QuantStudio 3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide (Pub. No. MAN0010407 F)

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

QuantStudio

™

3 and 5 Real‑Time PCR

Systems

INSTALLATION, USE, AND MAINTENANCE

Firmware v1.6

Publication Number MAN0010407

Revision F

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.

Revision history: MAN0010407 F (English)

Revision Date Description

F 8 August 2024

•

Information about using tubes/tube strips was added (“Options for loading MicroAmp

™

consumables with

the QuantStudio

™

3 and 5 Real‑Time PCR Systems” on page40 and “Prepare samples using MicroAmp

™

tubes/tube strips with separate cap strips” on page43).

•

Caution information about ﬂat caps for tubes was moved to “Prepare samples using MicroAmp

™

tubes/tube

strips with separate cap strips” on page43.

•

Information about instrument power issues during runs was added (“View run history and delete or transfer

ﬁles from the instrument” on page47).

•

Minor verbiage was updated.

E.0 31 January 2024

v1.6

•

The information about instrument settings was updated to indicate that this feature is available only to users

that are signed in when SAE mode is enabled (“Conﬁgure instrument settings” on page27).

•

The instructions to delete a run from the run history were updated to indicate that only an Administrator

can perform this function when SAE mode is enabled (

“View run history and delete or transfer ﬁles from the

instrument” on page47).

•

A data management feature was added to the settings (“Conﬁgure instrument settings” on page27).

•

Instructions were added to perform a self-veriﬁcation test, to view the instrument logs, and to connect the

instrument to a network drive.

•

The instructions to set the date and time were updated. The date and time cannot be set if the instrument is

linked to the Thermo Fisher

™

Connect Platform.

•

The instructions to test the connection to the Thermo Fisher

™

Connect Platform were removed. This feature

is not available.

•

The requirements for the computer for the desktop software were updated.

•

The support that is provided for the computer for the desktop software was updated.

D.0 21 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

Revision Date Description

D.0

(contin

ued)

21 July 2021

•

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 16 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

B.0 1 October 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 23 April 2015

New document. Describes installation, operation, and maintenance of the QuantStudio

™

3 and 5 Real‑Time PCR

Systems.

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.

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 trademark of Roche Molecular Systems, Inc., used under permission and license. Cy is a registered trademark of GE Healthcare.

Windows is a trademark of Microsoft Corporation. Chrome is a trademark of Google LLC. Core and Intel are trademarks of Intel

Corporation.

Contents

About thisguide .......................................................... 10

Purpose ...................................................................... 10

■

CHAPTER1Productinformation ................................................ 11

Network and password security requirements ..................................... 11

Network conﬁguration andsecurity .......................................... 11

Passwordsecurity ......................................................... 11

Perform internal validations before software upgrades .............................. 11

Update the instrumentﬁrmware .................................................. 12

Back up theinstrument ..................................................... 12

Instrument hardwaredescription ................................................. 12

Instrument overview ....................................................... 12

Parts of theinstrument ..................................................... 16

Softwaredescription ........................................................... 16

Instrument, desktop, and cloud software features .............................. 16

Folders, templates, experiments, and projects ................................. 17

Third-party software ....................................................... 19

Network connectionoptions ..................................................... 19

Types ofruns .................................................................. 19

■

CHAPTER2Start, sign on, and conﬁgure theinstrument ..................... 22

Installation and instrumentveriﬁcation ............................................ 22

Precautions foruse ............................................................. 23

Power on theinstrument ........................................................ 23

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

Use the instrument without signingin ............................................. 26

Create a new instrumentproﬁle .................................................. 26

Signin ........................................................................ 27

Signout ...................................................................... 27

Conﬁgure instrumentsettings .................................................... 27

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

■

CHAPTER3Create and run experiments on theinstrument .................. 31

Workﬂow ..................................................................... 32

Options for running an experiment ............................................... 33

Create and run an experiment from a template ................................ 33

Run an experiment from a savedﬁle ......................................... 33

Repeat the last instrumentrun ............................................... 34

Edit an experiment before starting arun .......................................... 35

Enter or edit template properties ............................................. 35

Edit the runmethod ........................................................ 36

Deﬁne, assign, and view welldetails ......................................... 39

Options for loading MicroAmp

™

consumables with the QuantStudio

™

3 and 5

Real‑Time PCR Systems ...................................................... 40

Load and unload the plate ...................................................... 40

Load and unload a plate in theinstrument .................................... 40

(If applicable) load and unload a plate in the instrument with a compressionpad ... 41

Prepare samples using MicroAmp

™

tubes/tube strips with separate capstrips ......... 43

View, pause, or stop arun ....................................................... 45

View real-time data and plots on the instrument touchscreen .................... 45

Pause or stop an instrumentrun ............................................. 45

Adjust the display of real-time plots on the instrument touchscreen .............. 46

Lock the touchscreen during arun ........................................... 46

Transfer, view, or manage ﬁles and results ......................................... 46

Transfer EDS ﬁles from the instrument home screen ............................ 46

View run history and delete or transfer ﬁles from theinstrument ................. 47

Manage templates (EDTﬁles) ................................................ 47

■

CHAPTER4Calibrate and verify instrument performance ..................... 49

Calibration and veriﬁcationschedule ............................................. 49

Calibrationdescriptions ......................................................... 50

View the calibration status and set reminders ...................................... 51

View calibration status and set reminders in theinstrument ..................... 51

View calibration status and set reminders in Thermo Fisher

™

ConnectPlatform .... 51

Perform ROI/uniformity, background, and dye calibrations .......................... 52

Workﬂow: Calibration ...................................................... 52

Prepare a calibration plate .................................................. 53

Perform calibrations ........................................................ 54

View calibration images and transfer results to a USBdrive ..................... 56

Troubleshoot calibration failure .............................................. 57

Identifycontamination ...................................................... 57

Create a background plate (optional) ......................................... 58

Contents

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Perform instrument veriﬁcation using RNase P plates ............................... 59

Instrument veriﬁcationdescription ........................................... 59

RNaseP instrument veriﬁcation plate ........................................ 59

Performance speciﬁcations pass criteria ...................................... 61

Prepare an RNase P plate ................................................... 61

Perform RNasePveriﬁcation ................................................ 62

Troubleshoot veriﬁcation failure .............................................. 63

Calibrate customdyes .......................................................... 65

Custom dyes overview ..................................................... 65

Use a dilution series to determine an optimal custom dye concentration .......... 65

Calibrate the customdye ................................................... 68

Calibrate for a custom melt curve experiment ...................................... 72

■

CHAPTER5Maintain theinstrument ............................................ 74

Back up or restore theinstrument ................................................ 74

Perform a self-veriﬁcation test ................................................... 75

View instrumentlogs ........................................................... 75

Conﬁgure the networkdrive ..................................................... 75

Create a shared networkfolder .............................................. 76

Determine the IP address of the computer .................................... 77

Determine the DNSname ................................................... 77

Decontaminate the sampleblock ................................................ 77

Materials required .......................................................... 77

Clean the sampleblock ..................................................... 78

Detailed procedures for cleaning the sampleblock ............................. 79

Replace the instrumentfuses .................................................... 80

Materials required .......................................................... 80

Replace thefuses .......................................................... 80

Power on or o, store, andmove ................................................. 81

Enable sleepmode ........................................................ 81

Power on theinstrument .................................................... 81

Power o theinstrument .................................................... 82

Prepare the instrument to store, move, orship ................................. 82

Move theinstrument ....................................................... 82

Return the instrument for service ............................................ 83

Contents

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

■

CHAPTER6Conﬁgure the instrument and manage instrumentproﬁles ..... 84

Initial start‑up .................................................................. 84

Manageproﬁles ................................................................ 85

Create an administrator instrument proﬁle during initial start-up ................. 85

Manage all instrument proﬁles (Administratoronly) ............................. 85

Edit an instrumentproﬁle ................................................... 86

Link an instrument proﬁle to Thermo Fisher

™

Connect .............................. 86

Recommended order to set upproﬁles ....................................... 87

Overview of local instrument proﬁles and Thermo Fisher

™

Connectproﬁles ....... 87

Thermo Fisher

™

Connect Platform instrument proﬁle roles andfunctions ......... 88

Link the instrument to your Thermo Fisher

™

Connect Platformaccount ........... 88

Link a local proﬁle to a Thermo Fisher

™

Connectproﬁle ......................... 89

Unlink a Thermo Fisher

™

Connectaccount .................................... 91

If you link when you are signed in to theinstrument ............................ 91

Change the PIN for a Thermo Fisher

™

Connectproﬁle .......................... 92

Enable SAE mode (Administratoronly) ............................................ 92

Require instrument proﬁle sign-in (Administratoronly) .............................. 93

Enable remote instrument monitoring (Administratoronly) ........................... 93

Update instrument software (Administratoronly) ................................... 94

Restore factorydefaults ......................................................... 94

Conﬁgure thenetwork .......................................................... 94

Set up a wiredconnection .................................................. 95

Set up a wirelessconnection ................................................ 95

Select a region for the Thermo Fisher

™

Connect Platform (Administratoronly) ......... 96

Manage the instrument name (Administratoronly) .................................. 96

Set the date and time (Administratoronly) ......................................... 96

Manage the signout timer (Administrator only) ..................................... 97

■

APPENDIXAInstall and connect the instrument to anetwork ................ 98

Workﬂow: Install and connect to anetwork ........................................ 98

Before youbegin ............................................................... 99

Unpack and install theinstrument ................................................ 99

Power on and follow the startup wizard .......................................... 100

Connect the computer to the instrument directly or to aLAN ....................... 100

Instrument and computerconnections ........................................... 101

Contents

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Download and install the desktop software ....................................... 102

Computer requirements for the desktop software ............................. 102

Download the desktop software ............................................ 103

Install the desktop software ................................................ 103

Networking ................................................................... 103

Supported options for instrument and computerconnections .................. 103

Control and monitor networkedinstruments .................................. 105

Ethernet port overview .................................................... 105

Firewall ports that must beopen ............................................ 105

Networking guidelines and best practices ................................... 106

■

APPENDIXBTroubleshooting .................................................. 107

■

APPENDIXCParts and materials .............................................. 109

Kits, consumables, accessories, and reagents .................................... 109

Consumables (96‑well, 0.2‑mLformat) ........................................... 109

384-wellconsumables ......................................................... 110

Consumables (96-well, 0.1-mLformat) .......................................... 111

Accessories .................................................................. 112

General-use materials andconsumables ......................................... 112

■

APPENDIXDInstrument speciﬁcation andlayout ............................ 113

Conﬁgured systemdimensions ................................................. 114

Instrument clearances ..................................................... 115

Electrical requirements ........................................................ 115

Environmental requirements .................................................... 116

Network requirements ......................................................... 116

■

APPENDIXESafety .............................................................. 118

Symbols on thisinstrument .................................................... 118

Conformitysymbols ...................................................... 120

Safety alerts on thisinstrument ................................................. 121

Location of safety labels on theinstrument .................................. 121

Safety information for instruments not manufactured by Thermo FisherScientiﬁc ..... 122

Instrumentsafety ............................................................. 122

General ................................................................. 122

Physical injury ............................................................ 123

Electricalsafety .......................................................... 124

Cleaning anddecontamination ............................................. 124

Contents

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Safety and electromagnetic compatibility (EMC) standards ......................... 124

Safetycompliance ........................................................ 125

EMC .................................................................... 125

Environmentaldesign ..................................................... 126

Chemicalsafety .............................................................. 127

Biological hazardsafety ....................................................... 128

■

APPENDIXFDocumentation and support ..................................... 129

Relateddocumentation ........................................................ 129

Obtain information from the Help system ........................................ 129

Customer and technical support ................................................ 129

Limited product warranty ...................................................... 130

Index ..................................................................................... 131

Contents

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

Product information

■

Network and password security requirements ............................................ 11

■

Perform internal validations before software upgrades ..................................... 11

■

Update the instrumentﬁrmware ........................................................ 12

■

Instrument hardwaredescription ....................................................... 12

■

Softwaredescription .................................................................. 16

■

Network connectionoptions ........................................................... 19

■

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.

