) Export the raw data, then calculate the average fluorescence value for each
concentration.

5. Select the lowest (optimal) dye concentration that falls within the acceptable signal range.

Calibrate the custom dye

Create a custom dye calibration plate
IMPORTANT! Wear powder-free gloves while creating the dye plate.

Create a full plate of the custom dye diluted to the optimal concentration:

1. Dilute the custom dye to the optimal concentration in buffer.

Prepare an adequate volume, using a volume range of 10–20 µL/well for a 96‑well plate or
5 µL/well for a 384-well plate.

2. Pipet the appropriate volume of the diluted custom dye to the plate wells.

3. Seal the plate.

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

5. 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.

IMPORTANT! Keep the bottom of the plate clean. Fluids and other contaminants on the bottom
of the plate can contaminate the sample block and cause an abnormally high background signal.

62 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 4 Calibrate and verify instrument performance
Calibrate custom dyes 4

Add a custom dye to the instrument

1. In the instrument home screen, touch Settings4Maintenance and
Service4Calibrations4Custom4Custom Dye.

2. Touch Add Custom Dye.

3. Enter the dye information:

Field/option Action
Custom Dye Name Enter a name for the custom dye.
IMPORTANT!
· Do not use a system dye name for a custom dye name.
· Dye names are spacing sensitive and cannot contain special characters.

Type Select:
• Reporter—The dye works in conjunction with a quencher dye to report an
increase of PCR product.
• Quencher—The dye suppresses the fluorescence of a reporter dye until
amplification of PCR product.
• Both—The dye can be used as a reporter or quencher dye.

4. Touch Save.

IMPORTANT! You must also add the custom dye to the desktop software dye library before
creating, running, or analyzing experiments that use the custom dye. For detailed information, see
the QuantStudio™ Design and Analysis Desktop Software User Guide.

Perform a custom dye calibration

1. Load the plate into the instrument.

CAUTION! The instrument should be used by trained operators who have been warned of the
moving parts hazard.

2. In the instrument home screen, touch Settings4Maintenance and

Service4Calibrations4Custom4Custom Dye.

3. Touch the custom dye to calibrate.

4. Review the custom dye information, (optional) make changes, then touch Update.

5. Enter the calibration temperature.

6. (Optional) Touch Reagents, then enter reagent information.

7. Touch Start.

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 Chapter 4 Calibrate and verify instrument performance
4 Calibrate custom dyes

8. When the run is complete and the screen displays Calibration Complete, touch View
Results4Details.

9. Review the plot. Passing calibration results show uniform signals with peaks that are aligned with
the dye wavelength.

Filter wavelength (nm)[1]

Peak filter
Excitation Emission
x1-m1 470 ± 15 520 ± 15
x2-m2 520 ± 10 558 ± 12
x3-m3 550 ± 10 587 ± 10
x4-m4 580 ± 10 623 ± 14
x5-m5 640 ± 10 682 ± 14
x6-m6 662 ± 10 711 ± 12
[1] The central wavelengths are the optimized wavelengths.

Note: Example dye calibration plot.

The peaks for your dye may align with a different filter set.

10. Select an action depending on whether the custom dye calibration passed or failed.

Calibration status Action

Passed • Touch Accept Results or Reject Results.
Note: Accepting the results saves the calibration data to the instrument
and overwrites existing data.
• (Optional) Touch Transfer EDS to transfer the calibration data to a USB.

Failed • Perform the calibration again using a new custom dye plate.
• See “Troubleshoot calibration failure” on page 51.

11. Unload the plate from the instrument.

CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the plate temperature
can reach 100°C. Allow it to cool to room temperature before handling.

Note: If the instrument does not eject the plate, contact Support.

64 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 4 Calibrate and verify instrument performance
Calibrate for a custom melt curve experiment 4

Calibrate for a custom melt curve experiment

Note: A custom melt calibration calibrates a custom dye and a melt calibration at the same time.

Before running the custom melt calibration:

• Ensure that all calibrations are current (touch Settings4Maintenance and
Service4Calibrations4History and Reminders).
• “Add a custom dye to the instrument” on page 63.

In the home screen:

1. Touch Settings4Maintenance and Service4Calibrations4Custom4Custom Melt.

2. Touch PCR + Melt or Melt only as appropriate for the kit you are using.

3. Load the plate into the instrument.

4. Select or add a dye, then select a filter set appropriate for your dye's wavelength (see filter-
wavelength table below).

Note: Refer to your reagent kit documentation for dye name and wavelength information.

Filter wavelength (nm)[1]

Peak filter
Excitation Emission
x1-m1 470 ± 15 520 ± 15
x2-m2 520 ± 10 558 ± 12
x3-m3 550 ± 10 587 ± 10
x4-m4 580 ± 10 623 ± 14
x5-m5 640 ± 10 682 ± 14
x6-m6 662 ± 10 711 ± 12
[1] The central wavelengths are the optimized wavelengths.

IMPORTANT! If the selected filter set does not match your reagent kit documentation, then the
incorrect wavelength may be collected during a run.

5. (Optional) Touch Reagents, then enter reagent information.

6. Touch Start.

7. When the run is complete and the screen displays Calibration Complete, touch View
Results4Details.

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 Chapter 4 Calibrate and verify instrument performance
4 Calibrate for a custom melt curve experiment

8. Review the plot. Passing calibration results show uniform signals with peaks that are aligned with
the dye wavelength.

Note: Example dye calibration plot.

The peaks for your dye may align with a different filter set.

9. Select an action depending on whether the custom dye calibration passed or failed.

Calibration status Action

Passed • Touch Accept Results or Reject Results.
Note: Accepting the results saves the calibration data to the instrument
and overwrites existing data.
• (Optional) Touch Transfer EDS to transfer the calibration data to a USB.

Failed • Perform the calibration again using a new custom dye plate.
• See “Troubleshoot calibration failure” on page 51.

10. Unload the plate from the instrument.

Note: You must also add the custom dye to the desktop software dye library before creating, running,
or analyzing experiments that use the custom dye. For detailed information, see the QuantStudio™
Design and Analysis Desktop Software User Guide.

Note: To perform a custom melt experiment, you can either create a Standard Curve or a Custom
experiment with melt, then specify the data points per degree in the method.

66 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 5 Maintain the instrument

■ Backup or restore the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

■ Decontaminate the sample block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
■ Replace the instrument fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
■ Power on or off, store, and move . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

IMPORTANT! This chapter contains user maintenance procedures for the instrument. Procedures
other than those described in this document must be performed by a qualified Thermo Fisher Scientific
service representative.

Backup or restore the instrument

In the home screen, touch Settings4Maintenance and Service4Backup/Restore.

To Action
Backup 1. Touch Backup Instrument.
2. Select a location to store the backup settings for your instrument.
3. If backing up to a USB drive, insert a USB drive into the front-panel USB
port.
4. Enter a backup file name, then touch Done.
5. Select the elements to backup, or leave them all selected.
6. Touch Backup.

Restore (Administrator 1. Touch Restore a Backup.

only)
2. Select the storage location of the backup settings.
3. If restoring from a USB drive, insert a USB drive into the front-panel USB
port.
4. Select the backup file, then touch Restore.

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 Chapter 5 Maintain the instrument
5 Decontaminate the sample block

Decontaminate the sample block

Perform this procedure to eliminate fluorescent contaminants from the instrument sample block.
Contamination is generally evident in failed background calibrations where one or more wells
consistently exhibit abnormally high signals.

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 Support.

CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the sample block
temperature can reach 100°C. Allow it to cool to room temperature before handling.

CAUTION! Before using a cleaning or decontamination method other than those recommended by
Thermo Fisher Scientific, confirm with Thermo Fisher Scientific that the proposed method will not
damage the equipment.

Materials required
• Safety glasses
• Powder-free gloves
• Tissue, lint-free
• Cotton or nylon swabs and lint-free cloths
• Pipette (100-µL) with pipette tips
• Deionized water
• Ethanol, 95% solution
• Na-hypochlorite, (0.1% v/v) solution

Clean the sample block

CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the sample block
temperature can reach 100°C. Allow it to cool to room temperature before handling.

IMPORTANT! Wear powder-free gloves when you perform this procedure.

IMPORTANT! Always use deionized water to rinse wells after cleaning with bleach or ethanol solution.

1. Identify the contaminated wells of the sample block (see “Identify contamination” on page 52).

2. Prepare the instrument and access the sample block:

a. Power off and unplug the instrument, then allow it to cool for 15 minutes.

68 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 5 Maintain the instrument
Decontaminate the sample block 5

b. Touch to eject the instrument drawer.

3. Rinse the contaminated wells with deionized water (see “Detailed procedures for cleaning the
sample block” on page 70).

4. Close the drawer and test the sample block for contamination:
a. Push the instrument drawer back in to the instrument.

b. Plug in, then power on the instrument.

c. Perform a background calibration to confirm that you have eliminated the contamination.

5. If the contamination remains, clean the contaminated wells using a 95% ethanol solution:
a. Repeat step 2 – step 3.

b. Clean the contaminated wells using a 95% ethanol solution (see “Detailed procedures for
cleaning the sample block” on page 70).

c. Repeat step 3 – step 4 to rinse the sample block with deionized water and to confirm that you
have eliminated the contamination.
IMPORTANT! Always use deionized water to rinse wells after cleaning with bleach or ethanol
solution.

6. If the contamination still remains, clean the contaminated wells using a Na-hypochlorite (0.1% v/v)
solution:
a. Repeat step 2 – step 3.

b. Clean the contaminated wells using a Na-hypochlorite (0.1% v/v) solution (see “Detailed
procedures for cleaning the sample block” on page 70).

c. Repeat step 3 – step 4 to rinse the sample block with deionized water and to confirm that you
have eliminated the contamination.
IMPORTANT! Always use deionized water to rinse wells after cleaning with Na-hypochlorite
or ethanol solution.

7. If the contamination continues to remain, contact Support.

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 Chapter 5 Maintain the instrument
5 Decontaminate the sample block

Detailed procedures for cleaning the sample block

IMPORTANT! Use these cleaning procedures only in conjunction with the complete decontamination
procedure (see “Clean the sample block” on page 68).

• Rinse the sample block with deionized water.

a. Pipet a small volume of deionized water into each contaminated well.

b. In each well, pipet the water up and down several times to rinse the well.

c. Pipet the water to a waste beaker.

d. Use a cotton swab to scrub inside of each contaminated well.

e. Use a lint-free cloth to absorb the excess deionized water.