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Update the instrument ﬁrmware

If your instrument is not on version 1.6 or later of the ﬁrmware you must update the ﬁrmware to

access the features and updates described in Revision E.0 of the revision history. 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 “Back up the instrument” on page12.

Back up the instrument

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

Touch Backup Instrument.

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

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

Enter a backup ﬁle name, then touch Done.

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

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).

Chapter1Product information

Update the instrument ﬁrmware

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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

™

0.1-mL Block (4Color)

•

96-Well VeriFlex

™

0.2-mL Block (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.

Peak

ﬁlter

Color

Filter wavelength (nm)

[1]

Factory-calibrated dyes Example customdyes

Excitation Emission

x1-m1 Blue 470 ± 15nm 520 ± 15nm

FAM

™

dye, SYBR

™

Green

dye

SYT09

x2-m2 Green 520 ± 10nm 558 ± 12nm VIC

™

dye

JOE

™

dye,

HEX

™

dye, TET

™

dye

[2]

x3-m3 Yellow 550 ± 10nm 587 ± 10nm

NED

™

dye, TAMRA

™

dye,

ABY

™

dye

3 dye

x4-m4 Orange 580 ± 10nm 623 ± 14nm ROX

™

dye, JUN

™

dye Texas Red

™

dye

x5-m5 Red 640 ± 10nm 682 ± 14nm

MUSTANG PURPLE

™

dye,

LIZ

™

dye

x6-m6

Deep-

Red

662 ± 10nm 711 ± 12nm None

[3]

5.5 dye

[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.

Chapter1Product information

Instrument hardware description

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Filters

Wavelength

(nm)

x1-m1 x2-m2

x3-m3

x4-m4

x5-m5 x6-m6

Emission

Spectra

x1-m1 — FAM

™

dye, SYBR

™

Green dye

x2-m2 — VIC

™

dye

x3-m3 — ABY

™

dye, NED

™

dye, Cy

3 dye, TAMRA

™

dye

x4-m4 — JUN

™

dye, ROX

™

dye, Texas Red

™

dye

x5-m5 — Cy

5 dye, 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65).

•

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13).

•

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.

Chapter1Product information

Instrument hardware description

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

About data collection

The instrument collects raw ﬂuorescence data at dierent points during the PCR cycle, depending on

the type of run performed.

When you create 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 dierent ﬁlter set for the melt curve stages.

Run type Experiment type Data collection point

Real-time

•

Standard curve

•

Relative standard

curve

•

Comparative C

(ΔΔC

)

•

Melt curve

During the thermal cycling protocol.

Typical timing is to collect data at each cycle of a PCR stage

or continuously during a melt stage.

Post-PCR

(endpoint)

•

Genotyping

•

Presence/ Absence

•

After thermal cycling is completed.

For Presence/Absence and Genotyping 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 oer

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]

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

Chapter1

Product information

Instrument hardware description

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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

Touchscreen – Controls the instrument.

USB port – For connection to an external network drive or external data storage device.

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 Platform) include the features described below.

Feature

Instrument Desktop

Thermo Fisher

™

Connect Platform

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 ✓ ✓ —

Chapter1Product information

Software description

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

(continued)

Feature Instrument Desktop

Thermo Fisher

™

Connect Platform

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]

™

5 System only)

Folders, templates, experiments, and projects

Term

Deﬁnition Supported in

Folders in Load

Experiment

Location in which you can store templates (EDT ﬁles) on the

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

Instrument

Chapter1Product information

Software description

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

(continued)

Term

Deﬁnition Supported in

Experiment

Template File

(EDT)

Default settings for an instrument run, can be modiﬁed before

instrument run.

Two types:

•

Factory-provided, accessed from Open Template (instrument)

or Create Experiment (desktop or Thermo Fisher

™

Connect

Platform)

•

User-created, accessed from Load Experiment

Instrument

Desktop

Thermo Fisher

™

Connect Platform

Experiment Run

File (EDS)

Settings and data for a completed instrument run. Instrument

Desktop

Thermo Fisher

™

Connect Platform

Template and

experiment

components

Instrument Desktop

Thermo Fisher

™

Connect

Platform

Properties

•

Experiment ﬁle name

•

Reagent information

(Reagent barcode, Lot#)

•

Plate barcode

•

Data management (location

for auto-transfer of data)

•

Comments (Tags are not

used at this time)

•

Experiment ﬁle name

•

Plate barcode

•

User name

•

Instrument type

•

Block type

•

Experiment type

•

Chemistry (reagent information)

•

Run mode

•

Comments

•

(Thermo Fisher

™

Connect Platform only) Notiﬁcations

Method Thermal cycling conditions Thermal cycling conditions

Plate Sample names

You cannot edit targets/SNP

assays or tasks on the

instrument.

Deﬁne and assign samples, targets or SNP assays, and tasks in

the Quick Setup and Advanced Setup panes of the Plate tab.

Run Start and monitor a run in

progress

View: time remaining and

temperature, method, plots

Pause, resume, stop a run

Start and monitor a run in

progress

View: time remaining and

temperature, method, plots

Monitor a run in progress (link

to Thermo Fisher

™

Connect

Platform Instrument Details)

View: time remaining and

temperature, method, plots

Chapter1Product information

Software description

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

(continued)

Template and

experiment

components

Instrument Desktop

Thermo Fisher

™

Connect

Platform

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

You can connect an instrument to a network or computer in the conﬁgurations listed below. For speciﬁc

information on networking, see “Networking” on page103.

Direct connection

Local area network (LAN) connection

Thermo Fisher

™

Connect Platform

connection

wired wired or wireless wired or wireless

LAN

Types of runs

Purpose

Description

Standard curve run

Determines absolute

target quantity in

samples.

The software measures ampliﬁcation of the target in a standard dilution series and

in test samples.

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

series.

The software uses the standard curve to interpolate the absolute quantity of target

in the test samples.

Chapter1Product information

Network connection options

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Purpose

Description

Relative standard curve run

Determines relative target

quantity in samples.

The software measures ampliﬁcation of the target of interest and of an endogenous

control target in a standard dilution series, in a reference (calibrator) sample, and in

test samples.

The endogenous control is a target that is expressed equally in all samples;

examples of endogenous controls are β‐actin, GAPDH, and 18S ribosomal RNA.

The software can algorithmically incorporate multiple endogenous control targets in

relative

quantiﬁcation calculations.

The reference sample is used as the basis for relative quantiﬁcation results (or

1× sample). For example, in a study of drug eects on gene expression, an

untreated control is an appropriate reference sample.

The software generates standard curves for the target of interest and the

endogenous control using data from the corresponding standard dilution series.

The software uses the standard curves to interpolate the quantities of the target of

interest and the endogenous control in each sample. The target quantity in each

sample is then normalized to the sample's endogenous control quantity.

To determine the relative quantity of the target in test samples, the software divides

the normalized target quantity in the sample by the normalized target quantity in

the reference sample.

Comparative C

(ΔΔC

) run

Determines relative target

quantity in samples.

The software measures ampliﬁcation of the target of interest and of an endogenous

control target in a reference (calibrator) sample and in test samples.

The endogenous control is a target that is expressed equally in all samples;

examples of endogenous controls are β‐actin, GAPDH, and 18S ribosomal RNA.

The software can algorithmically incorporate multiple endogenous control targets in

relative

quantiﬁcation calculations.

The reference sample is used as the basis for relative quantiﬁcation results (or

1× sample). For example, in a study of drug eects on gene expression, an

untreated control is an appropriate reference sample.

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

control.

To determine the relative quantity of the target in test samples, the software

compares the normalized ΔC

(ΔC

or ΔC

) for the sample to the normalized

ΔC

(ΔC

or ΔC

) for the reference sample.

Chapter1Product information

Types of runs

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Purpose

Description

Genotyping run

Detects single nucleotide

polymorphism (SNP)

variants of a target

nucleic acid sequence.

Genotyping runs use preformulated TaqMan

™

SNP Genotyping Assays that include the

following components:

•

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

of interest

•

Two allele-speciﬁc TaqMan

™

probes for Allele 1 and Allele 2

The software normalizes the ﬂuorescence of the reporter dyes to the ﬂuorescence

of the passive reference dye in each well.

The software plots the normalized reporter dye signal of each sample well on

an Allelic Discrimination Plot, which contrasts the reporter dye intensities of the

allele-speciﬁc probes.

The software algorithmically clusters the sample data, and assigns a genotype call

to the samples of each cluster according to its position on the plot.

Presence/absence run

Determines the presence

or absence of a target

nucleic acid sequence in

a sample.

The software calls the target present or absent based on an algorithmically determined

call threshold. (The call threshold is dierent from the C

threshold; the C

threshold is

not used to make calls.)

Melt curve run

Determines the melting

temperature (T

) of the

ampliﬁcation products

of a PCR that used

intercalating dyes.

In the software, melt curve analysis is included in the default run method for any run

type that uses intercalating dyes.

The software plots a melt curve based on the ﬂuorescence of the dye with respect

to change in temperature.

Using the melt curve, the software calculates the melting temperature (T

Chapter1Product information

Types of runs

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Start, sign on, and conﬁgure the

instrument

■

Installation and instrumentveriﬁcation .................................................. 22

■

Precautions foruse ................................................................... 23

■

Power on theinstrument .............................................................. 23

■

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

■

Use the instrument without signingin ................................................... 26

■

Create a new instrumentproﬁle ........................................................ 26

■

Signin .............................................................................. 27

■

Signout ............................................................................. 27

■

Conﬁgure instrumentsettings .......................................................... 27

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99).

•

Verify instrument performance (see “Perform instrument veriﬁcation using RNase P plates” on

page59).

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49).

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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

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.

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.

Chapter2Start, sign on, and conﬁgure the instrument

Precautions for use

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Parts of the home screen

8 7

Avatar and Instrument name

Eject icon

Help icon

Status dial

Current user name; instrument block type

Settings button

Buttons for accessing EDT ﬁles

Connectivity icons

Chapter2Start, sign on, and conﬁgure the instrument

Parts of the home screen

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Table1Parts of the home screen

Element of the home

screen

Function

For more information,

see...