• Clean the sample block with 95% ethanol.

a. Pipet a small volume of 95% ethanol solution into each contaminated well.

b. In each well, pipet the solution up and down several times to rinse the well.

c. Pipet the ethanol solution to a waste beaker.

IMPORTANT! Always use deionized water to rinse wells after cleaning with bleach or ethanol
solution.

• Clean the sample block with Na-hypochlorite (0.1% v/v) solution.

a. Pipet a small volume of Na-hypochlorite (0.1% v/v) solution into each contaminated well.

b. In each well, pipet the solution up and down several times to rinse the well.

c. Pipet the bleach solution to a waste beaker.

IMPORTANT! Always use deionized water to rinse wells after cleaning with bleach or ethanol
solution.

70 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 5 Maintain the instrument
Replace the instrument fuses 5

Replace the instrument fuses

CAUTION! FIRE HAZARD. For continued protection against the risk of fire, replace fuses only with
listed and certified fuses of the same type and rating as those currently in the instrument.

Materials required
• Fuses (2) – 10A, Time-Lag T, 250VAC, 5 × 20mm
• Safety glasses
• Powder-free gloves
• Screwdriver, flathead

Replace the fuses

1. Power off and unplug the instrument, then allow it to cool for 15 minutes.

2. Using a flat-head screwdriver, unscrew and remove the fuse holder.

3. Remove each fuse from its fuse holder and inspect it for damage. Carbon typically coats the inside
of failed fuses.

Good Failed

4. Replace each failed fuse.

Note: The voltage and amperage ratings are on the fuse holder.

5. Install the fuse holder back into the instrument.

6. Plug in, then power on the instrument.

The installation is successful if the instrument powers on.

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 Chapter 5 Maintain the instrument
5 Power on or off, store, and move

Note: Fuse failure can result from fluctuations in the supplied power to the system. To prevent further
failures, consider installing an electrical protective device, such as a UPS or a surge protector. If issues
with the fuse persist, contact Support.

Power on or off, store, and move

Enable Sleep Mode
1. In the home screen, touch Settings4Instrument Settings4Sleep Mode.

2. Slide the control On to enable sleep mode.

3. Touch Edit Time, then enter the time length of inactivity before the instrument enters sleep mode.

4. Touch Enter, then touch OK.

Power on the instrument

1. Touch anywhere on the touchscreen to determine if the instrument is in sleep mode. If the home
screen is displayed, the instrument is already powered on.

2. If the home screen does not display, power on the

instrument by pressing the switch on the rear panel.

If left unattended, the instrument automatically enters sleep

mode (enabled by default) to conserve power.

Note: To customize the sleep mode setting, touch

Settings4Instrument Settings4Sleep Mode.

Power off the instrument

The instrument operates in low-power mode when not in use. However, the instrument can be powered
off completely so that the components use no power.

Note: To power off the instrument for >1 week, see “Prepare the instrument to store, move, or ship” on
page 73.

1. Power off the instrument using the power switch on the back of the instrument.

2. Power off the computer.

72 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 5 Maintain the instrument
Power on or off, store, and move 5

Prepare the instrument to store, move, or ship

In the home screen:

1. Touch Settings4Maintenance and Service4Ship Prep Mode4Next.

2. Touch to eject the instrument drawer.

3. Load the packing plate or an empty plate, then touch to close the drawer.

4. Touch Lock Block.

5. Power off the instrument using the power switch on the back of the instrument.

The instrument is now ready to store, move, or ship.

Move the instrument

CAUTION! PHYSICAL INJURY HAZARD. Do not attempt to lift the instrument or any other heavy
objects unless you have received related training. Incorrect lifting can cause painful and sometimes
permanent back injury. Use proper lifting techniques when lifting or moving the instrument. At least
two people are required to lift it.

IMPORTANT! Moving your instrument can create subtle changes in the alignment of the instrument
optics. Recalibrate the instrument if necessary.

• Ensure that the surface on which you place the instrument can support at least 35 kg (77 lbs).
• Ensure that the path to transport the instrument is clear of obstructions.
• At least two people are needed to lift and carry the instrument.
• Keep your spine in a good neutral position.
• Bend at the knees and lift with your legs.
• Do not lift an object and twist your torso at the same time.
• Coordinate your intentions with your assistant before lifting and carrying.

IMPORTANT! After moving the instrument, perform an RNase P instrument verification run. If the run
fails, perform ROI/ uniformity, background, and dye calibrations.

Return the instrument for service

The service process requires 2 to 3 weeks.
Before returning the instrument for service, perform the following tasks.
1. Back up the instrument (see “Backup or restore the instrument” on page 67).
2. In the home screen, touch Settings4Instrument Settings4Reset Factory defaults.
3. Set the instrument to Ship Prep Mode (see “Prepare the instrument to store, move, or ship” on
page 73).

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 Chapter 5 Maintain the instrument
5 Power on or off, store, and move

To return the instrument for service, perform the following tasks.

1. Contact your local customer care center or technical support group to obtain a copy of the
Certificate of Instrument Decontamination, a service notification, a service call number, and
packaging materials (if required).

2. Follow the instructions in the form to decontaminate the instrument.

IMPORTANT! The instrument must be decontaminated before packing it for shipping.

3. Complete and sign a copy of the Certificate of Instrument Decontamination.

4. Fax the Certificate of Instrument Decontamination to the customer care center.

5. Pack the instrument in the provided packaging and follow the instructions in the table below.

Prepare Include Exclude

1. Transfer any data files from • Instrument Any accessories, including:

the instrument. • Completed and signed • Power cord
2. Load an empty plate in the Certificate of Instrument • Ethernet cable
sample block. Decontamination
• USB drive
3. Use the touchscreen to Note: The instrument will not be • Wireless adapter
place the instrument in ship accepted for service without a
mode. hard copy of the Certificate of Note: If included with the
Instrument Decontamination. instrument, these items will be
Note: The empty plate and disposed of during service and
ship mode protects the internal not returned.
components of the instrument
during transport.

6. Attach the postage provided with the Certificate of Instrument Decontamination to the box, then
ship the instrument to the designated facility.

74 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 6 Configure the instrument and
manage instrument profiles

■ Initial start‑up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
■ Manage profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
■ Link an instrument profile to Thermo Fisher™ Connect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
■ Enable SAE mode (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
■ Require instrument profile sign-in (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
■ Enable remote instrument monitoring (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
■ Update instrument software (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
■ Restore factory defaults . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
■ Configure the network . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
■ Select a region for Thermo Fisher™ Connect (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
■ Manage the instrument name (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
■ Set the date and time (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
■ Manage the Sign Out Timer (Administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Initial start‑up
Perform these tasks during initial instrument start‑up or after you restore factory defaults (see “Restore
factory defaults” on page 87).

1. (Optional) Select one of the following options.

• Configure the instrument for either wired connection or wireless network connection (see
“Configure the network” on page 87).
• Touch Neither/Decide Later.

2. (Optional) Enter an instrument name (see “Manage the instrument name (Administrator only)” on
page 88).

3. Set the date and time (see “Set the date and time (Administrator only)” on page 89).

4. Select one of the following options.

• Select a region for Thermo Fisher™ Connect.
• Touch Next to continue.

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 Chapter 6 Configure the instrument and manage instrument profiles
6 Manage profiles

5. Create an administrator profile (see “Create an administrator instrument profile during initial start-
up” on page 76).

6. Select one of the following options.

• Link the instrument profile to Thermo Fisher™ Connect (see “Link an instrument profile to
Thermo Fisher™ Connect” on page 77).
• Touch Skip.

Manage profiles
To See

Create a profile • “Create an administrator instrument profile during initial start-up” on page 76
• “Create a new instrument profile” on page 25

Configure a profile • “Link an instrument profile to Thermo Fisher™ Connect” on page 77

• “Edit an instrument profile” on page 77

View or manage all • “Manage all instrument profiles (Administrator only)” on page 76
profiles

Create an administrator instrument profile during initial start-up

During initial start-up, the user is automatically prompted to create an administrator instrument profile.
See “Initial start‑up” on page 75.
• The first instrument profile that is created during installation is given administrator privileges.
• Administrators can grant administrative privileges to other users. See “Manage all instrument
profiles (Administrator only)” on page 76.

1. Touch Name, enter a username, then touch Done.

2. Touch PIN, enter a four-digit numerical password, then touch Enter.

Note: Touch the Show PIN checkbox to switch PIN display on or off.

3. Touch Confirm PIN, then repeat step 2.

4. Touch Create profile.

Manage all instrument profiles (Administrator only)

1. In the home screen, access the All Profiles tab.
• Touch My Profile4All Profiles.
• Touch Settings4Manage Users4Manage Profiles4All Profiles.

A list of users, the date the profile was created, and the user type displays.

76 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Chapter 6 Configure the instrument and manage instrument profiles
Link an instrument profile to Thermo Fisher™ Connect 6

2. Select the instrument profile to edit.

3. Edit the profile.

• To delete the profile, touch Delete profile4Delete.
• To reset the PIN, touch Reset PIN4Reset.
– The user will be directed to enter a new PIN at the next sign in.
• To enable or disable administrative privileges, slide the control to Administrator or Standard,
respectively.

4. Touch Done.

Edit an instrument profile

1. In the home screen, touch My Profile.

Note: Administrators can also navigate to this screen by touching Settings4Manage

Users4Manage Profiles.

2. Touch Edit.

3. Select the fields to edit, then make changes.

4. Touch Done.

Link an instrument profile to Thermo Fisher™ Connect

Linking your instrument profile to Thermo Fisher™ Connect cloud-based platform allows you to access
the following functions:
• View an instrument status from the cloud.
• Download templates from your cloud storage to the instrument.
• Transfer run data from the instrument to your cloud storage.

To link an instrument profile to Thermo Fisher™ Connect, see the following sections:
• “Recommended order to set up profiles” on page 78
• “Overview of local instrument profiles and Thermo Fisher™ Connect profiles” on page 78
• “Thermo Fisher™ Connect instrument profile roles and functions” on page 79
• “Link the instrument to your Thermo Fisher™ Connect account” on page 80
• “Link a local profile to a Thermo Fisher™ Connect profile” on page 82
• “Unlink a Thermo Fisher™ Connect account” on page 83
• “If you link when you are signed in to the instrument” on page 84
• “Change the PIN for a Thermo Fisher™ Connect profile” on page 85

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 Chapter 6 Configure the instrument and manage instrument profiles
6 Link an instrument profile to Thermo Fisher™ Connect

Recommended order to set up profiles

Task Description

The first profile on the instrument becomes the instrument

Create a profile for the instrument administrator.
administrator. See “Create an administrator instrument profile during initial start-up”
on page 76.