Avatar and Instrument

name

Set by the administrator to uniquely identify instrument. “Manage the instrument

name (Administrator

only)” on page96.

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.

—

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 name

and block type

Displays the user name of the current signed-in user and the

instrument block 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 the

instrument.

“Conﬁgure instrument

settings” on page27.

Buttons for accessing

experiment and

template ﬁles

Load Experiment – Touch to open a user-created EDT ﬁle from

a Thermo Fisher

™

Connect Platform account, USB, instrument

folder, or network drive.

“Run an experiment

from a saved ﬁle” on

page33.

Open Template – Touch to open a system EDT template ﬁle. “Create and run an

experiment from a

template” on page33.

Run Last – Touch to open the last EDT ﬁle run on the instrument.

•

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.

“Repeat the last

instrument run” on

page34.

Connectivity icons

•

—The instrument is connected to a wired network.

•

—The instrument is wirelessly connected.

•

—A USB drive is plugged into the instrument.

•

—The instrument is linked to a Thermo Fisher

™

Connect

Platform account.

—

Chapter2Start, sign on, and conﬁgure the instrument

Parts of the home screen

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Table 1 Parts of the home screen(continued)

Element of the home

screen

Function

For more information,

see...

(My Proﬁle button

when a user is signed

in)

•

Touch Sign In to sign into an instrument proﬁle and link to

a Thermo Fisher

™

Connect Platform account.

•

Touch My Proﬁle to change instrument proﬁle settings,

link to a Thermo Fisher

™

Connect Platform account, or lock

the instrument during a run.

“Sign in” on page27.

Use the instrument without signing in

If the instrument is conﬁgured by an Administrator to allow guest access ( Settings4Manage

Users4Sign In Required set to o), 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 Platform (only to USB or network drive).

Create a new instrument proﬁle

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

Touch Name, enter a username, then touch Done.

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

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

Touch Conﬁrm PIN, then repeat step2.

Touch Create proﬁle.

Note: To enable access to Thermo Fisher

™

Connect Platform, see “Link an instrument proﬁle to

Thermo Fisher

™

Connect” on page86.

Chapter2Start, sign on, and conﬁgure the instrument

Use the instrument without signing in

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Create an instrument proﬁle before signing into the instrument. See “Create a new instrument proﬁle”

on page26.

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.

In the home screen, touch SignIn.

Touch SignIn, then select your username.

Enter your PIN, then touch Enter.

Note: To enable access to Thermo Fisher

™

Connect Platform, see “Link an instrument proﬁle to

Thermo Fisher

™

Connect” on page86.

Sign out

In the home screen, touch MyProﬁle.

Touch SignOut.

Conﬁgure instrument settings

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

Note: When SAE mode is enabled, the Settings button is not available if a user is not signed in.

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

Chapter2

Start, sign on, and conﬁgure the instrument

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Options Description

Instrument Settings

Instrument Name

(Administrator only)

Instrument name. If connected to a network, the instrument name must be unique.

(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 o 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

(Administrator only)

Required for API access to the instrument. When enabled, the desktop cannot connect

to the instrument.

API access to the instrument is exclusive to authorized OEM partners.

Cloud Region

(Administrator only)

Specify the regional server location to access Thermo Fisher

™

Connect Platform.

Note: Once you set a region for the cloud platform, restore factory defaults to change

the region.

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 “Back up

or restore the instrument” on page74).

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

(Administrator only)

(QuantStudio

™

5 Real‑Time

PCR Instrument only)

When enabled the following items apply:

•

The home screen displays SAE mode.

•

Runs must be started from the desktop software. The instrument locks out 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.

•

The Settings button is not available if a user is not signed in.

Chapter2Start, sign on, and conﬁgure the instrument

Conﬁgure instrument settings

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Options Description

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

(Administrator only)

Update the instrument software.

Monitoring

(Administrator only)

Enable:

•

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.

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.

Chapter2Start, sign on, and conﬁgure the instrument

Conﬁgure instrument settings

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Options Description

Manage Users

(Administrator only)

Enable the restriction of instrument use to only signed-in users (disables Guest proﬁle

use).

Sign Out Timer

(Administrator only)

Set the duration of inactivity before a user is automatically signed out.

Manage Proﬁles

(Administrator only)

•

Instrument

•

Cloud

•

All Proﬁles

Displays the proﬁle information for the instrument and the associated Thermo Fisher

™

Connect Platform account.

Data Management

User deﬁned or System

deﬁned

(Administrator only)

When data management is system-deﬁned, the destination to save the data cannot be

edited by an individual user.

When data management is system-deﬁned, the Thermo Fisher

™

Connect Platform

cannot be selected as a location to save the data. The Thermo Fisher

™

Connect

Platform is speciﬁc to each user and cannot be system-deﬁned.

When data management is user-deﬁned, each individual user can select the

destination to save the data.

USB and Network

(Administrator only)

Select the default destination to save the data.

Automatically transfer run

data (EDS ﬁles)

Select the Automatically transfer run data (EDS ﬁles) checkbox to automatically

transfer EDS ﬁles after the run. The Automatically transfer run data (EDS ﬁles)

checkbox is available for both the USB drive destination and the network drive

destination.

Chapter2Start, sign on, and conﬁgure the instrument

Conﬁgure instrument settings

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Create and run experiments on the

instrument

■

Workﬂow ............................................................................ 32

■

Options for running an experiment ...................................................... 33

■

Edit an experiment before starting arun ................................................. 35

■

Options for loading MicroAmp

™

consumables with the QuantStudio

™

3 and 5 Real‑Time

PCR Systems ........................................................................ 40

■

Load and unload the plate ............................................................ 40

■

Prepare samples using MicroAmp

™

tubes/tube strips with separate capstrips ............... 43

■

View, pause, or stop arun ............................................................. 45

■

Transfer, view, or manage ﬁles and results ............................................... 46

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Workﬂow

Start the instrument

▼

(Optional) Sign in to your instrument proﬁle

(Optional) Link to your Thermo Fisher

™

Connect Platform 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 Platform

▼

Transfer results (EDS ﬁle) to the desktop software or Thermo Fisher

™

Connect Platform, then analyze

Chapter3Create and run experiments on the instrument

Workﬂow

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Options for running an experiment

Create and run an experiment from a template

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

In the home screen, touch Open Template.

(Optional) Touch a category in the left column.

Touch the ﬁle name.

(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”).

(Optional) Edit the run method (see “Edit the run method” on page36).

•

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.

(Optional) Deﬁne plate wells with sample names and view Well ID, Targets, or Dyes (see “Deﬁne,

assign, and view well details”).

Load a plate into the instrument (see “Load and unload the plate” on page40).

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

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

In the home screen, touch Load Experiment.

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.

Touch the ﬁle name.

(Optional) “Manage templates (EDT ﬁles)” in either USB or

MyInstrument.

Chapter3

Create and run experiments on the instrument

Options for running an experiment

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

(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”).

(Optional) Edit the run method (see “Edit the run method” on page36).

•

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.

(Optional) Deﬁne plate wells with sample names and view Well ID, Targets, or Dyes (see “Deﬁne,

assign, and view well details”).

Load a plate into the instrument (see “Load and unload the plate” on page40).

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.

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

In the home screen, touch Run Last.

(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”).

(Optional) Edit the run method (see “Edit the run method” on page36).

•

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.

(Optional) Deﬁne plate wells with sample names and view Well ID, Targets, or Dyes (see “Deﬁne,

assign, and view well details”).

Load a plate into the instrument (see “Load and unload the plate” on page40).

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.

Chapter3

Create and run experiments on the instrument

Options for running an experiment

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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33.

•

“Run an experiment from a saved ﬁle” on page33.

•

“Repeat the last instrument run” on page34.

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

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

•

Edit the ﬁle name for the EDS ﬁle for the run.

Touch the Run File Name ﬁeld.

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

•

Enter a plate barcode.

Touch the Plate Barcode ﬁeld.

Enter or scan the plate barcode, then touch Done.

•

Record reagents and their expiration dates.

Touch Reagent Information.

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

Touch the Name, Type, Lot #, Reagent Barcode, Part #, or Expiration Date ﬁeld to enter

individual reagent information.

Touch Done.

•

Automatically transfer run data (EDS ﬁle) when an instrument run ends.

Touch Data Destination.

Touch the appropriate icon to select a data destination.

Under the desired data destination, select Automatically transfer experiment.

Touch Done.

•

Enter a comment.

Touch Comments.

Enter text, then touch Done.

Chapter3

Create and run experiments on the instrument

Edit an experiment before starting a run

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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.

Click the Barcode ﬁeld.

Hold the scanner 20–30 cm away from a plate or container label and aim at the center of the

barcode, then press the trigger.

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

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

•

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

•

Transmits other reagent information (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33.

•

“Run an experiment from a saved ﬁle” on page33.

•

“Repeat the last instrument run” on page34.

For an overview of the method as it is graphically represented on the touchscreen, see “Method

elements” on page37.

In the Method screen:

Touch Edit.

Touch a ﬁeld, enter changes, then touch Enter.

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

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39).

Chapter3Create and run experiments on the instrument

Edit an experiment before starting a run

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Method elements

Method tab

Heated cover temperature

Reaction volume

Stage of thermal protocol

Step within a stage

Number of cycles for the stage

Temperature for the step

Hold time for the step

Data collection point

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39).

•

In the Method screen, touch Edit4Manage Steps.

Option

Procedure

Add a step

Touch Add/Remove steps4Add steps.

Touch on the left or right border of a step to add a step before or after the

step, respectively.

Enter parameters for the new step, then touch Enter.

Touch Done.

Remove a step

Touch Add/Remove steps4Remove steps.

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

Chapter3Create and run experiments on the instrument

Edit an experiment before starting a run

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

(continued)

Option Procedure

Add a stage

Touch Add/Remove stages4Add stages.

Touch on the left or right border of a stage to add a stage before or after

the stage, respectively.

Edit parameters of the new stage in the Method screen. See “Edit the run

method” on page36.

Touch Done.

Remove a stage

Touch Add/Remove stages4Remove stages.

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

Add a melt curve

Touch Melt curves4Add melt curve.

Touch on the left or right border of a step to add a melt curve before or

after the step, respectively.

Select Continuous or Step and hold.

Touch melt curve parameters to edit, then touch Done.

Touch Done.

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

or placement of melt curves.

Remove a melt

curve

Touch Remove melt curve.

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

Add or remove

data collection

points

Touch Data collection location.

Touch to switch data collection on or o.

Chapter3Create and run experiments on the instrument

Edit an experiment before starting a run

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Conﬁgure VeriFlex

™

Zones, ramp rates, and pause settings

•

In the Method screen, touch Edit4Manage Steps4Advanced Options.

Option Procedure

Use VeriFlex

™

Zones (96‑well

blocks only)

Touch VeriFlex

™

Zones.

Touch on the step to apply VeriFlex

™

Zones.

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.

(Optional) Apply additional VeriFlex

™

Zones.

Touch Done.

Edit ramp rates

Touch Ramp Rates.

Touch the ramp rates ﬁelds.

Touch Enter.

(Optional) Edit additional steps, then touch Done.

Add a pause into

the method

Touch Add Pause.

Touch in a stage.

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

Touch Enter.

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

Touch Done.

Deﬁne, assign, and view well details

Access a template (EDT ﬁle). For more information, see the following sections.

•

“Create and run an experiment from a template” on page33.

•

“Run an experiment from a saved ﬁle” on page33.

•

“Repeat the last instrument run” on page34.

Chapter3Create and run experiments on the instrument

Edit an experiment before starting a run

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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

Option Procedure

Deﬁne and assign samples in

the plate layout view

Touch .

Touch Manage or touch an individual well.

Touch the Samples subtab.

Select one or more wells, then touch Edit.

Enter sample names for the selected wells, then touch Done.

Deﬁne and assign samples in

the well table view

Touch .

Touch Edit to edit sample names for individual wells.

Touch a sample name ﬁeld, enter a new name, then touch Done.

View target information

Touch .

Touch Manage or touch an individual well.

Touch the Targets subtab.

Touch Details to view target information, then touch Done.

Touch Done to return to the Plate tab.

Options for loading MicroAmp

™

consumables with the

QuantStudio

™

3 and 5 Real‑Time PCR Systems

(Recommended) If using MicroAmp

™

reaction plates, proceed to “Load and unload the plate” on

page40.

If using MicroAmp

™

tubes/tube strips, proceed to “Prepare samples using MicroAmp

™

tubes/tube strips

with separate cap strips” on page43.

Load and unload the plate

If a compression pad is not used, see “Load and unload a plate in the instrument” on page40.

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 “(If applicable) load and unload a plate in the instrument with a

compression pad” on page41.

Load and unload a plate in the instrument

Load the plate.

Touch to eject the instrument drawer.

Chapter3

Create and run experiments on the instrument

Options for loading MicroAmp

™

consumables with the QuantStudio

™

3 and 5 Real‑Time PCR Systems

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Load the plate onto the plate adaptor so that the following criteria are met.

•

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

•

The barcode faces the front of the instrument.

IMPORTANT! The instrument should be loaded and unloaded 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.

Touch to close the instrument drawer.

When the run ends, unload the plate.

Touch to eject the instrument drawer.

Remove the plate.

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.

(If applicable)

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.

Load the plate.

Touch to eject the instrument drawer.

Chapter3

Create and run experiments on the instrument

Load and unload the plate

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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.

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 help 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.

Touch to close the instrument drawer.

When the run ends, unload the plate.

Touch to eject the instrument drawer.

Remove the plate.

Chapter3

Create and run experiments on the instrument

Load and unload the plate

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Touch to close the instrument drawer.

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 inspect 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.

Prepare samples using MicroAmp

™

tubes/tube strips with

separate cap strips

CAUTION!

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

cover.

The following procedure describes how to properly load and seal MicroAmp tube strips using cap strips

and the MicroAmp 96-well tray/retainer set. For a visual demonstration, watch the video "How to use

adapter tray retainers" by visiting PCR/qPCR Plastics and Seals Education at thermoﬁsher.com.

The MicroAmp

™

96-Well Tray/Retainer Set for Veriti

™

Systems (Cat.No. 4381850) for 0.2mL format has

a blue tray and retainer.

The MicroAmp

™

96-Well Tray for VeriFlex

™

Block (Cat.No. 4379983) for 0.1mL format has a black tray

and retainer.

Separate the blue or black tray and retainer by squeezing the release catch as indicated in the

graphic.

Release catch

MicroAmp

™

96-Well Retainer

MicroAmp

™

96-Well Tray

Chapter3Create and run experiments on the instrument

Prepare samples using MicroAmp

™

tubes/tube strips with separate cap strips

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Place the blue or black tray on the 96-well base.

Load the tube strips on the tray.

Pipette the reaction mixture into the tubes.

Place the blue or black retainer over the tubes and snap the retainer into the tray.

Seal the tube strip using a MicroAmp

™

cap strip.

Remove the blue or black tray/retainer assembly containing the sealed tube strips from the

96-well base and place the assembly on the instrument block with the black adapter on the block.

Note: Ensure the tubes and blue or black tray and retainer ﬁt properly into the wells on the block.

The tube, tray, and retainer assembly may feel loose and demonstrate some movement within the

block, which is standard. The appropriate amount of pressure will be applied when the heated

cover is lowered onto it.

MicroAmp

™

8-Cap strip

MicroAmp

™

96-Well Retainer

MicroAmp

™

8-Tube Strip (0.2-mL) or MicroAmp

™

Reaction Tube without Cap (0.2-mL)

MicroAmp

™

96-Well Tray

MicroAmp

™

Splash Free 96-Well Base

Chapter3Create and run experiments on the instrument

Prepare samples using MicroAmp

™

tubes/tube strips with separate cap strips

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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45).

•

Adjust the display of real-time plots (see “Adjust the display of real-time plots on the instrument

touchscreen” on page46).

–

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45).

View real-time data and plots on the instrument touchscreen

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

Touch Well details.

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

Touch Close to return to the home screen.

Pause or stop an instrument run

In the home screen, during an instrument run:

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

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.

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

Chapter3Create and run experiments on the instrument

View, pause, or stop a run

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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

In the instrument home screen, during an instrument run, touch or swipe left twice to view

real-time data and plots.

Touch Zoom.

Touch or to zoom in or out.

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

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.

Lock the touchscreen.

In the home screen, touch My Proﬁle.

Touch Lock Screen, then touch Lock.

Unlock the touchscreen.

Touch anywhere on the touchscreen.

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

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

In the home screen, when a run ends, touch Transfer File.

Select the data destination for the EDS ﬁle.

Navigate to and select a folder.

Touch OK.

Touch Transfer.

Chapter3

Create and run experiments on the instrument

Transfer, view, or manage ﬁles and results

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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

View run history and delete or transfer ﬁles from the instrument

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

When SAE mode is enabled, only an Administrator can delete a run.

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: The instrument automatically resumes interrupted runs due to power outages within an hour,

even without software connection. If network issues disrupt the connection during a desktop-initiated

run, the run completes on the instrument with data saved in its history. For incomplete desktop-initiated

runs, data must be manually transferred to a USB or network drive. Data stays in the internal memory

on the instrument until manually deleted or reset.

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46.

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

In the home screen, touch Load Experiment.

Touch USB or

My Instrument.

Touch Manage Files.

(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.

Touch one or more ﬁles to select for managing.

Chapter3

Create and run experiments on the instrument

Transfer, view, or manage ﬁles and results

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Delete or copy the ﬁles.

•

Touch Delete Files, then conﬁrm deletion.

•

Touch Copy Files, select a ﬁle destination, then touch Paste Files.

Touch Done.

Chapter3Create and run experiments on the instrument

Transfer, view, or manage ﬁles and results

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Calibrate and verify instrument

performance

■

Calibration and veriﬁcationschedule .................................................... 49

■

Calibrationdescriptions ............................................................... 50

■

View the calibration status and set reminders ............................................ 51

■

Perform ROI/uniformity, background, and dye calibrations ................................. 52

■

Perform instrument veriﬁcation using RNase P plates ..................................... 59

■

Calibrate customdyes ................................................................ 65

■

Calibrate for a custom melt curve experiment ............................................ 72

Calibration and veriﬁcation schedule

The instrument is factory-calibrated and does not require calibration at installation. To help 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116. Exposure to extreme temperatures can

adversely aect 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

(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

veriﬁcation

•

After installing or moving the instrument

•

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65.

Calibration descriptions

Calibration description and purpose

Pass Criteria

ROI/Uniformity

•

The software captures images for each optical ﬁlter.

•

The software uses calibration data to map the increase in ﬂuorescence

to the plate wells during subsequent runs and to evaluate well-to-well

consistency of the signals.

The image for each ﬁlter

distinguishes all wells of the

plate.

Each well in the image is

distinct.

Background

•

The software captures background images for each optical ﬁlter in the

absence of sample and reagent, and it checks that the ﬂuorescence from

each well is below a ﬂuorescence threshold.

•

The software uses calibration data to remove background ﬂuorescence

during a run.

Note: You can also run this calibration to determine if contamination is

related to the sample block or the plate.

The plate images for all

ﬁlters are free of abnormal

ﬂuorescence.

Chapter4Calibrate and verify instrument performance

Calibration descriptions

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

(continued)

Calibration description and purpose

Pass Criteria

Dye

•

The software extracts a spectral proﬁle for each dye standard, then

produces a set of spectral proﬁles plotted as ﬂuorescence vs ﬁlter.

•

The software uses calibration data to characterize and distinguish the

individual contribution of each dye in the total ﬂuorescence signals collected

by the instrument.

Dye spectra peak within the

same ﬁlter as their group.

View the calibration status and set reminders

View calibration status and set reminders in the instrument

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

In the home screen, touch Settings4Maintenance and Service4Calibrations4History and

Reminders.

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

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

Done.

Touch Edit to set the calibration reminder settings. For each calibration type:

Slide the control On to enable the calibration reminder.

Edit the Exp interval and Remind me ﬁelds.

Touch Save.

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

Touch Done.

View calibration status and set reminders in Thermo Fisher

™

Connect

Platform

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

network.

In Thermo Fisher

™

Connect Platform, click

for the Instrument Connect page.

Select any of your registered instruments.

Chapter4

Calibrate and verify instrument performance

View the calibration status and set reminders

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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.

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65)

Perform any time that ROI and background calibrations are current.

Chapter4Calibrate and verify instrument performance

Perform ROI/uniformity, background, and dye calibrations

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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

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.

While wearing powder‐free gloves, remove the calibration plate from its packaging and retain the

packaging. Do not remove the optical ﬁlm.

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

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

centrifuge the plate again.

Chapter4Calibrate and verify instrument performance

Perform ROI/uniformity, background, and dye calibrations

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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

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.

Follow the instructions on the screen to start the calibration.

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

Load the plate.

Touch to eject the instrument drawer.

Load the plate onto the plate adaptor so that the following criteria are met.

•

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

•

The barcode faces the front of the instrument.

IMPORTANT!

The instrument should be loaded and unloaded 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.

Chapter4

Calibrate and verify instrument performance

Perform ROI/uniformity, background, and dye calibrations

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Touch to close the instrument drawer.

Touch Start.

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57.

Note:

You can view the calibration images only after the ROI/Uniformity and Background

calibrations pass.

When the run ends, unload the plate.

Touch to eject the instrument drawer.

Remove the plate.

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.

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

Chapter4Calibrate and verify instrument performance

Perform ROI/uniformity, background, and dye calibrations

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

View calibration images and transfer results to a USB drive

The instrument performs the ROI, Uniformity, and Background calibrations in sequence. You can view

the calibration images after the Background calibration is complete.

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

In the Calibration Status screen, touch Details.

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

Calibration Example results indicating successful calibration

ROI

Note: Select the desired ﬁlter

combination from the Filter Set

dropdown list.

Green circles around all wells and bright well centers.

Uniformity Signals from each well following a uniform trend.

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.

Chapter4Calibrate and verify instrument performance

Perform ROI/uniformity, background, and dye calibrations

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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.

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

Troubleshoot calibration failure

Observation Possible cause Recommended action

Calibration failed

The plate was improperly prepared. Ensure the following:

• The correct plate was used for the calibration

performed.