A Thermo Fisher™ Connect administrator is distinct from an

instrument administrator.
The first Thermo Fisher™ Connect profile to be linked to the
instrument is automatically assigned the role of a Thermo Fisher™
Select a Thermo Fisher™ Connect
Connect administrator. It is recommended that the first Connect
administrator.
profile to be linked is the one that should be a Thermo Fisher™
Connect administrator.
The roles can be updated at a later time on the Thermo Fisher™
Connect platform.

Create a local instrument profile. Thermo Fisher™ Connect -enabled

features are not available.
(Optional) Link a local instrument profile to a Thermo Fisher™ Connect
Each person creates a profile. profile.

Sign in with a Thermo Fisher™ Connect profile. Thermo Fisher™

Connect-enabled features are available.

Any of the profiles can be assigned the role of instrument

Assign additional instrument administrators. administrator. The local profile must be created first or the Thermo
Fisher™ Connect profile must be linked first.

Overview of local instrument profiles and Thermo Fisher™ Connect profiles

• Local instrument profile
– Experiment template files and data files are stored on the instrument.
– Experiment template files and data files can be transferred to the desktop software.
– Email notifications are not available.
– Separate profiles are required for each instrument if multiple instruments are used.
• Thermo Fisher™ Connect profile
– Experiment template files and data files are stored on the instrument.
– Experiment template files and data files can be transferred to the Thermo Fisher™ Connect
platform or the desktop software.
– Email notifications are available.
– The same profile can be used for multiple instruments.

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Link an instrument profile to Thermo Fisher™ Connect 6

Thermo Fisher™ Connect instrument profile roles and functions

The first user who links their local instrument profile to their Thermo Fisher™ Connect account is
assigned a Thermo Fisher™ Connect profile with administrator role.

Instrument profile Location Functions allowed

Standard Thermo • Create, save, open, import, and run template files
Fisher™ • Create and modify run settings
Connect
• View and export data files

Administrator Thermo All the permissions of a local administrator profile, plus the following
Fisher™ functions performed in Thermo Fisher™ Connect:
Connect • See a list of all the Thermo Fisher™ Connect profiles that are linked
to the instrument
• Assign Thermo Fisher™ Connect administrator roles to one or more
users
• Remove a user from an instrument
• Disconnect the instrument from Thermo Fisher™ Connect
• Change the instrument name

Test the connection to the Thermo Fisher™ Connect platform

1. In the home screen, tap (Settings)4Maintenance and service4Connect services.
The Connect Services screen is displayed.

2. Tap Test connection.

If the connection can be established, You are able to connect to the Connect platform will be
displayed.

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 Chapter 6 Configure the instrument and manage instrument profiles
6 Link an instrument profile to Thermo Fisher™ Connect

If the connection cannot be established, Unable to connect will be displayed.

3. Tap Close.

Link the instrument to your Thermo Fisher™ Connect account

This section describes using your Thermo Fisher™ Connect account when you use the instrument for
the first time.
The first time you use your Thermo Fisher™ Connect account on an instrument, you will be prompted to
create a four-digit numerical PIN. This PIN is to use when signing in to the instrument with your Thermo
Fisher™ Connect account. It will apply to all other instruments when you use your Thermo Fisher™
Connect account. This does not change the password when signing in to your Thermo Fisher™ Connect
account on a browser.

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Link an instrument profile to Thermo Fisher™ Connect 6

After the PIN is set up on the instrument, it must be changed with your Thermo Fisher™ Connect
account on a browser, see “Create an administrator instrument profile during initial start-up” on
page 76.
The first time the instrument is used with a Thermo Fisher™ Connect account, a region must be
selected.

1. In the Sign In screen, tap Get started4Create a local instrument file4Connect to your
Thermo Fisher™ Connect account.

2. (Optional) Select the appropriate region.

Option Description
China For users in China
U.S. For users in any country other than China

3. Tap a connection option.

Option Action
Mobile
devices Note: Before selecting this option, install and sign in to the Thermo Fisher™ Connect
application on your mobile device.

On the instrument:
1. Tap Mobile devices.
2. Hold the camera on your mobile device over the QR code that is displayed on the
touchscreen.
3. Tap Close.

PC A link code is displayed on the instrument.

On a computer:
1. Access the Thermo Fisher™ Connect platform.
2. Click Add instrument.
3. Select QuantStudio.
4. Enter the link code.

4. (Optional) In the Enter PIN screen, tap the PIN (4 digits required) field, enter a four-digit numerical
PIN, then tap Enter.
Tap the Show PIN checkbox to show or hide the PIN.

5. (Optional) Tap the Confirm PIN field, enter the four-digit numerical PIN again, then tap Enter.

6. Tap Done.

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6 Link an instrument profile to Thermo Fisher™ Connect

Link a local profile to a Thermo Fisher™ Connect profile

This section describes linking a local instrument profile to a Thermo Fisher™ Connect profile, if a local
instrument profile was created first.
The first time you use your Thermo Fisher™ Connect account on an instrument, you will be prompted to
create a four-digit numerical PIN. This PIN is to use when signing in to the instrument with your Thermo
Fisher™ Connect account. It will apply to all other instruments when you use your Thermo Fisher™
Connect account. This does not change the password when signing in to your Thermo Fisher™ Connect
account on a browser.
After the PIN is set up on the instrument, it must be changed with your Thermo Fisher™ Connect
account on a browser, see “Change the PIN for a Thermo Fisher™ Connect profile” on page 85.
The first time the instrument is used with a Thermo Fisher™ Connect account, a region must be
selected.
For a detailed description of the profile, see “If you link when you are signed in to the instrument” on
page 84.
(Optional) Test the connection, see “Test the connection to the Thermo Fisher™ Connect platform” on
page 79.

1. In the home screen, tap (Profile).

The My Profile screen is displayed.

2. Tap Connect4Link Account.

The Connect to Connect Platform screen is displayed.

3. (Optional) Select the appropriate region.

Option Description
China For users in China
U.S. For users in any country other than China

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Link an instrument profile to Thermo Fisher™ Connect 6

4. Tap a connection option.

Option Action
Mobile
devices Note: Before selecting this option, install and sign in to the Thermo Fisher™ Connect
application on your mobile device.

On the instrument:
1. Tap Mobile devices.
2. Hold the camera on your mobile device over the QR code that is displayed on the
touchscreen.
3. Tap Close.

PC A link code is displayed on the instrument.

On a computer:
1. Access the Thermo Fisher™ Connect platform.
2. Click Add instrument.
3. Select QuantStudio.
4. Enter the link code.

5. (Optional) In the Enter PIN screen, tap the PIN (4 digits required) field, enter a four-digit numerical
PIN, then tap Enter.
Tap the Show PIN checkbox to show or hide the PIN.

6. (Optional) Tap the Confirm PIN field, enter the four-digit numerical PIN again, then tap Enter.

7. Tap Done.

Unlink a Thermo Fisher™ Connect account

Unlinking a Thermo Fisher™ Connect is done from the Thermo Fisher™ Connect platform on your
computer.
For more information about unlinking a Thermo Fisher™ Connect account, see “If you link when you are
signed in to the instrument” on page 84.

1. Sign in to your account on the desktop Thermo Fisher™ Connect platform.

2. In the left pane, click (Instrument).

3. Select the instrument, then click Disconnect.

4. Tap Confirm.

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6 Link an instrument profile to Thermo Fisher™ Connect

If you link when you are signed in to the instrument

In this scenario, your local instrument profile name is created manually on the instrument before you
link. Your local instrument profile name differs from your Thermo Fisher™ Connect instrument profile
name.

Phase Steps that occur

Before you link: • You enter your local instrument profile name in the Sign In screen.
• Your local instrument profile (UserABC) is displayed in the home screen of the
instrument.
• All plates and results that you create are accessible only when you are signed in
with your local instrument profile.

When you link: • You link your local instrument profile (see “Link a local profile to a Thermo Fisher™
Connect profile” on page 82).
• If this is the first time you link, a Thermo Fisher™ Connect instrument
profile is created using the FirstNameLastInitial of the user name from your
thermofisher.com account.
Example: [email protected] First name is User, Last name is Gray.
Thermo Fisher™ Connect account username is User G.
• Your local instrument profile (UserABC) is linked to your Thermo Fisher™ Connect
account ([email protected]).
• Your Thermo Fisher™ Connect instrument profile (User G.) replaces your local
instrument profile.

After you link: • Your Thermo Fisher™ Connect instrument profile (User G.) and is displayed in
the home screen of the instrument.
• Plate files and data files from your local instrument profile can be transferred to
Thermo Fisher™ Connect.
• New plate files and data files are saved under your Thermo Fisher™ Connect
instrument profile.

If your Thermo Fisher™ • Your local instrument profile (UserABC) is displayed in the home screen of the
Connect account is instrument.
unlinked: • Plate files and data files that were saved under your Thermo Fisher™ Connect
instrument profile are accessible under your local instrument profile.
• Plate files and data files are saved under local instrument profile and can be
copied to Thermo Fisher™ Connect (see “Manage templates (EDT files)” on
page 42 and “Transfer EDS files from the instrument home screen” on page 41).
• Your local instrument profile name (UserABC) is available for selection in the Sign
In screen.

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Enable SAE mode (Administrator only) 6

Change the PIN for a Thermo Fisher™ Connect profile

This section describes changing a PIN for a Thermo Fisher™ Connect profile. To change a PIN for a
local instrument profile, see “Manage all instrument profiles (Administrator only)” on page 76.

1. Sign in to Thermo Fisher™ Connect on a browser.

2. Click Update PIN number.

3. In the Update PIN number dialog box, enter a new PIN, then enter the new PIN a second time to
confirm it.

4. Click Send.

The 4-digit PIN to sign in to instruments with your Thermo Fisher™ Connect profile is updated. This
change applies to all of the instruments that you access with your Thermo Fisher™ Connect profile.

Enable SAE mode (Administrator only)

Security, Audit, and e-Signature (SAE) functions are only available for the QuantStudio™ 5 System.
The SAE module works with the instrument and desktop software to record and restrict various user
activities. Audits and e-Signatures are tracked in the desktop software.
In the home screen:

1. Touch Settings4Instrument Settings4SAE Mode.

2. Slide the control On to enable SAE on the instrument.

3. Touch OK.

The following instrument functions are disabled in SAE mode.

• Start a run from the instrument.