• The plate was properly thawed.

• The plate was properly centrifuged.

• The plate was properly sealed.

The plate is damaged or

contaminated.

Check for damage, improper plate seal, or

contamination.

Order a replacement plate. If the replacement

plate fails, contact Support.

High ﬂuorescence

signal in individual wells

Signals that exceed the limit of

normal ﬂuorescence may indicate

ﬂuorescent contaminants on the

plate or the sample block.

See “Identify contamination” on page57.

Calibration failed but

plate is undamaged

The incorrect plate was used for

calibration performed.

Use the plate that matches the calibration

performed.

The plate was improperly prepared. Repeat the calibration with the plate properly

prepared.

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.

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

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

Chapter4Calibrate and verify instrument performance

Perform ROI/uniformity, background, and dye calibrations

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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77).

Reversed The plate is contaminated.

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

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 buer that accurately simulates the reagents used for PCR, and, therefore, produces high-

quality calibration data.

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

Required materials:

•

MicroAmp

™

optical 96-well reaction plate

•

Optical adhesive cover or optical ﬂat caps

•

Pipettor, 200‐µL (with pipette tips)

•

Powder‐free gloves

•

Safety glasses

•

Deionized water

IMPORTANT!

Wear powder-free gloves while creating the background plate.

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

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.

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

Use the plate for background calibration.

Chapter4Calibrate and verify instrument performance

Perform ROI/uniformity, background, and dye calibrations

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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

performance of

the instrument.

Quantiﬁes the number of

copies of the human RNaseP

gene in samples with

known concentrations of the

corresponding DNA template.

The instrument passes performance speciﬁcations if the

following inequality is true and the instrument successfully

distinguishes between unknown populations AandB.

[(C

) – 3(σ

CtA

)] > [(C

) + 3(σ

CtB

)]

where:

•

= Average C

of unknown populationA

•

CtA

= Standard deviation of unknown populationA

•

= Average C

of unknown populationB

•

CtB

= 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.

Chapter4Calibrate and verify instrument performance

Perform instrument veriﬁcation using RNase P plates

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Figure1 96-well RNase P plate

Unknown A (5,000)

NTC (no template control)

STD 1,250 copies

STD 2,500 copies

STD 5,000 copies

STD 10,000 copies

STD 20,000 copies

Unknown B (10,000)

Figure2

384-well RNase P plate

NTC (no template control)

STD 1,250 copies

STD 2,500 copies

STD 5,000 copies

STD 10,000 copies

Unknown A (5,000)

Unknown B (10,000)

Chapter4Calibrate and verify instrument performance

Perform instrument veriﬁcation using RNase P plates

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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.

[(C

) – 3(σ

CtA

)] > [(C

) + 3(σ

CtB

)]

•

= Average C

of unknown populationA

•

CtA

= Standard deviation of unknown populationA

•

= Average C

of unknown populationB

•

CtB

= 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.

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.

Conﬁrm that the bench, vortex, and centrifuge are clean. Before use, wipe the vortex and

centrifuge using a lint‑free tissue.

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

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

Chapter4Calibrate and verify instrument performance

Perform instrument veriﬁcation using RNase P plates

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

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

Load the plate.

Touch to eject the instrument drawer.

Load the plate onto the plate adaptor so that the following criteria are met.

•

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

•

The barcode faces the front of the instrument.

IMPORTANT!

The instrument should be loaded and unloaded 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.

Chapter4

Calibrate and verify instrument performance

Perform instrument veriﬁcation using RNase P plates

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Touch to close the instrument drawer.

Touch Start.

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63.

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 drive

When the run ends, unload the plate.

Touch to eject the instrument drawer.

Remove the plate.

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

prepared.

Ensure the following:

• 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 the Thermo Fisher

™

Connect Platform to view

the ﬂags and troubleshooting details for failed wells.

The plate is damaged or

contaminated.

Check for damage, improper plate seal, or contamination.

Order a replacement plate. If the replacement plate fails,

contact Support.

Chapter4Calibrate and verify instrument performance

Perform instrument veriﬁcation using RNase P plates

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Observation Possible cause Recommended action

High ﬂuorescence

signal

The reaction volume is not

correct.

Ensure that reaction volumes in the plate are correct and

match the volume that is entered in the Method tab.

Signals that exceed the

limit of normal ﬂuorescence

may indicate ﬂuorescent

contaminants on the plate or

the sample block.

Examine the bottom of the reaction plate. If there is

contamination, prepare a new plate and run the experiment

again.

Identify the location of contamination on the plate or sample

block.

Obtain a background plate.

Follow the procedures that are described in “Identify

contamination” on page57.

Veriﬁcation failed

but plate is

undamaged

The incorrect plate was used

for veriﬁcation.

Use the correct RNase P plate for veriﬁcation.

The plate was improperly

prepared.

Repeat the veriﬁcation with a new properly 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 the Thermo Fisher

™

Connect Platform 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.

Chapter4Calibrate and verify instrument performance

Perform instrument veriﬁcation using RNase P plates

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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14.

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 dierence 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 buer compatible with your master mix.

•

(Intercalating dyes only) Add the appropriate amount of ampliﬁed PCR product to generate

ﬂuorescence.

Chapter4

Calibrate and verify instrument performance

Calibrate custom dyes

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Prepare a custom dye dilution plate

IMPORTANT! Wear powder-free gloves throughout the procedure.

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

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

1,600nM

8 9 10

100nM

200nM

400nM

800nM

1,600nM

100nM

200nM

400nM

800nM

1,600nM

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

Chapter4Calibrate and verify instrument performance

Calibrate custom dyes

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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.

Run the dilution plate as an experiment

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

Load the plate into the instrument.

CAUTION!

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

moving parts hazard.

Set up a genotyping experiment on the instrument.

•

Load an experiment created in the desktop or cloud software.

In the home screen, touch Load Experiment.

Select the experiment location, then the experiment ﬁle.

•

Create a new experiment on the instrument touchscreen.

In the home screen, touch Open Template4Genotyping4Genotyping Post.

(Optional) In the Properties tab, edit the experiment properties.

In the Method tab, set the hold temperature to 60°C with a 2 minute hold and enter the

appropriate reaction volume.

In the Plate tab, enter the dilution series information for the appropriate wells.

Touch Start Run.

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

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.

Chapter4

Calibrate and verify instrument performance

Calibrate custom dyes

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Determine the optimal dye concentration

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

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.

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

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.

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

concentration.

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:

Dilute the custom dye to the optimal concentration in buer.

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.

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

Seal the plate.

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

Chapter4Calibrate and verify instrument performance

Calibrate custom dyes

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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.

Add a custom dye to the instrument

In the instrument home screen, touch Settings4Maintenance and

Service4Calibrations4Custom4Custom Dye.

Touch Add Custom Dye.

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.

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 documents

for the desktop software.

Chapter4Calibrate and verify instrument performance

Calibrate custom dyes

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Perform a custom dye calibration

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

Load the plate into the instrument.

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

moving parts hazard.

In the instrument home screen, touch Settings4Maintenance and

Service4Calibrations4Custom4Custom Dye.

Touch the custom dye to calibrate.

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

Enter the calibration temperature.

(Optional) Touch Reagents, then enter reagent information.

Touch Start.

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

Results4Details.

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

the dye wavelength.

Peak

ﬁlter

Filter wavelength (nm)

[1]

Excitation Emission

x1-m1 470 ± 15nm 520 ± 15nm

x2-m2 520 ± 10nm 558 ± 12nm

x3-m3 550 ± 10nm 587 ± 10nm

x4-m4 580 ± 10nm 623 ± 14nm

Chapter4Calibrate and verify instrument performance

Calibrate custom dyes

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

(continued)

Peak ﬁlter

Filter wavelength (nm)

[1]

Excitation Emission

x5-m5 640 ± 10nm 682 ± 14nm

x6-m6 662 ± 10nm 711 ± 12nm

[1]

The central wavelengths are the optimized wavelengths.

Note: Example dye calibration plot.

The peaks for your dye may align with a dierent 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57.

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.

Chapter4

Calibrate and verify instrument performance

Calibrate custom dyes

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Calibrate for a custom melt curve experiment

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

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

Before performing a calibration for a custom melt curve experiment, ensure that all calibrations are

current (touch Settings4Maintenance and Service4Calibrations4History and Reminders).

Add a custom dye to the software (see “Add a custom dye to the instrument” on page69).

In the home screen, touch Settings4Maintenance and

Service4Calibrations4Custom4Custom Melt.

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

Load the plate into the instrument.

Select or add a dye, then select a ﬁlter set appropriate for your dye's wavelength (see ﬁlter-

wavelength table below).

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

Peak

ﬁlter

Filter wavelength (nm)

[1]

Excitation Emission

x1-m1 470 ± 15nm 520 ± 15nm

x2-m2 520 ± 10nm 558 ± 12nm

x3-m3 550 ± 10nm 587 ± 10nm

x4-m4 580 ± 10nm 623 ± 14nm

x5-m5 640 ± 10nm 682 ± 14nm

x6-m6 662 ± 10nm 711 ± 12nm

[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.

(Optional) Touch Reagents, then enter reagent information.

Touch Start.

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

Results4Details.

Chapter4

Calibrate and verify instrument performance

Calibrate for a custom melt curve experiment

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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 dierent ﬁlter set.

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57.

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 documentation for

the desktop software.

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.

Chapter4Calibrate and verify instrument performance

Calibrate for a custom melt curve experiment

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Maintain the instrument

■

Back up or restore theinstrument ...................................................... 74

■

Perform a self-veriﬁcation test .......................................................... 75

■

View instrumentlogs .................................................................. 75

■

Conﬁgure the networkdrive ............................................................ 75

■

Decontaminate the sampleblock ....................................................... 77

■

Replace the instrumentfuses .......................................................... 80

■

Power on or o, store, andmove ....................................................... 81

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.

Back up or restore the instrument

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

Action

Back up

Touch Backup Instrument.

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

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

Enter a backup ﬁle name, then touch Done.

Select the elements to back up, or leave them all selected.

Touch Backup.

Restore (Administrator

only)

Touch Restore a Backup.

Select the storage location of the backup settings.

If restoring from a USB drive, insert a USB drive into the front-panel USB port.

Select the backup ﬁle, then touch Restore.

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Perform a self-veriﬁcation test

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

In the home screen, touch Settings4Maintenance and Service4Self Veriﬁcation Test.

IMPORTANT! Ensure the front of the instrument is not obstructed. The instrument drawer will be

ejected during the test. The test will take approximately ten minutes.

Touch Start Test.

View instrument logs

If an Administrator has set data management as system-deﬁned, you cannot select the location to save

the data. See “Conﬁgure instrument settings” on page27.

In the home screen, touch Settings4Maintenance and Service4Log.

Touch Instrument Run Log to view the log records.

(Optional) Touch a category on the left to ﬁlter the log table by event type.

(Optional) Touch an individual log record to view details.

(Optional) Export log records.

•

Touch Export4 USB.

•

Touch Export4 Thermo Fisher

™

Connect Platform, then touch Export.

•

Touch Export4 Network.