Note: All instrument runs must be started from desktop software that has SAE functions enabled.
• Edit an instrument name.
• Edit an instrument date or time.
• Restore to factory defaults.
• Perform a software update.

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6 Require instrument profile sign-in (Administrator only)

Require instrument profile sign-in (Administrator only)

1. In the home screen, touch Settings4Manage Users4Sign In Required.

2. Slide the control On.

Only signed-in users are allowed to access the instrument for any task, including access to
Settings.

3. Touch Done.

Enable remote instrument monitoring (Administrator only)

1. In the home screen, touch Settings4Maintenance and Service4Monitoring.

2. Configure the instrument monitoring settings.

Option Description
Remote Slide the control On to enable the Remote Monitoring Service.
Monitoring Enabling the Remote Monitoring Service allows the instrument to automatically
Service notify Thermo Fisher Scientific support teams in real time of potential instrument
issues. The service monitors and sends general instrument data, but the service
does not monitor or send customer data.
Thermo Fisher™ Slide the control On to enable users to access real‑time monitoring of
Connect Monitor amplification plots from the Thermo Fisher™ Connect dashboard (cloud-based
platform).

3. Touch OK.

Update instrument software (Administrator only)

1. In the home screen, touch Settings4Maintenance and Service4Software Update.

2. Select the location of the update files.

3. When prompted, confirm your request to update the software.

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Restore factory defaults 6

Restore factory defaults

This procedure can only be performed by an Administrator.

IMPORTANT! Back up the instrument before restoring factory defaults (see “Backup or restore the
instrument” on page 67).

1. In the home screen, touch Settings4Instrument Settings4Restore Factory Defaults.

2. Touch Restore Factory Defaults.

3. Power Off, then power On the instrument to apply the change.

• Instrument profiles and files stored on the instrument are deleted, including all EDS files and
any custom dye calibrations.
• The most recent valid ROI/Uniformity, Background, and system dye calibrations are not
deleted.

After restoring factory defaults, perform initial start‑up tasks. See “Initial start‑up” on page 75.

Configure the network

IMPORTANT! Configure the instrument for either wired connection or wireless connection but not
both.

“Set up a wired connection” on page 87

“Set up a wireless connection” on page 88

Set up a wired connection

1. In the home screen, touch Settings4Instrument Settings4Network Connection4 Wired.

2. In the Network Configuration screen, touch a radio button to connect to a network either by
DHCP or by a Static IP address.
Option Action
Automatic Touch DHCP.
Manual 1. Touch Static IP.
2. Enter the IP address for the instrument, the Subnet Mask, the Default Gateway, and
(optional) the Primary DNS Server and the Secondary DNS Server.
Addresses are in the form of X.X.X.X, where each X is a number from 0 to 255.

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6 Select a region for Thermo Fisher™ Connect (Administrator only)

Note: Ask your system administrator if the IP address is assigned statically or dynamically. For
static addresses, you need to know the IP address for the instrument, the Subnet Mask, and the
Default Gateway.

3. Touch OK.

Set up a wireless connection

1. In the home screen, touch Settings4Instrument Settings4Network Connection4
Wireless to display a list of the available networks.

2. Select a network or touch Join other network, enter the network password, then touch Enter.
If you select Join other network, enter the network name and security type.

3. Touch Join to continue.

4. In the Network Connection Complete screen, touch Next.

5. Touch OK.

6. In the Network Configuration screen, edit the Network details or touch Done.

Select a region for Thermo Fisher™ Connect (Administrator

only)
During the initial startup, you will be automatically prompted to select a region for Thermo Fisher™
Connect. Return to the selection through Settings, if necessary.

1. In the home screen, touch Settings4Instrument Settings4Thermo Fisher Connect Region.

2. Touch a region.
The server used to store your data is located in this region.

3. Touch OK.

Manage the instrument name (Administrator only)

1. In the home screen, touch Settings4Instrument Settings4Instrument Name.

2. Touch the Instrument Name field, enter an instrument name, then touch Done.

3. Touch OK.

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Set the date and time (Administrator only) 6

Set the date and time (Administrator only)

1. In the home screen, touch Settings4Instrument Settings4Date/Time.

2. Select a time zone from the dropdown list.

3. Select a date format.

a. Touch Date Format, then select the preferred date format.

b. Touch Next, touch the date field, then enter the date.

c. Touch Enter, then touch Done.

4. Select a time format.

a. Touch Time Format.

b. Slide the control to select a 12‑hour or 24‑hour clock.

c. Touch Next, touch the time field, then enter the time.

d. Touch Enter, then touch Done.

5. Touch Done.

Manage the Sign Out Timer (Administrator only)

1. In the home screen, touch Settings4Manage Users4Sign Out Timer.

2. Touch the Edit Time field, then enter the desired duration of inactivity before automatic user sign
out.

3. Touch Enter, then touch Done.

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 A Install and connect the instrument to
a network

■ Workflow: Install and connect to a network . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

■ Before you begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
■ Unpack and install the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
■ Power on and follow the startup wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
■ Connect the computer to the instrument directly or to a LAN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
■ Instrument and computer connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
■ Download and install the desktop software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
■ Networking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

Workflow: Install and connect to a network

Perform all steps in “Before you begin” on page 91
▼

“Unpack and install the instrument” on page 91

▼

“Power on and follow the startup wizard” on page 92

▼

“Perform instrument verification using RNase P plates” on page 53

▼

“Connect the computer to the instrument directly or to a LAN” on page 92

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 Appendix A Install and connect the instrument to a network
Before you begin A

Before you begin

This section provides instructions for customer installation of the computer and the instrument. For
installation by a field service engineer (FSE), contact Support to order a service call.
Before starting the installation, complete the following tasks:
• Determine the configuration for your instrument and obtain the network information you need (see
“Networking” on page 95).
• Review site requirements (see QuantStudio™ 3 and 5 Real‑Time PCR Systems Site Preparation
Guide (Pub. No. MAN0010405).
• Review instrument and computer connections (see “Instrument and computer connections” on
page 93).

Unpack and install the instrument

1. Prepare the installation site as described in the QuantStudio™ 3 and 5 Real‑Time PCR Systems Site
Preparation Guide (Pub. No. MAN0010405).

2. Follow the pre-printed instructions on the instrument box to unpack the instrument, accessories,
and reference documentation. Save the packing material for future use or recycle it.
The instrument box contains:
• Reference documentation: Welcome note, unpacking and set up instructions card, system
documentation insert
• One instrument
• Accessories: power cable, Ethernet cable, USB drive, reaction tube retainer
• Shipping plate

Note: Save the shipping plate but do not use it to operate the instrument.

If you ordered the wireless adapter, it is provided separately.

3. Place the instrument on the bench.

4. Plug the power cable into the power port on the back panel of the instrument, then plug the cable
into an electrical receptacle.

5. Connect your instrument as required by your network configuration (see “Supported options for
instrument and computer connections” on page 95 and “Instrument and computer connections”
on page 93).
• Connect an Ethernet cable to the Ethernet port on the back panel of the instrument, then
connect the cable to a computer or a networking port.
or
• Connect wirelessly via the wireless adapter.

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 Appendix A Install and connect the instrument to a network
A Power on and follow the startup wizard

Note: Do not connect the High Power USB WiFi Module (Cat. No. A26774) to the instrument if
it is connected to a network by an Ethernet cable. Configuring the instrument for both wired and
wireless connection can interfere with instrument operation.

Power on and follow the startup wizard

1. Power on the instrument.

2. Follow the startup wizard through the following tasks:

• Select the language for the instrument.
• Accept the license agreement.
• Select a Wired or Wireless networking option, as needed for your configuration (see
“Supported options for instrument and computer connections” on page 95).
• Configure the instrument date and time.
• Create an administrator instrument profile.

Note: You can perform any of the steps above at a later time if you do not have the information
needed to complete the startup screens. See “Configure instrument settings” on page 26.

IMPORTANT! Before using the instrument for the first time, we recommend that you perform
instrument verification using RNase P plates (see “Perform instrument verification using RNase P
plates” on page 53).

Connect the computer to the instrument directly or to a

LAN
This section describes the direct wired connection of the computer to the instrument or to a LAN.

1. Connect an Ethernet cable from the instrument or a LAN to the computer.

2. Power on the computer, then log in using a Windows™ Administrator account.

3. Open the Control Panel, then open the Network and Sharing Center.

4. In the left pane of the Network and Sharing Center window, click Change Adapter Settings.

5. Right-click on Broadband Connection, then select Properties.

6. In the Networking tab, select Internet Protocol Version 4 (TCP/IPv4).

7. Click Properties.

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 Appendix A Install and connect the instrument to a network
Instrument and computer connections A

8. In the Internet Protocol Version 4 (TCP/IPv4) Properties dialog box, select one of the following
options.
• Obtain an IP address automatically
• Use the following IP address

9. If Use the following IP address was selected, enter the IP address.

10. Close all dialog boxes by clicking OK, then re-start the computer.

Instrument and computer connections

5
6
7

Figure 3 Instrument back panel

1 USB ports 4 RS232 Port—For service use only
2 WiFi USB port—Connect USB wireless adapter for 5 Fuse Cover
wireless network access (ordered separately) 6 Power Switch
3 Ethernet Port—RJ45 port for 100/1,000 Mbps Ethernet 7 Power Port—100 to 240 VAC
communication with the instrument

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 93
 Appendix A Install and connect the instrument to a network
A Download and install the desktop software

3 2
1 1

Figure 4 Instrument‑to‑computer connections (barcode scanner connected to the computer)

Minitower configuration

1 Detachable power supply cord compatible with local power supply receptacle.
2 Connection between the computer and the instrument.
3 Connection between the computer and the monitor, keyboard, and mouse.
4 Connection between the computer and the (optional) handheld barcode scanner.

Download and install the desktop software

Computer requirements for the desktop software
If you purchased a computer provided by Thermo Fisher Scientific, you can install the desktop software
and use it to control the instrument.
This instrument uses QuantStudio™ Design and Analysis Software v1.5.x. QuantStudio™ Design and
Analysis Software v2.x can also be used to setup and analyze files.
Thermo Fisher Scientific does not support the use of customer-provided computers to control the
instrument.
However, if desired, you can install the desktop software on a customer-provided computer and use
the software to create templates and analyze data. Minimum requirements for a customer-provided
computer are:
• Operating system—Windows™ 10 (64‑bit)
• Processor—Pentium® 4 or comparable
• Memory—4 GB RAM
• Hard drive—500 GB
• Monitor—1280 × 1024 resolution

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 Appendix A Install and connect the instrument to a network
Networking A

Download the desktop software

1. Sign in to your account at thermofisher.com.

Note: If you do not have an account, create an account.