Conﬁgure the network drive

When importing or exporting ﬁles from and to a network drive, you are prompted to specify the network

drive location and information.

If the instrument is already connected to a network drive, the folder structure of the network drive is

displayed.

The network drive can be identiﬁed by the IP address of the computer. It can be identiﬁed by the

domain name system (DNS) name for v1.5.2 or later.

For v1.6 or later, the location of the network drive can be set in the data management settings. If the

network drive is deﬁned in the data management settings, it cannot be changed at the time that ﬁles are

exported. For more information, see “Conﬁgure instrument settings” on page27.

Set up the network drive as a shared folder (see “Create a shared network folder” on page76).

If the network drive is identiﬁed by the IP address of the computer, determine the IP address of the

computer (see “Determine the IP address of the computer” on page77).

Chapter5

Maintain the instrument

Perform a self-veriﬁcation test

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

If the network drive is identiﬁed by the DNS name, determine the DNS name (see “Determine the DNS

name” on page77).

In the home screen, touch Settings4Instrument Settings4Network Drive.

Select the drive location.

The drive location is required.

For IP address, the drive location is <IP address>/<folder name>.

For DNS name, the drive location is <DNS>/<folder name>.

Enter the following information, then touch Connect.

•

Domain name

•

User name

•

Password

The domain name, username, and password can be required, depending on the network

requirements.

The username and password are for the network. They are not the username and password for the

instrument.

Create a shared network folder

Files can be transferred from the instrument to a folder on the network.

The folder on the network must be set up as a shared folder.

To designate a folder as shared, right-click on the folder, then click Properties.

In the Properties dialog box, click the Sharing tab.

Click Advanced Sharing.

In the Advanced Sharing dialog box, select the Share this folder checkbox, then click

Permissions.

Ensure that Everyone is selected in the Group or user name ﬁeld.

Ensure that the checkboxes for Allow are selected for the permissions.

The permissions are Full Control, Change, and Read.

In the Permissions dialog box, click OK.

In the Advanced Sharing dialog box, click Apply4OK.

In the Properties dialog box, click Close.

Chapter5

Maintain the instrument

Conﬁgure the network drive

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Determine the IP address of the computer

In Windows

™

search bar, enter cmd to open the Command Prompt.

In the Command Prompt, enter ipconﬁg/all, then press Enter.

Locate the IPv4 Address.

The IP address is listed on the IPv4 Address line.

Determine the DNS name

In the Windows

™

search bar, enter

cmd

to open the Command Prompt.

In the Command Prompt, enter ipconﬁg/all, then press Enter.

Locate the DNS names.

The text indicating the DNS names might be dierent, depending on the conﬁguration. The text

DNS is displayed and there might be more than one ﬁeld for the DNS names. Contact your IT

administrator for assistance to determine the correct DNS name.

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

Chapter5

Maintain the instrument

Decontaminate the sample block

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

•

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.

Identify the contaminated wells of the sample block (see “Identify contamination” on page57).

Prepare the instrument and access the sample block:

Power o and unplug the instrument, then allow it to cool for 15 minutes.

Touch to eject the instrument drawer.

Rinse the contaminated wells with deionized water (see “Detailed procedures for cleaning the

sample block” on page79).

Close the drawer and test the sample block for contamination:

Push the instrument drawer back in to the instrument.

Plug in, then power on the instrument.

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

If the contamination remains, clean the contaminated wells using a 95% ethanol solution:

Repeat step 2 – step 3.

Clean the contaminated wells using a 95% ethanol solution (see “Detailed procedures for

cleaning the sample block” on page79).

Chapter5

Maintain the instrument

Decontaminate the sample block

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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.

If the contamination still remains, clean the contaminated wells using a Na-hypochlorite (0.1% v/v)

solution:

Repeat step 2 – step 3.

Clean the contaminated wells using a Na-hypochlorite (0.1% v/v) solution (see “Detailed

procedures for cleaning the sample block” on page79).

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.

If the contamination continues to remain, contact Support.

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78).

•

Rinse the sample block with deionized water.

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

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

Pipet the water to a waste beaker.

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

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

•

Clean the sample block with 95% ethanol.

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

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

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.

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

Chapter5

Maintain the instrument

Decontaminate the sample block

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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

Pipet the bleach solution to a waste beaker.

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

solution.

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

Power o and unplug the instrument, then allow it to cool for 15 minutes.

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

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

of failed fuses.

Good

Failed

Chapter5Maintain the instrument

Replace the instrument fuses

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Replace each failed fuse.

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

Install the fuse holder back into the instrument.

Plug in, then power on the instrument.

The installation is successful if the instrument powers on.

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 o, store, and move

Enable sleep mode

In the home screen, touch Settings4Instrument Settings4Sleep Mode.

Slide the control On to enable sleep mode.

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

Touch Enter, then touch OK.

Power on the instrument

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.

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.

Chapter5Maintain the instrument

Power on or o, store, and move

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Power o the instrument

The instrument operates in low-power mode when not in use. However, the instrument can be powered

o completely so that the components use no power.

Note: To power o the instrument for >1 week, see “Prepare the instrument to store, move, or ship” on

page82.

Power o the instrument using the power switch on the back of the instrument.

Power o the computer.

Prepare the instrument to store, move, or ship

In the home screen:

Touch Settings4Maintenance and Service4Ship Prep Mode4Next.

Touch to eject the instrument drawer.

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

Touch Lock Block.

Power o 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.

Chapter5

Maintain the instrument

Power on or o, store, and move

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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.

Back up the instrument (see “Back up or restore the instrument” on page74).

In the home screen, touch Settings4Instrument Settings4Reset Factory defaults.

Set the instrument to Ship Prep Mode (see “Prepare the instrument to store, move, or ship” on

page82).

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

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).

Follow the instructions in the form to decontaminate the instrument.

IMPORTANT!

The instrument must be decontaminated before packing it for shipping.

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

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

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

Prepare

Include Exclude

Transfer any data ﬁles from the

instrument.

Load an empty plate in the

sample block.

Use the touchscreen to place

the instrument in ship mode.

Note: The empty plate and

ship mode protects the internal

components of the instrument during

transport.

•

Instrument

•

Completed and signed

Certiﬁcate of Instrument

Decontamination

Note: The instrument will not be

accepted for service without a

hard copy of the Certiﬁcate of

Instrument Decontamination.

Any accessories, including:

•

Power cord

•

Ethernet cable

•

USB drive

•

Wireless adapter

Note: If included with

the instrument, these items

will be disposed of during

service and not returned.

Attach the postage provided with the Certiﬁcate of Instrument Decontamination to the box, then

ship the instrument to the designated facility.

Chapter5

Maintain the instrument

Power on or o, store, and move

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Conﬁgure the instrument and

manage instrument proﬁles

■

Initial start‑up ........................................................................ 84

■

Manageproﬁles ...................................................................... 85

■

Link an instrument proﬁle to Thermo Fisher

™

Connect .................................... 86

■

Enable SAE mode (Administratoronly) .................................................. 92

■

Require instrument proﬁle sign-in (Administratoronly) ..................................... 93

■

Enable remote instrument monitoring (Administratoronly) ................................. 93

■

Update instrument software (Administratoronly) .......................................... 94

■

Restore factorydefaults ............................................................... 94

■

Conﬁgure thenetwork ................................................................ 94

■

Select a region for the Thermo Fisher

™

Connect Platform (Administratoronly) ............... 96

■

Manage the instrument name (Administratoronly) ........................................ 96

■

Set the date and time (Administratoronly) ............................................... 96

■

Manage the signout timer (Administrator only) ........................................... 97

Initial start‑up

Perform these tasks during initial instrument start‑up or after you restore factory defaults (see “Restore

factory defaults” on page94).

(Optional) Select one of the following options.

•

Conﬁgure the instrument for either wired connection or wireless network connection (see

“Conﬁgure the network” on page94).

•

Touch Neither/Decide Later.

(Optional) Enter an instrument name (see “Manage the instrument name (Administrator only)” on

page96).

Set the date and time (see “Set the date and time (Administrator only)” on page96).

Select one of the following options.

• Select a region for the Thermo Fisher

™

Connect Platform.

• Touch Next to continue.

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Create an administrator proﬁle (see “Create an administrator instrument proﬁle during initial start-

up” on page85).

Select one of the following options.

•

Link the instrument proﬁle to the Thermo Fisher

™

Connect Platform (see “Link an instrument

proﬁle to Thermo Fisher

™

Connect” on page86).

•

Touch Skip.

Manage proﬁles

See

Create a proﬁle

•

“Create an administrator instrument proﬁle during initial start-up” on page85

•

“Create a new instrument proﬁle” on page26

Conﬁgure a proﬁle

•

“Link an instrument proﬁle to Thermo Fisher

™

Connect” on page86

•

“Edit an instrument proﬁle” on page86

View or manage all proﬁles

•

“Manage all instrument proﬁles (Administrator only)” on page85

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84.

•

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85.

Touch Name, enter a username, then touch Done.

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

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

Touch Conﬁrm PIN, then repeat step2.

Touch Create proﬁle.

Manage all instrument proﬁles (Administrator only)

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.

Chapter6

Conﬁgure the instrument and manage instrument proﬁles

Manage proﬁles

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Select the instrument proﬁle to edit.

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.

Touch Done.

Edit an instrument proﬁle

In the home screen, touch MyProﬁle.

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

Users4Manage Proﬁles.

Touch Edit.

Select the ﬁelds to edit, then make changes.

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87

•

“Overview of local instrument proﬁles and Thermo Fisher

™

Connect proﬁles” on page87

•

“Thermo Fisher

™

Connect Platform instrument proﬁle roles and functions” on page88

•

“Link the instrument to your Thermo Fisher

™

Connect Platform account” on page88

•

“Link a local proﬁle to a Thermo Fisher

™

Connect proﬁle” on page89

•

“Unlink a Thermo Fisher

™

Connect account” on page91

•

“If you link when you are signed in to the instrument” on page91

•

“Change the PIN for a Thermo Fisher

™

Connect proﬁle” on page92

Chapter6

Conﬁgure the instrument and manage instrument proﬁles

Link an instrument proﬁle to Thermo Fisher

™

Connect

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Recommended order to set up proﬁles

Task

Description

Create a proﬁle for the

instrument administrator.

The ﬁrst proﬁle on the instrument becomes the instrument administrator.

See “Create an administrator instrument proﬁle during initial start-up” on page85.

Select a Thermo Fisher

™

Connect administrator.

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

™

Connect administrator. It is recommended that

the ﬁrst Connect 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.

Each person creates a

proﬁle.

Create a local instrument proﬁle. Thermo Fisher

™

Connect -enabled features are not

available.

(Optional) Link a local instrument proﬁle to a Thermo Fisher

™

Connect proﬁle.

™

Connect proﬁle. Thermo Fisher

™

Connect-enabled

features are available.

Assign additional

instrument administrators.

Any of the proﬁles can be assigned the role of instrument 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.

Chapter6Conﬁgure the instrument and manage instrument proﬁles

Link an instrument proﬁle to Thermo Fisher

™

Connect

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Thermo Fisher

™

Connect Platform instrument proﬁle roles and functions

The ﬁrst user who links their local instrument proﬁle to their Thermo Fisher

™

Connect Platform account

is assigned a Connect Platform proﬁle with the administrator role.

Instrument

proﬁle

Location Functions allowed

Standard Connect

Platform

•

Create, save, open, import, and run template ﬁles

•

Create and modify run settings

•

View and export data ﬁles

Administrator Connect

Platform

All the permissions of a local administrator proﬁle, plus the following functions

performed in the Connect Platform:

•

See a list of all the Connect Platform proﬁles that are linked to the

instrument

•

Assign Connect Platform administrator roles to one or more users

•

Remove a user from an instrument

•

Disconnect the instrument from the Connect Platform

•

Change the instrument name

Link the instrument to your Thermo Fisher

™

Connect Platform account

This section describes using your Thermo Fisher

™

Connect Platform account when you use the

instrument for the ﬁrst time.

The ﬁrst time that you use your Connect Platform 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 Connect

Platform account. It will apply to all other instruments when you use your Connect Platform account.

This does not change the password when signing in to your Connect Platform account on a browser.

After the PIN is set up on the instrument, it must be changed with your Connect Platform account on a

browser, see “Create an administrator instrument proﬁle during initial start-up” on page85.

The ﬁrst time the instrument is used with a Connect Platform account, a region must be selected.

In the Sign In screen, tap Get started4Create a local instrument ﬁle4Connect to your

Thermo Fisher

™

Connect Platform account.

(Optional) Select the appropriate region.

Option

Description

China For users in China

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

Chapter6Conﬁgure the instrument and manage instrument proﬁles

Link an instrument proﬁle to Thermo Fisher

™

Connect

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Tap a connection option.

Option Action

Mobile

devices

Note: Before selecting this option, install and sign in to the Connect Platform

application on your mobile device.

On the instrument:

Tap

Mobile devices.

Hold the camera on your mobile device over the QR code that is displayed on the

touchscreen.

Tap Close.

PC A link code is displayed on the instrument.

On a computer:

Access the Connect Platform.

Click Add instrument.

Select QuantStudio.

Enter the link code.

(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.

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

Tap Done.

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 that you use your Thermo Fisher

™

Connect account on an instrument, you are 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 applies 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92.

The ﬁrst time the instrument is used with a Thermo Fisher

™

Connect account, a region must be

selected.

Chapter6

Conﬁgure the instrument and manage instrument proﬁles

Link an instrument proﬁle to Thermo Fisher

™

Connect

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

For a detailed description of the proﬁle, see “If you link when you are signed in to the instrument” on

page91.

In the home screen, tap (Proﬁle).

The My Proﬁle screen is displayed.

Tap Connect4Link Account.

The Connect to Connect Platform screen is displayed.

(Optional) Select the appropriate region.

Option Description

China For users in China

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

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:

Tap

Mobile devices.

Hold the camera on your mobile device over the QR code that is displayed on the

touchscreen.

Tap Close.

PC A link code is displayed on the instrument.

On a computer:

Access the Thermo Fisher

™

Connect platform.

Click Add instrument.

Select QuantStudio.

Enter the link code.

(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.

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

Tap Done.

Chapter6

Conﬁgure the instrument and manage instrument proﬁles

Link an instrument proﬁle to Thermo Fisher

™

Connect

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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91.

™

Connect platform.

In the left pane, click

(Instrument).

Select the instrument, then click Disconnect.

Tap Conﬁrm.

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 diers 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89).

•

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: User1@thermoﬁsher.com 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

(

User1@thermoﬁsher.com).

•

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.

Chapter6Conﬁgure the instrument and manage instrument proﬁles

Link an instrument proﬁle to Thermo Fisher

™

Connect

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

(continued)

Phase Steps that occur

If your

Thermo

Fisher

™

Connect

account is

unlinked:

•

Your local instrument proﬁle (UserABC) is displayed in the home screen of the instrument.

•

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47 and “Transfer EDS ﬁles from

the instrument home screen” on page46).

•

Your local instrument proﬁle name (UserABC) is available for selection in the Sign In screen.

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85.

™

Connect on a browser.

Click Update PIN number.

In the Update PIN number dialog box, enter a new PIN, then enter the new PIN a second time to

conﬁrm it.

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 available only for the QuantStudio

™

5 Real‑Time

PCR 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:

Touch Settings4Instrument Settings4SAE Mode.

Slide the control On to enable SAE on the instrument.

Touch OK.

Chapter6

Conﬁgure the instrument and manage instrument proﬁles

Enable SAE mode (Administrator only)

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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.

•

Access the instrument settings if you are not signed in.

Require instrument proﬁle sign-in (Administrator only)

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

Slide the control On.

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

Settings.

Touch Done.

Enable remote instrument monitoring (Administrator only)

In the home screen, touch Settings4Maintenance and Service4Monitoring.

Conﬁgure the instrument monitoring settings.

Option

Description

Remote

Monitoring

Service

Slide the control On to enable the Remote Monitoring Service.

Enabling the Remote Monitoring Service allows the instrument to automatically

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

™

Connect Monitor

Slide the control On to enable users to access real‑time monitoring of

ampliﬁcation plots from the Thermo Fisher

™

Connect dashboard (cloud-based

platform).

Touch OK.

Chapter6Conﬁgure the instrument and manage instrument proﬁles

Require instrument proﬁle sign-in (Administrator only)

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Update instrument software (Administrator only)

In the home screen, touch Settings4Maintenance and Service4Software Update.

Select the location of the update ﬁles.

When prompted, conﬁrm your request to update the software.

Restore factory defaults

This procedure can only be performed by an Administrator.

IMPORTANT!

Back up the instrument before restoring factory defaults (see “Back up or restore the

instrument” on page74).

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

Touch Restore Factory Defaults.

Power O, 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84.

Conﬁgure the network

IMPORTANT!

Conﬁgure the instrument for either wired connection or wireless connection but not

both.

“Set up a wired connection” on page95

“Set up a wireless connection” on page95

Chapter6Conﬁgure the instrument and manage instrument proﬁles

Update instrument software (Administrator only)

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Set up a wired connection

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

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

Touch Static IP.

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.

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.

Touch OK.

Set up a wireless connection

In the home screen, touch Settings4Instrument Settings4Network Connection4

Wireless to display a list of the available networks.

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.

Touch Join to continue.

In the Network Connection Complete screen, touch Next.

Touch OK.

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

Chapter6Conﬁgure the instrument and manage instrument proﬁles

Conﬁgure the network

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Select a region for the Thermo Fisher

™

Connect Platform

(Administrator only)

During the initial startup, you are automatically prompted to select a region for the Thermo Fisher

™

Connect Platform. Return to the selection through Settings, if necessary.

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

Touch a region.

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

Touch OK.

Manage the instrument name (Administrator only)

In the home screen, touch Settings4Instrument Settings4Instrument Name.

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

Touch OK.

Set the date and time (Administrator only)

The date and time cannot be set if the instrument is linked to the Thermo Fisher

™

Connect Platform.

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

Select a time zone from the dropdown list.

Select a date format.

Touch Date Format, then select the preferred date format.

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

Touch Enter, then touch Done.

Select a time format.

Touch Time Format.

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

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

Touch Enter, then touch Done.

Touch Done.

Chapter6

Conﬁgure the instrument and manage instrument proﬁles

Select a region for the Thermo Fisher

™

Connect Platform (Administrator only)

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Manage the signout timer (Administrator only)

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

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

out.

Touch Enter, then touch Done.

Chapter6Conﬁgure the instrument and manage instrument proﬁles

Manage the signout timer (Administrator only)

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Install and connect the instrument to

a network

■

Workﬂow: Install and connect to anetwork .............................................. 98

■

Before youbegin ..................................................................... 99

■

Unpack and install theinstrument ...................................................... 99

■

Power on and follow the startup wizard ................................................ 100

■

Connect the computer to the instrument directly or to aLAN .............................. 100

■

Instrument and computerconnections ................................................. 101

■

Download and install the desktop software ............................................. 102

■

Networking ......................................................................... 103

Workﬂow: Install and connect to a network

Perform all steps in

“Before you begin” on page99

▼

“Unpack and install the instrument” on page99

▼

“Power on and follow the startup wizard” on page100

▼

“Perform instrument veriﬁcation using RNase P plates” on page59

▼

“Connect the computer to the instrument directly or to a LAN” on page100

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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103).

•

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101).

Unpack and install the instrument

Prepare the installation site as described in the QuantStudio

™

3 and 5 Real‑Time PCR Systems Site

Preparation Guide (Pub. No.MAN0010405).

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.

Place the instrument on the bench.

Plug the power cable into the power port on the back panel of the instrument, then plug the cable

into an electrical receptacle.

Connect your instrument as required by your network conﬁguration (see “Supported options for

instrument and computer connections” on page103 and “Instrument and computer connections”

on page101).

•

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.

•

Connect wirelessly via the wireless adapter.

AppendixA

Install and connect the instrument to a network

Before you begin

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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

Power on the instrument.

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103).

•

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27.

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59).

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.

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

Power on the computer, then log in using a Windows

™

Administrator account.

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

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

Right-click on Broadband Connection, then select Properties.

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

Click Properties.

AppendixA

Install and connect the instrument to a network

Power on and follow the startup wizard

100

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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

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

Figure3Instrument back panel

USB ports

WiFi USB port—Connect USB wireless adapter for

wireless network access (ordered separately)

Ethernet Port—RJ45 port for 100/1,000 Mbps Ethernet

communication with the instrument

RS232 Port—For service use only

Fuse Cover

Power Switch

Power Port—100 to 240 VAC

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

Instrument and computer connections

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

101

1 1

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

conﬁguration

Detachable power supply cord compatible with local power supply receptacle.

Connection between the computer and the instrument.

Connection between the computer and the monitor, keyboard, and mouse.

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.x. QuantStudio

™

Design and

Analysis Software v2.x can also be used to set up and analyze ﬁles.

Thermo Fisher Scientiﬁc does not provide technical support for customer-provided computers. Thermo

Fisher Scientiﬁc provides limited support for Thermo Fisher Scientiﬁc‑supplied computers that have

been altered from their default conﬁguration.

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—Intel

™

Core

™

or compatible

•

Memory—4 GB RAM

•

Hard drive—20 GB free space

•

Monitor—1280 × 1024 resolution

AppendixA

Install and connect the instrument to a network

Download and install the desktop software

102

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Download the desktop software

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

Go to thermoﬁsher.com/quantstudio3-5softwaredownloads.

Download the software and the example ﬁles.

Install the desktop software

Use a Windows

™

Administrator account to log in to the computer on which you are installing the

desktop software.

Unzip the downloaded software and example ﬁles.

Double-click setup.exe.

Follow the InstallShield Wizard prompts to install the software.

Accept the License Agreement.

Select Typical as the setup preference, then click Next.

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.

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

Platform 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.

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

Networking

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

103

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 Platform conﬁgurations.