2. Go to thermofisher.com/quantstudio3-5softwaredownloads.

3. Download the software and the example files.

Install the desktop software

1. Use a Windows™ Administrator account to log in to the computer on which you are installing the
desktop software.

2. Unzip the downloaded software and example files.

3. Double-click setup.exe.

4. Follow the InstallShield Wizard prompts to install the software.

5. Accept the License Agreement.

6. Select Typical as the setup preference, then click Next.

7. If you are installing the software on a computer provided by Thermo Fisher Scientific, install
the software on the D:\ drive. If you are installing on a customer-provided computer, install the
software in your preferred location.

8. Click Finish.

Networking
IMPORTANT! This section provides general networking information. It does not provide adequate
detail to integrate the instrument into all possible network architectures. Because a network may
contain advanced features (such as a firewall or network domains), we recommend that you consult
a network administrator before connecting the instrument to your laboratory network.

Supported options for instrument and computer connections

We support the following direct, networked (LAN– local area network), or Thermo Fisher™ Connect
configurations. Configurations other than those listed are not recommended. Select a configuration that
meets the needs of your laboratory's instrument, software, and workflow requirements.

IMPORTANT! Do not connect both an Ethernet cable and the Wi‑Fi module (Cat. No. A26774) to
the instrument. Configuring the instrument for both wired and wireless connection can interfere with
instrument operation.

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 Appendix A Install and connect the instrument to a network
A Networking

Note: For detailed information about networking your instrument, see the QuantStudio™ 3 and 5
Real‑Time PCR Systems IT Checklist (Pub. No. MAN0013738).

Direct configuration option

• A computer provided by Thermo Fisher Scientific with the QuantStudio™ Design and Analysis Software

• Computer‑to‑instrument connection:
– Direct, wired connection between the computer and the instrument
using an Ethernet cable

IMPORTANT! A direct instrument‑to‑computer connection cannot be

combined with the LAN or the Thermo Fisher™ Connect configurations. LAN

Networked configuration option

• A computer provided by Thermo Fisher Scientific with the QuantStudio™ Design and Analysis Software
• The computer and instrument must have the same subnet mask within the same network.

• Computer‑to‑LAN connection (select an option):

– Wired connection to the network using an Ethernet cable – or – LAN

– Wireless connection to the network

• Instrument‑to‑LAN connection (select an option):

– Wired connection to the network using an Ethernet cable – or –
– Wireless connection to the network using the instrument Wi‑Fi module

Thermo Fisher™ Connect configuration option

• Internet access and a computer with the Chrome™ web browser to access Thermo Fisher™ Connect

• Computer‑to‑Thermo Fisher™ Connect connection (select an option):

– Wired connection to the internet using an Ethernet cable – or –
LAN
– Wireless connection to the internet

• Instrument‑to‑Thermo Fisher™ Connect connection (select an option):

– Wired connection to the network using an Ethernet cable – or –
– Wireless connection to the network using the instrument Wi‑Fi module

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Networking A

Control and monitor networked instruments

When the instrument is connected to a network:
• Computers on the network that are running the desktop software can control the instrument.
Networked instruments can be controlled by only one computer at a time.
• Instruments linked to Thermo Fisher™ Connect cannot be controlled remotely. However, you can
perform the following functions:
– Remotely access Thermo Fisher™ Connect to create (and analyze) experiments.
– From the instrument, download the experiments and start a run.
– Monitor a run from Thermo Fisher™ Connect in real time.

Ethernet port overview

The Ethernet port of the instrument supports:
• Static IP network service with subnet mask, primary and secondary data network service (DNS),
and default gateway settings, or dynamic host configuration protocol (DHCP) network service.
• mDNS/DNS for local domains.

Note: Because mDNS is limited to direct network connections, an instrument configured for
mDNS may not be visible to other nodes that are separated by a router, hub, or another network
device.
• IPv4 linknlocal (IPV4LL) in the RFC (also known as Automatic Private IP Addressing [APIPA] or
Internet Protocol Automatic Configuration [IPAC]).

Note: When an instrument is set for DHCP, APIPA is automatically enabled, and the instrument
provides an IP address when no address is supplied by the DHCP server.

Firewall ports that must be open

Ports Condition

Standard ports for instrument-to-Thermo Fisher™ Connect and computer-to-

80/443
Thermo Fisher™ Connect connections

mDNS, 7443 Instrument-to-computer connection

mDNS, 5353 Instrument discovery

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 Appendix A Install and connect the instrument to a network
A Networking

Networking guidelines and best practices

• Consult a network administrator before connecting the instrument to a network.
• To enable the full functionality of the software, the computer requires a network connection.
• Open the firewall port for the instruments to be discovered. See “Firewall ports that must be open”
on page 97.
• Observe the restrictions to mDNS and Autodiscovery.
The instrument supports mDNS but only when the instrument and computer share a direct network
connection and are within the same subnet. Network computers that are separated from the
instrument by a router, hub, or another network device may not be able to access the instrument by
its host name.
• Confirm the uniqueness of the instrument name.
– The instrument name must be unique within the subnet. The desktop software can
automatically discover instruments on the link-local network.
– The instrument does not test the uniqueness of the instrument name within the subnet when it
is set.

98 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 B Troubleshooting

Observation Possible cause Recommended action

Inconsistent communication The instrument is configured Ensure only one connectivity option is plugged
between instrument and for both wired and wireless into the instrument (either an Ethernet cable or
computer or instrument and network connection. a wireless adapter, but not both).
Thermo Fisher™ Connect
Configure for wired or wireless network
connection.
Weak or unstable internet Change the configuration to a wired
connection, especially if connection.
configured for wireless. Use a wireless network with a stronger or
more consistent signal.
The connection between the The connection is not fully Power the instrument off, then power it on
instrument and the computer is established. again.
not recognized
If using a networked Contact your information technologies
configuration, the instrument department to have them ensure that the
and computer are not on the instrument and computer are on the same
same subnet mask. subnet mask.
If using a networked Contact your information technologies
configuration, the instrument department to have them ensure that the IP
or computer has an invalid IP addresses are valid.
address.
Insufficient disk space Insufficient disk space to save 1. In the home screen, touch
message a run. Settings4Run History4Manage.
2. Delete or transfer experiments from the
instrument.
The touchscreen is black The instrument is in sleep Touch anywhere on the instrument
mode. touchscreen.
The instrument is not powered If you touch the instrument touchscreen and
on. it remains black, check if the instrument is
powered on. The power switch is located on
the rear panel of the instrument.
If the instrument does not power on, check
that the instrument is properly plugged in.
If the instrument does not power on and
the instrument is properly plugged in, contact
Support.
Forgot PIN for instrument Non-administrator forgot See “Manage all instrument profiles
profile instrument profile PIN. (Administrator only)” on page 76.

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 99
 Appendix B Troubleshooting
B Networking

Observation Possible cause Recommended action

Forgot PIN for instrument Administrator forgot instrument Have another administrator reset the PIN for
profile profile PIN. the forgotten-PIN profile (see “Manage all
(continued) instrument profiles (Administrator only)” on
page 76).
If there is not another administrator profile
on the instrument, you must restore factory
defaults (see “Restore factory defaults” on
page 87).

100 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 C Parts and materials

■ Kits, consumables, accessories, and reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101

■ Consumables (96‑well, 0.2‑mL format) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
■ 384-well consumables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
■ Consumables (96-well, 0.1-mL format) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
■ Accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
■ General-use materials and consumables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104

Kits, consumables, accessories, and reagents

Unless otherwise indicated, all materials are available through thermofisher.com.
Store all calibration and RNase P plates at –20°C. All other items can be stored at 15–30°C. Use all
materials by the expiration date on the packaging.
Catalog numbers that appear as links open the web pages for those products.

Consumables (96‑well, 0.2‑mL format)

Consumable Amount Cat. No.

MicroAmp™ Optical 8-Cap Strips 300 strips 4323032

MicroAmp™ Optical 8-Tube Strip, 0.2 mL 125 strips 4316567

MicroAmp™ Optical Tube without Cap, 0.2 mL 2,000 tubes N8010933

MicroAmp™ 96-Well Tray/Retainer Set for Veriti™ Systems 10 trays 4381850

10 plates N8010560
MicroAmp™ Optical 96-Well Reaction Plate
500 plates 4316813

20 plates 4306737
MicroAmp™ Optical 96-Well Reaction Plate with Barcode
500 plates 4326659

MicroAmp™ EnduraPlate™ Optical 96-Well Clear Reaction Plates with 20 plates 4483354
Barcode 500 plates 4483352

MicroAmp™ EnduraPlate™ Optical 96-Well Clear GPLE Reaction

20 plates 4483348
Plates with Barcode

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 101
 Appendix C Parts and materials
C 384-well consumables

(continued)
Consumable Amount Cat. No.

MicroAmp™ EnduraPlate™ Optical 96-Well Clear GPLE Reaction

500 plates 4483351
Plates with Barcode
MicroAmp™ EnduraPlate™ Optical 96-Well Fast Clear Reaction Plates
with Barcode 20 plates 4483485

MicroAmp™ EnduraPlate™ Optical 384-Well Clear Reaction Plates

with Barcode 20 plates 4483285

MicroAmp™ Optical Adhesive Film Kit 1 kit 4313663

MicroAmp™ Optical Film Compression Pad (Optional, used for some

5 each 4312639
applications)

Instrument verification or calibration plate Cat. No.

TaqMan™ RNase P Instrument Verification Plate, 96‑Well 0.2‑mL 4432382

Region of Interest (ROI) and Background Plates, 96‑Well 0.2‑mL (2 plates) 4432364

QuantStudio™ 3/5 10‑Dye Spectral Calibration Kit, 96‑Well 0.2‑mL

A26343
(contains all 3 spectral calibration plates listed below)

QuantStudio™ 3/5 Spectral Calibration Plate 1

A26331
(FAM™, VIC™, ROX™, and SYBR™ dyes), 96‑Well 0.2‑mL

QuantStudio™ 3/5 Spectral Calibration Plate 2, 96‑Well 0.2‑mL

A26332
(ABY™, JUN™, and MUSTANG PURPLE™ dyes)

QuantStudio™ 3/5 Spectral Calibration Plate 3, 96‑Well 0.2‑mL

A26333
(TAMRA™, NED™, and Cy®5 dyes)

384-well consumables
Consumable Contents Cat. no.

MicroAmp™ Optical 384-Well Reaction Plate with Barcode 50 plates 4309849

500 plates 4326270

1000 plates 4343814

MicroAmp™ EnduraPlate™ Optical 384-Well Reaction Plate with 20 plates 4483285

Barcode (clear)
500 plates 4483273

MicroAmp™ Optical Adhesive Film Kit 1 kit 4313663

102 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Appendix C Parts and materials
Consumables (96-well, 0.1-mL format) C

Calibration or instrument verification plate Cat. no.

384-Well Region of Interest (ROI) and Background Plates (2 plates) 4432320

QuantStudio™ 3 or 5 10-Dye Spectral Calibration Kit, 384-Well A26341

384-Well Spectral Calibration Plate 1

A26334
(containing FAM™, VIC™, ROX™, TAMRA™, and SYBR™ dyes)

384-Well Spectral Calibration Plate 2

A26335
(containing ABY™, JUN™, MUSTANG PURPLE™, NED™, and Cy®5 dyes)

384-Well TaqMan™ RNase P Instrument Verification Plate 4455280

Consumables (96-well, 0.1-mL format)

Consumable Contents Cat. no.

MicroAmp™ Optical 8-Cap Strip 300 strips 4323032

MicroAmp™ Optical Fast 8-Tube Strip (0.1 mL) 125 strips 4358293

MicroAmp™ Optical Fast Tube with Cap (0.1 mL) 1000 tubes 4358297

MicroAmp™ 96-Well Tray for VeriFlex™ Block 10 trays 4379983

MicroAmp™ Optical 96-Well Fast Reaction Plate (0.1 mL) 10 plates 4346907

MicroAmp™ EnduraPlate™ Optical 96-Well Fast Reaction Plate with 20 plates 4481194
Barcode (clear) (0.1 mL)
500 plates 4483494

MicroAmp™ Optical Adhesive Film Kit 1 kit 4313663

Calibration or instrument verification plate Cat. no.

96-Well Fast Region of Interest (ROI) and Background Plates (2 plates) 4432426

QuantStudio™ 3 or 5 10-Dye Spectral Calibration Kit, 96-Well 0.1-mL A26342

96-Well 0.1-mL Spectral Calibration Plate 1

A26336
(containing FAM™, VIC™, ROX™, and SYBR™ dyes

96-Well 0.1-mL Spectral Calibration Plate 2

A26337
(containing ABY™, JUN™, and MUSTANG PURPLE™ dyes)

96-Well 0.1-mL Spectral Calibration Plate 3

A26340
(containing TAMRA™, NED™, and Cy®5 dyes)

96Well Fast TaqMan™ RNase P Instrument Verification Plate 4351979

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 103
 Appendix C Parts and materials
C Accessories

Accessories
Item Amount Cat. No.

MicroAmp™ Multi Removal Tool 1 tool 4313950

MicroAmp™ Cap Installing Tool (handle style) 1 tool 4330015

MicroAmp™ Optical Adhesive Film 25 films 4360954

100 films 4311971

MicroAmp™ Adhesive Film Applicator 5 applicators 4333183

RT-PCR Grade Water 10 × 1.5 mL tubes AM9935

Handheld Barcode Scanner 1 scanner 4488442

High Power USB WiFi Module 1 module A26774

General-use materials and consumables

The following general-use materials and consumables are required to calibrate, maintain, and operate
the instrument.
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.

Material/Consumable Source

Centrifuge with 96‑well plate buckets MLS

Cotton or nylon swabs and lint‑free cloths MLS

Ethanol, 95% solution MLS

Optical clear adhesive film for PCR MLS

Na-hypochlorite, 0.1% v/v solution

Pipettors, 100‑µL and 200‑µL (with pipette tips) MLS

Powder‑free gloves MLS

Safety glasses MLS

Screwdriver, flathead MLS

Tissue, lint‑free MLS

Deionized water MLS

104 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 D Instrument specification and layout

■ Configured system dimensions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

■ Electrical requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
■ Environmental requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
■ Network requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 105
 Appendix D Instrument specification and layout
D Configured system dimensions

Configured system dimensions

Allow space for the configured instrument. A typical setup with a co-located minitower computer is
shown below.

Note: Dimensions are rounded to the nearest whole or half unit.

15 cm (6 in.)

50 cm (20 in.)
27 cm (10.5 in.)

30 cm (12 in.)
40 cm (16 in.)

207 cm (81.5 in.)

106 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Appendix D Instrument specification and layout
Electrical requirements D

Instrument clearances
During instrument installation and maintenance, it is necessary to access the back of the instrument. If
the back of the instrument faces a wall, ensure that there is sufficient clearance on the bench to rotate
the instrument for access.

IMPORTANT! For safety, the power outlet for the instrument must be accessible.

Component Top Front Sides Back

Instrument 30 cm (12 in.) 30 cm (12 in.) 15 cm (6 in.) 15 cm (6 in.)

Computer[1] — 15 cm (6 in.) — 15 cm (6 in.)

[1] Co-locating the computer with the instrument is optional.

Electrical requirements
WARNING! For safety, the power outlet used for powering the instrument must be accessible at all
times. See “Instrument clearances” on page 107 for information about the space needed between the
wall and the instrument. In case of emergency, you must be able to immediately disconnect the main
power supply to all the equipment. Allow adequate space between the wall and the equipment so
that the power cords can be disconnected in case of emergency.

WARNING! Use of accessories, transducers, and cables other than those specified or provided by
the manufacturer of the equipment could result in increased electromagnetic emissions or decreased
electromagnetic immunity of this equipment and result in improper operation.

• Electric receptacle with grounding capability

• Maximum power dissipation: ~960 W (not including computer and monitor)
• Mains AC line voltage tolerances must be up to ±10 percent of nominal voltage

Circuit Rated
Device Rated voltage Rated power
required frequency

Instrument 100–240 ±10% VAC[1] 10 A 50/60 Hz 960 W

Computer (laptop) 100–240 ±10% VAC 10 A 50/60 Hz 90 VA

Computer (desktop) 125 VA

100–240 ±10% VAC 10 A 50/60 Hz
Monitor 65 VA
[1] If the supplied power fluctuates beyond the rated voltage, a power line regulator may be required. High or low voltages can adversely
affect the electronic components of the instrument.

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 107
 Appendix D Instrument specification and layout
D Environmental requirements

Environmental requirements
Table 2 Environmental requirements

Condition Acceptable range

Installation site Indoor use only

Electromagnetic interference Do not use this device in close proximity to sources of strong electromagnetic
radiation (for example, unshielded intentional RF sources). Strong electromagnetic
radiation may interfere with the proper operation of the device.

Altitude Between sea level and 2000 m (6500 ft) above sea level

Operating conditions • Humidity: 15–80% relative humidity (noncondensing)

• Temperature: 15°C to 30°C (59°F to 86°F)
Note: For optimal performance, avoid rapid or extreme fluctuations in room
temperature.

Storage and transport • Humidity: 20–80% relative humidity (noncondensing)

conditions • Temperature: –30°C to 60°C (–22°F to 140°F)

Thermal output During operation, the net thermal output, based on the actual current draw of the
instrument, is expected to be approximately 960 W (3275 Btu/h).

Vibration Ensure that the instrument is not adjacent to strong vibration sources, such as
a centrifuge, pump, or compressor. Excessive vibration will affect instrument
performance.

Pollution degree The instrument has a Pollution Degree rating of II. The instrument may only
be installed in an environment that has nonconductive pollutants such as dust
particles or wood chips. Typical environments with a Pollution Degree II rating are
laboratories and sales and commercial areas.
The noise output of the instrument is £ 60 dB when running.

Other conditions Ensure the instrument is located away from any vents that could expel particulate
material onto the instrument components.
Avoid placing the instrument and computer adjacent to heaters, cooling ducts, or
in direct sunlight.

Network requirements
The instrument:
• Is factory-configured for IPv4 TCP/IP communication and includes an Ethernet adapter
(100/1,000 Mbps) with an RJ45-type connector for integrating the device into a local area network
(LAN).
• Can alternatively be configured for wireless networking (High Power USB WiFi Module required,
sold separately as an optional accessory).

108 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Appendix D Instrument specification and layout
Network requirements D

The instrument can be configured for either wired or wireless networking, not both.
If a Thermo Fisher Scientific service representative is to install the instrument:
• If the instrument will be connected to a LAN, an active, tested network jack must be in place before
the scheduled installation date.
• A representative from your information technologies department must be available during the
installation to help connect the instrument to your network.

Required materials to network the instrument:

• Wired—Ethernet cable of sufficient length with RJ45 connectors
– CAT5 cable for a 100 Mbps network connection
– CAT5e or CAT6 cable for a 1,000 Mbps network connection

–or–
• Wireless—High Power USB WiFi Module (Cat. No. A26774, sold separately)

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 109
 E Safety

■ Symbols on this instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110

■ Safety alerts on this instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
■ Safety information for instruments not manufactured by Thermo Fisher Scientific . . . . . . . . . . . . 114
■ Instrument safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
■ Safety and electromagnetic compatibility (EMC) standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
■ Chemical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
■ Biological hazard safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120

WARNING! GENERAL SAFETY. Using this product in a manner not specified in the user
documentation may result in personal injury or damage to the instrument or device. Ensure that
anyone using this product has received instructions in general safety practices for laboratories and
the safety information provided in this document.

· Before using an instrument or device, read and understand the safety information provided in the
user documentation provided by the manufacturer of the instrument or device.
· Before handling chemicals, read and understand all applicable Safety Data Sheets (SDSs) and use
appropriate personal protective equipment (gloves, gowns, eye protection, and so on). To obtain
SDSs, see the “Documentation and Support” section in this document.

Symbols on this instrument

Symbols may be found on the instrument to warn against potential hazards or convey important safety
information. In this document, the hazard symbol is used along with one of the following user attention
words:
• CAUTION!—Indicates a potentially hazardous situation that, if not avoided, may result in minor or
moderate injury. It may also be used to alert against unsafe practices.
• WARNING!—Indicates a potentially hazardous situation that, if not avoided, could result in death or
serious injury.
• DANGER!—Indicates an imminently hazardous situation that, if not avoided, will result in death or
serious injury.

Symbol English Français

Caution, risk of danger Attention, risque de danger

Consult the manual for further safety Consulter le manuel pour d’autres
information. renseignements de sécurité.