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–

–

Wireless connection to the network

LAN

•

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

Connect Platform conﬁguration option

•

Internet access and a computer with the Chrome

™

web browser to access the Thermo Fisher

™

Connect

Platform

•

Computer‑to‑Thermo Fisher

™

Connect Platform connection (select an option):

–

Wired connection to the internet using an Ethernet cable – or–

–

Wireless connection to the internet

LAN

•

Instrument‑to‑Thermo Fisher

™

Connect Platform 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

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

Networking

104

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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 Platform cannot be controlled remotely. However,

you can perform the following functions:

–

Remotely access Thermo Fisher

™

Connect Platform to create (and analyze) experiments.

–

From the instrument, download the experiments and start a run.

–

Monitor a run from Thermo Fisher

™

Connect Platform 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 link‑local (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

80/443

Standard ports for instrument-to-Thermo Fisher

™

Connect Platform and computer-to-Thermo

Fisher

™

Connect Platform connections

mDNS, 7443 Instrument-to-computer connection

mDNS, 5353 Instrument discovery

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

Networking

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™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

105

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105.

•

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.

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

Networking

106

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™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Troubleshooting

Observation Possible cause Recommended action

Inconsistent communication

between instrument and

computer or instrument and

Thermo Fisher

™

Connect

Platform

The instrument is conﬁgured

for both wired and wireless

network connection.

Ensure only one connectivity option is plugged

into the instrument (either an Ethernet cable or a

wireless adapter, but not both).

Conﬁgure for wired or wireless network connection.

Weak or unstable internet

connection, especially if

conﬁgured for wireless.

Change the conﬁguration to a wired connection.

Use a wireless network with a stronger or more

consistent signal.

The connection between the

instrument and the computer

is not recognized

The connection is not fully

established.

Power the instrument o, then power it on again.

If using a networked

conﬁguration, the instrument

and computer are not on the

same subnet mask.

Contact your information technologies department

to have them ensure that the instrument and

computer are on the same subnet mask.

If using a networked

conﬁguration, the instrument

or computer has an invalid

IP address.

Contact your information technologies department

to have them ensure that the IP addresses are

valid.

Insucient disk space

message

Insucient disk space to

save a run.

In the home screen, touch Settings4Run

History4Manage.

Delete or transfer experiments from the

instrument.

The touchscreen is black

The instrument is in sleep

mode.

Touch anywhere on the instrument touchscreen.

The instrument is not

powered on.

If you touch the instrument touchscreen and 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

proﬁle

Non-administrator forgot

instrument proﬁle PIN.

See “Manage all instrument proﬁles (Administrator

only)” on page85.

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

107

Observation Possible cause Recommended action

Forgot PIN for instrument

proﬁle

(continued)

Administrator forgot

instrument proﬁle PIN.

Have another administrator reset the PIN for the

forgotten-PIN proﬁle (see “Manage all instrument

proﬁles (Administrator only)” on page85).

If there is not another administrator proﬁle on the

instrument, you must restore factory defaults (see

“Restore factory defaults” on page94).

AppendixBTroubleshooting

Networking

108

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™

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Parts and materials

■

Kits, consumables, accessories, and reagents .......................................... 109

■

Consumables (96‑well, 0.2‑mLformat) ................................................. 109

■

384-wellconsumables ............................................................... 110

■

Consumables (96-well, 0.1-mLformat) ................................................. 111

■

Accessories ........................................................................ 112

■

General-use materials andconsumables ............................................... 112

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

MicroAmp

™

Optical 96-Well Reaction Plate

10 plates N8010560

500 plates 4316813

MicroAmp

™

Optical 96-Well Reaction Plate with Barcode

20 plates 4306737

500 plates 4326659

MicroAmp

™

EnduraPlate

™

Optical 96-Well Clear Reaction Plates with Barcode

20 plates 4483354

500 plates 4483352

MicroAmp

™

EnduraPlate

™

Optical 96-Well Clear GPLE Reaction Plates with

Barcode

20 plates 4483348

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

109

(continued)

Consumable

Amount Cat.No.

MicroAmp

™

EnduraPlate

™

Optical 96-Well Clear GPLE Reaction Plates with

Barcode

500 plates 4483351

MicroAmp

™

Optical Adhesive Film Kit 1 kit 4313663

MicroAmp

™

Optical Film Compression Pad (Optional, used for some applications) 5 each 4312639

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

(contains all 3 spectral calibration plates listed below)

A26343

QuantStudio

™

3/5 Spectral Calibration Plate 1, 96‑Well 0.2‑mL

(FAM

™

,VIC

™

,ROX

™

,SYBR

™

dyes)

A26331

QuantStudio

™

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

(ABY

™

,JUN

™

,MUSTANG PURPLE

™

dyes)

A26332

QuantStudio

™

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

(TAMRA

™

,NED

™

,Cy

5dyes)

A26333

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 Barcode (clear) 20 plates 4483285

500 plates 4483273

MicroAmp

™

Optical Adhesive Film Kit 1 kit 4313663

AppendixCParts and materials

384-well consumables

110

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™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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

(containing FAM

™

, VIC

™

, ROX

™

, TAMRA

™

, and SYBR

™

dyes)

A26334

384-Well Spectral Calibration Plate 2

(containing ABY

™

, JUN

™

, MUSTANG PURPLE

™

, NED

™

, and Cy

5 dyes)

A26335

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 Barcode (clear)

(0.1 mL)

20 plates 4481194

500 plates 4483494

MicroAmp

™

EnduraPlate

™

Optical 96-Well Fast Clear Reaction Plates with Barcode 20 plates 4483485

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

(containing FAM

™

, VIC

™

, ROX

™

, and SYBR

™

dyes

A26336

96-Well 0.1-mL Spectral Calibration Plate 2

(containing ABY

™

, JUN

™

, and MUSTANG PURPLE

™

dyes)

A26337

96-Well 0.1-mL Spectral Calibration Plate 3

(containing TAMRA

™

, NED

™

, and Cy

5 dyes)

A26340

96Well Fast TaqMan

™

RNase P Instrument Veriﬁcation Plate 4351979

AppendixCParts and materials

Consumables (96-well, 0.1-mL format)

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

111

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 MLS

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

AppendixCParts and materials

Accessories

112

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™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

Instrument speciﬁcation and layout

■

Conﬁgured systemdimensions ........................................................ 114

■

Electrical requirements ............................................................... 115

■

Environmental requirements .......................................................... 116

■

Network requirements ............................................................... 116

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™

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113

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.)

27 cm (10.5 in.)

50 cm (20 in.)

30 cm (12 in.)

40 cm (16 in.)

207 cm (81.5 in.)

AppendixDInstrument speciﬁcation and layout

Conﬁgured system dimensions

114

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™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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 sucient 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115 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

Device

Rated voltage Circuit required Rated frequency Rated power

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)

100–240 ±10% VAC 10 A 50/60 Hz

125 VA

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.

AppendixD

Instrument speciﬁcation and layout

Electrical requirements

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™

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115

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

conditions

•

Humidity: 20–80% relative humidity (noncondensing)

•

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 aect 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).

The instrument can be conﬁgured for either wired or wireless networking, not both.

AppendixD

Instrument speciﬁcation and layout

Environmental requirements

116

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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 sucient 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)

AppendixDInstrument speciﬁcation and layout

Network requirements

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™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

117

Safety

■

Symbols on thisinstrument ........................................................... 118

■

Safety alerts on thisinstrument ....................................................... 121

■

Safety information for instruments not manufactured by Thermo FisherScientiﬁc ............ 122

■

Instrumentsafety .................................................................... 122

■

Safety and electromagnetic compatibility (EMC) standards ............................... 124

■

Chemicalsafety ..................................................................... 127

■

Biological hazardsafety .............................................................. 128

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, visit thermoﬁsher.com/support.

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

Consult the manual for further safety

information.

Attention, risque de danger

Consulter le manuel pour d’autres

renseignements de sécurité.

118

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

(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)

O O (arrêt)

On/O On/O (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

alternating current or voltage

Borne pouvant recevoir ou envoyer une

tension ou un courant de type alternatif

Terminal that can receive or supply

alternating or direct current or voltage

Borne pouvant recevoir ou envoyer une

tension ou un courant continu ou alternatif

AppendixESafety

Symbols on this instrument

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

119

(continued)

Symbol English Français

Do not dispose of this product in

unsorted municipal waste

CAUTION! To minimize

negative environmental impact

from disposal of electronic

waste, do not dispose of

electronic waste in unsorted

municipal waste. Follow local

municipal waste ordinances for

proper disposal provision and

contact customer service for

information about responsible

disposal options.

Ne pas éliminer ce produit avec les déchets

usuels non soumis au tri sélectif.

MISE EN GARDE! Pour minimiser

les conséquences négatives sur l’en

vironnement à la suite de l’élimination

de déchets électroniques, ne pas éli

miner ce déchet électronique avec les

déchets usuels non soumis au tri sé

lectif. Se conformer aux ordonnances

locales sur les déchets municipaux

pour les dispositions d’élimination et

communiquer avec le service à la cli

entèle 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.

AppendixESafety

Symbols on this instrument

120

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™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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 the Safety Data Sheets (SDSs)

before handling.

MISE EN GARDE! Produits chimiques dange

reux. Lire les ﬁches signalétiques (FS) avant de ma

nipuler les produits.

CAUTION! Hazardous waste. Refer

to SDS(s) and local regulations for

handling and disposal.

MISE EN GARDE! Déchets dangereux. Lire les

ﬁches signalétiques (FS) et la réglementation locale

associées à la manipulation et à l’élimination des

déchets.

Location of safety labels on the instrument



AppendixESafety

Safety alerts on this instrument

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™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

121

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.

AppendixESafety

Safety information for instruments not manufactured by Thermo Fisher Scientiﬁc

122

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™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

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.

AppendixESafety

Instrument safety

QuantStudio

™

3 and 5 Real‑Time PCR Systems Installation, Use, and Maintenance Guide

123

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.

AppendixE

Safety

Safety and electromagnetic compatibility (EMC) standards

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Safety compliance

Reference

Description

EU Directive 2014/35/EU European Union “Low Voltage Directive”

IEC 61010-1

EN 61010-1

UL 61010-1

CSA C22.2 No. 61010-1

Safety requirements for electrical equipment for measurement, control, and

laboratory use – Part 1: General requirements

IEC 61010-2-010

EN 61010-2-010

Safety requirements for electrical equipment for measurement, control and

laboratory use – Part 2-010: Particular requirements for laboratory equipment for

the heating of materials

IEC 61010-2-081

EN 61010-2-081

Safety requirements for electrical equipment for measurement, control and

laboratory use – Part 2-081: Particular requirements for automatic and semi-

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.

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Safety and electromagnetic compatibility (EMC) standards

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Environmental design

Reference

Description

Directive 2012/19/EU European Union “WEEE Directive” – Waste electrical and

electronic equipment

EU Directive 2011/65/EU & Commission

Delegated Directive (EU) 2015/863

European Union “RoHS Directive” – Restriction of hazardous

substances in electrical and electronic equipment

Directive 2006/66/EC European Union “Battery Directive”

China EEP Hazardous Substances Information

Component Name QuantStudio

™

3 and 5 Real‑Time PCR Systems

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.

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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

sucient 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.

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Chemical safety

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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

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

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Documentation and support