110 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Appendix E Safety
Symbols on this instrument E

(continued)

Symbol English Français

Caution, risk of electrical shock Attention, risque de choc électrique

Moving parts Parties mobiles

Caution, hot surface Attention, surface chaude

Potential biohazard Danger biologique potentiel

Ultraviolet light Rayonnement ultraviolet

Potential slipping hazard Danger de glisser potentiel

On On (marche)

Off Off (arrêt)

On/Off On/Off (marche/arrêt)

Standby En attente

Earth (ground) terminal Borne de (mise à la) terre

Protective conductor terminal (main ground) Borne de conducteur de protection (mise à la

terre principale)

Terminal that can receive or supply Borne pouvant recevoir ou envoyer une
alternating current or voltage tension ou un courant de type alternatif

Terminal that can receive or supply Borne pouvant recevoir ou envoyer une
alternating or direct current or voltage tension ou un courant continu ou alternatif

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 111
 Appendix E Safety
E Symbols on this instrument

(continued)

Symbol English Français

Do not dispose of this product in unsorted Ne pas éliminer ce produit avec les déchets
municipal waste usuels non soumis au tri sélectif.

CAUTION! To minimize negative MISE EN GARDE ! Pour minimi‐

environmental impact from disposal ser les conséquences négatives sur
of electronic waste, do not l’environnement à la suite de l’éli‐
dispose of electronic waste in mination de déchets électroniques,
unsorted municipal waste. Follow ne pas éliminer ce déchet électro‐
local municipal waste ordinances nique avec les déchets usuels non
for proper disposal provision soumis au tri sélectif. Se conformer
and contact customer service aux ordonnances locales sur les dé‐
for information about responsible chets municipaux pour les disposi‐
disposal options. tions d’élimination et communiquer
avec le service à la clientèle pour
des renseignements sur les options
d’élimination responsable.

Conformity symbols
Conformity mark Description

Indicates conformity with safety requirements for Canada and U.S.A.

Indicates conformity with European Union requirements for safety and

electromagnetic compatibility.

Indicates conformity with Australian standards for electromagnetic compatibility.

112 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Appendix E Safety
Safety alerts on this instrument E

Safety alerts on this instrument

Additional text may be used with one of the symbols described above when more specific information
is needed to avoid exposure to a hazard. See the following table for safety alerts found on the
instrument.

English Français

CAUTION! Hazardous chemicals. Read MISE EN GARDE ! Produits chimiques

the Safety Data Sheets (SDSs) before dangereux. Lire les fiches signalétiques (FS)
handling. avant de manipuler les produits.

CAUTION! Hazardous waste. Refer to MISE EN GARDE ! Déchets dangereux.

SDS(s) and local regulations for handling Lire les fiches signalétiques (FS) et la régle‐
and disposal. mentation locale associées à la manipulation
et à l’élimination des déchets.

Location of safety labels on the instrument

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 113
 Appendix E Safety
E Safety information for instruments not manufactured by Thermo Fisher Scientific

Safety information for instruments not manufactured by

Thermo Fisher Scientific
Some of the accessories provided as part of the instrument system are not designed or built by Thermo
Fisher Scientific. Consult the manufacturer's documentation for the information needed for the safe use
of these products.

Instrument safety
General

CAUTION! Do not remove instrument protective covers. If you remove the protective instrument
panels or disable interlock devices, you may be exposed to serious hazards including, but not limited
to, severe electrical shock, laser exposure, crushing, or chemical exposure.

CAUTION! Solvents and Pressurized fluids. Wear eye protection when working with any
pressurized fluids. Use caution when working with any polymeric tubing that is under pressure:

· Extinguish any nearby flames if you use flammable solvents.

· Do not use polymeric tubing that has been severely stressed or kinked.
· Do not use polymeric tubing with tetrahydrofuran or nitric and sulfuric acids.
· Be aware that methylene chloride and dimethyl sulfoxide cause polymeric tubing to swell and
greatly reduce the rupture pressure of the tubing.
· Be aware that high solvent flow rates (~40mL/min) may cause a static charge to build up on the
surface of the tubing and electrical sparks may result.

114 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Appendix E Safety
Instrument safety E

Physical injury

CAUTION! Moving and Lifting Injury. The instrument is to be moved and positioned only by the
personnel or vendor specified in the applicable site preparation guide. Improper lifting can cause
painful and permanent back injury.
Things to consider before lifting or moving the instrument or accessories:
· Depending on the weight, moving or lifting may require two or more persons.
· If you decide to lift or move the instrument after it has been installed, do not attempt to do so
without the assistance of others, the use of appropriate moving equipment, and proper lifting
techniques.
· Ensure you have a secure, comfortable grip on the instrument or accessory.
· Make sure that the path from where the object is to where it is being moved is clear of
obstructions.
· Do not lift an object and twist your torso at the same time. Keep your spine in a good neutral
position while lifting with your legs.
· Participants should coordinate lift and move intentions with each other before lifting and carrying.
· For smaller packages, rather than lifting the object from the packing box, carefully tilt the box on its
side and hold it stationary while someone else slides the contents out of the box.

CAUTION! Moving Parts. Moving parts can crush, pinch and cut. Keep hands clear of moving parts
while operating the instrument. Disconnect power before servicing.

WARNING! Do not attempt to lift or move the instrument without the assistance of others. Use
appropriate moving equipment and proper lifting technique, improper lifting may result in serious
injury.

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 115
 Appendix E Safety
E Safety and electromagnetic compatibility (EMC) standards

Electrical safety

WARNING! Fuse Installation. Before installing the instrument, verify that the fuses are properly
installed and the fuse voltage matches the supply voltage. Replace fuses only with the type and
rating specified for the unit. Improper fuses can damage the instrument wiring system and cause a
fire.

WARNING! Ensure appropriate electrical supply. For safe operation of the instrument:
· Plug the system into a properly grounded receptacle with adequate current capacity.
· Ensure the electrical supply is of suitable voltage.
· Never operate the instrument with the ground disconnected. Grounding continuity is required for
safe operation of the instrument.

WARNING! Power Supply Line Cords. Use properly configured and approved line cords for the
power supply in your facility.

WARNING! Disconnecting Power. To fully disconnect power either detach or unplug the power
cord, positioning the instrument such that the power cord is accessible.

Cleaning and decontamination

CAUTION! Cleaning and Decontamination. Use only the cleaning and decontamination methods
specified in the manufacturer's user documentation. It is the responsibility of the operator (or other
responsible person) to ensure the following requirements are met:

· No decontamination or cleaning agents are used that could cause a HAZARD as a result of a
reaction with parts of the equipment or with material contained in the equipment.
· The instrument is properly decontaminated a) if hazardous material is spilled onto or into the
equipment, and/or b) prior to having the instrument serviced at your facility or sending the
instrument for repair, maintenance, trade-in, disposal, or termination of a loan (decontamination
forms may be requested from customer service).
· Before using any cleaning or decontamination methods (except those recommended by the
manufacturer), users should confirm with the manufacturer that the proposed method will not
damage the equipment.

Safety and electromagnetic compatibility (EMC) standards

The instrument design and manufacture complies with the following standards and requirements for
safety and electromagnetic compatibility.

116 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Appendix E Safety
Safety and electromagnetic compatibility (EMC) standards E

Safety compliance
Reference Description

EU Directive 2014/35/EU European Union “Low Voltage Directive”

IEC 61010-1 Safety requirements for electrical equipment for measurement, control, and
laboratory use – Part 1: General requirements
EN 61010-1
UL 61010-1
CSA C22.2 No. 61010-1

IEC 61010-2-010 Safety requirements for electrical equipment for measurement, control and
laboratory use – Part 2-010: Particular requirements for laboratory equipment
EN 61010-2-010
for the heating of materials

IEC 61010-2-081 Safety requirements for electrical equipment for measurement, control and
laboratory use – Part 2-081: Particular requirements for automatic and semi-
EN 61010-2-081
automatic laboratory equipment for analysis and other purposes

EMC
Reference Description

Directive 2014/30/EU European Union “EMC Directive”

EN 61326-1/ IEC 61326-1 Electrical Equipment for Measurement, Control and Laboratory Use –
EMC Requirements – Part 1: General Requirements

AS/NZS CISPR 11 Limits and Methods of Measurement of Electromagnetic Disturbance

Characteristics of Industrial, Scientific, and Medical (ISM)
Radiofrequency Equipment

ICES-001, Issue 4 Industrial, Scientific and Medical (ISM) Radio Frequency Generators

FCC Part 15 Subpart B (47 CFR) U.S. Standard Radio Frequency Devices

This equipment has been tested and found to comply with the limits for a Class A digital device,
pursuant to part 15 of the FCC Rules. These limits are designed to provide reasonable protection
against harmful interference when the equipment is operated in a commercial environment. This
equipment generates, uses, and can radiate radio frequency energy and, if not installed and used
in accordance with the instruction manual, may cause harmful interference to radio communications.
Operation of this equipment in a residential area is likely to cause harmful interference in which case the
user will be required to correct the interference at his own expense.

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 117
 Appendix E Safety
E Safety and electromagnetic compatibility (EMC) standards

Environmental design
Reference Description

Directive 2012/19/EU European Union “WEEE Directive” – Waste electrical and electronic equipment

EU Directive 2011/65/EU European Union “RoHS Directive” – Restriction of hazardous substances in

& Commission Delegated electrical and electronic equipment
Directive (EU) 2015/863

Directive 2006/66/EC European Union “Battery Directive”

China EEP Hazardous Substances Information

Component QuantStudio™ 3 and 5 Real‑Time PCR Systems

Name
Hazardous Substances

(Pb) (Hg) (Cd) (Cr(VI)) (PBB) (PBDE)

PCBA X O O O O O

SJ/T11364. This table is compiled according to SJ/T 11364 standard.

O: GB/T26572.
Indicates that the concentration of the hazardous substance in all homogeneous materials for the part is
below the relevant threshold of the GB/T 26572 standard.
X: GB/T26572.
Indicates that the concentration of the hazardous substance in at least one homogenous material of the
part is above the relevant threshold of the GB/T 26572 standard.

118 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Appendix E Safety
Chemical safety E

Chemical safety
WARNING! GENERAL CHEMICAL HANDLING. To minimize hazards, ensure laboratory personnel
read and practice the general safety guidelines for chemical usage, storage, and waste provided
below. Consult the relevant SDS for specific precautions and instructions:

· Read and understand the Safety Data Sheets (SDSs) provided by the chemical manufacturer
before you store, handle, or work with any chemicals or hazardous materials. To obtain SDSs, see
the "Documentation and Support" section in this document.
· Minimize contact with chemicals. Wear appropriate personal protective equipment when handling
chemicals (for example, safety glasses, gloves, or protective clothing).
· Minimize the inhalation of chemicals. Do not leave chemical containers open. Use only with
sufficient ventilation (for example, fume hood).
· Check regularly for chemical leaks or spills. If a leak or spill occurs, follow the manufacturer
cleanup procedures as recommended in the SDS.
· Handle chemical wastes in a fume hood.
· Ensure use of primary and secondary waste containers. (A primary waste container holds the
immediate waste. A secondary container contains spills or leaks from the primary container.
Both containers must be compatible with the waste material and meet federal, state, and local
requirements for container storage.)
· After emptying a waste container, seal it with the cap provided.
· Characterize (by analysis if needed) the waste generated by the particular applications, reagents,
and substrates used in your laboratory.
· Ensure that the waste is stored, transferred, transported, and disposed of according to all local,
state/provincial, and/or national regulations.
· IMPORTANT! Radioactive or biohazardous materials may require special handling, and disposal
limitations may apply.

WARNING! HAZARDOUS WASTE (from instruments). Waste produced by the instrument is

potentially hazardous. Follow the guidelines noted in the preceding General Chemical Handling
warning.

WARNING! 4L Reagent and Waste Bottle Safety. Four-liter reagent and waste bottles can crack
and leak. Each 4-liter bottle should be secured in a low-density polyethylene safety container with the
cover fastened and the handles locked in the upright position.

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 119
 Appendix E Safety
E Biological hazard safety

Biological hazard safety

WARNING! Potential Biohazard. Depending on the samples used on this instrument, the surface
may be considered a biohazard. Use appropriate decontamination methods when working with
biohazards.

WARNING! BIOHAZARD. Biological samples such as tissues, body fluids, infectious agents,
and blood of humans and other animals have the potential to transmit infectious diseases.
Conduct all work in properly equipped facilities with the appropriate safety equipment (for example,
physical containment devices). Safety equipment can also include items for personal protection,
such as gloves, coats, gowns, shoe covers, boots, respirators, face shields, safety glasses, or
goggles. Individuals should be trained according to applicable regulatory and company/ institution
requirements before working with potentially biohazardous materials. Follow all applicable local,
state/provincial, and/or national regulations. The following references provide general guidelines when
handling biological samples in laboratory environment.

· U.S. Department of Health and Human Services, Biosafety in Microbiological and Biomedical
Laboratories (BMBL), 6th Edition, HHS Publication No. (CDC) 300859, Revised June 2020
https://www.cdc.gov/labs/pdf/CDC-BiosafetymicrobiologicalBiomedicalLaboratories-2020-
P.pdf
· Laboratory biosafety manual, fourth edition. Geneva: World Health Organization; 2020 (Laboratory
biosafety manual, fourth edition and associated monographs)
www.who.int/publications/i/item/9789240011311

120 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 F Documentation and support

Related documentation
Publication
Document Description
number

QuantStudio™ 3 and 5 Real‑Time MAN0010408 Describes the hardware and software

PCR Systems Installation, Use, and and provides information on preparing,
Maintenance Guide using, maintaining, and troubleshooting the
system.

QuantStudio™ Real‑Time PCR System Help MAN0010422 Describes the instrument touchscreen and
provides procedures for configuration,
calibration, and performing a run.

QuantStudio™ Design and Analysis MAN0010409 Describes how to use the command-line
Desktop Software Command-Line software application and provides the
Application Guide procedure to automate the creation of
new experiment files and export data from
existing files.

QuantStudio™ Design and Analysis MAN0010408 Describes how to design and perform
Desktop Software User Guide experiments using the software.

QuantStudio™ Design and Analysis MAN0010415 Describes the software and provides
Desktop Software Help procedures for common tasks.

QuantStudio™ 5 Real‑Time PCR System MAN0010417 Describes the SAE Administrator Console
SAE Admin Console Help and provides procedures for common
tasks.

QuantStudio™ 5 Real‑Time PCR System MAN0010410 Describes how to use the SAE
SAE Admin Console User Guide Administrator Console.

QuantStudio™ Design and Analysis Cloud MAN0010414 Describes the Cloud version of the
Software Help software and provides procedures for
common tasks.

QuantStudio™ 3 and 5 Real‑Time PCR MAN0010405 Explains how to prepare your site to
Systems Site Preparation Guide receive and install the system. Intended
for personnel who schedule, manage, and
perform the tasks required to prepare the
site for installation.

Note: For additional documentation, see “Customer and technical support” on page 122.

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 121
 Appendix F Documentation and support
F Obtain information from the Help system

Obtain information from the Help system

The instrument has a Help system that describes how to use each feature of the touchscreen. Touch
on the instrument touchscreen to access the Help system.

Customer and technical support

Visit thermofisher.com/support for the latest service and support information.
• Worldwide contact telephone numbers
• Product support information
– Product FAQs
– Software, patches, and updates
– Training for many applications and instruments
• Order and web support
• Product documentation
– User guides, manuals, and protocols
– Certificates of Analysis
– Safety Data Sheets (SDSs; also known as MSDSs)

Note: For SDSs for reagents and chemicals from other manufacturers, contact the
manufacturer.

Limited product warranty

Life Technologies Corporation and/or its affiliate(s) warrant their products as set forth in the
Life Technologies' General Terms and Conditions of Sale at www.thermofisher.com/us/en/home/
global/terms-and-conditions.html. If you have any questions, please contact Life Technologies at
www.thermofisher.com/support.

122 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Index

A set up 92
Connect
accessories 104
Link to instrument 80
add to method 35
Roles
administrator instrument profile 76
Administrator 79
Administrator profile 79
Standard 79
Unlink from instrument 83
B Connect profile, Overview 78
connect to network, workflow 90
background calibration
connection, not recognized
create plate 52
consumables
description 44
384-well 102
plate, prepare 47
96-well 0.1-mL 103
Background calibration
96-well 0.2-mL 101
run 48
contamination, identify 52
when to perform 43
custom dye
backup instrument 11, 67
add to the instrument 63
barcode scan 33
calibration plate, create 62
biohazard safety 120
calibration, perform 63
description 13
C dilution guidelines 59
optimal concentration 61
calibration
wavelength requirements 59
reminders 45
custom dye calibration, workflow 59
Background 48
custom dye dilution plate, prepare 60
custom dye. See custom dye
custom melt calibration 65
custom melt 65
Dye 48
plate, prepare 47 D
reminders 45
data collection 14
ROI/Uniformity 48
data collection points, add to method 34
schedule 43
date and time 89
status 45
delete files 42
transfer results 50
desktop software
view images 50
download 95
workflow 46
download and install 94
calibration failure, troubleshoot 51
install 95
Change password 85
disk space message
Change PIN 85
documentation, related 121
Cloud server, select location 88
download desktop software 95
comparative Ct runs 19
dye calibration
computer
description 44
connection to instrument or LAN 95
plate, prepare 47
connections 93
Dye calibration
requirements for desktop software 94
run 48

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 123
Index

when to perform 43 return for service 73

dyes touchscreen black
custom 13, 59 instrument filters 12
system 12 instrument layout 105
instrument settings 26
instrument specification 105
E instrument verification. See RNase P verification
Edit profile 85
EDS files, transfer 41
EDT files, copy or delete 42 L
Ethernet port 97 limited product warranty 122
experiment load plate 37, 38
create from template 30 Local instrument profile, Overview 78
edit 32 lock the touchscreen 41
run from saved file 30
run last 31
M
maintenance 67
F melt curve runs 19
factory defaults 87 melt curves, add to method 34
firewall ports 97 method
fluorescence high add melt curves 34
fuses, replace 71 add stages 34
add steps 34
data collection points 34
G edit 33
genotyping runs 19 parts of 34
guest profile pause 35
disable 86 ramp rate 35
limits 25

N
H network
Help system, access 122 configurations supported 95
home screen, parts of 23 guidelines and best practices 98
wired connection set up 87
wireless connection set up 88
I network configuration and security 10
install, desktop software 95 networking 95
installation
before you begin 91
desktop software 94 O
workflow 90 online Help. See Help system
instrument Order to set up profiles 78
profile, create 25
connections 93
enable for monitoring 86 P
move 73 Password, Change 85
name 88 password security 10
overview 11 pause run 40
parts of 15 performance verification. See RNase P verification
power off 72 PIN, Change 85
power on 22, 72 PIN reset 76
prepare to store or move or ship 73 presence/absence runs 19

124 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
 Index

Profile S
Connect
SAE mode (Security, Audit, and e‑Signature) 85
Link 80
safety, biohazard 120
Unlink 83
sample block
Edit 85
clean 68
profiles
decontaminate 68
administrator 76
settings 26
delete 76
sign in, require 86
edit 77
sign out
guest, disable 86
profile 26
instrument 25
timer, set 89
require sign-in 86
sleep mode 72
reset PIN 76
software features 15
sign in 25
software updates 86
Profiles
stages, add to method 34
Connect
standard curve runs 19
Administrator 79
Standard profile 79
Standard 79
standby mode 72
Order to set up 78
startup wizard 92
properties, enter or edit 32
steps, add to method 34
protocol. See method
stop run 40
support, customer and technical 122
R supported dyes 12
real-time plots symbols, safety 110
view on instrument touchscreen 40 system dyes 12
zoom 41
related documentation 121 T
relative standard curve runs 19
template properties. See properties
Replace with index term
terms and conditions 122
require sign in 86
thermal protocol. See method
restore instrument 11, 67
Thermo Fisher Connect profile, Edit 85
RNase P verification
third-party software 18
pass criteria 55
transfer files 42
plate description 53
troubleshooting 99
run 56
RNase P verification, plate, prepare 55
ROI/uniformity calibration U
description 44
uniformity calibration
plate, prepare 47
description 44
ROI/Uniformity calibration
plate, prepare 47
run 48
unload plate 37, 38
when to perform 43
unpack instrument 91
run
use the instrument, workflow 29
pause or stop 40
post-PCR 14
real-time 14 V
run data, transfer 41
verification failure, troubleshoot 57
run history 42
run last experiment 31
run protocol. See method W
runs, types 19
warranty 122
well details

QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide 125
Index

define, assign, view 36 Z

view on instrument touchscreen 40
zoom 41
workflow, use the instrument 29

126 QuantStudio™ 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide
QS 35 Instrument UG_RUO_MAN0010407EN no translations-v12-GUID-88D256DF-7F65-4A04-
B662-0DCAA6DC61A6-2021/07/21 16:29:30 en
16:15:10.886+01:00
thermofisher.com/support | thermofisher.com/askaquestion
thermofisher.com

22 July 2021