ThermoFisher Scientific QuantStudio 3 Quick start guide

For Research Use Only. Not for use in diagnostic procedures.
QuantStudio™3 and 5 Real-Time PCR Systems
INSTALLATION, USE, AND MAINTENANCE
Firmware v1.2.x
Publication Number MAN0010407
Revision C.0

The information in this guide is subject to change without notice.
DISCLAIMER
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PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.
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Notice to Purchaser: The purchase of this instrument conveys to the purchaser the limited, non-transferable right to use the purchased instrument
only, under intellectual property rights that are owned and/or controlled by Life Technologies and relate specifically to the instrument. Purchase of the
instrument includes the right to use the instrument for internal research and to perform services (including the right to report the results of services
for a fee) by the purchaser only, but does not convey rights to use any other products, reagents, assays or methods such as the 5' nuclease assay
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components, and no such rights are conveyed expressly, by implication, or by estoppel. For information on obtaining additional rights, please contact
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©2015 Thermo Fisher Scientific Inc. All rights reserved.

Contents
About this guide ............................................................ 8
Revision history ................................................................. 8
Purpose ....................................................................... 9
■CHAPTER 1 Product information ...................................... 10
Instrument hardware description ................................................ 10
Instrument overview ....................................................... 10
Parts of the instrument ..................................................... 13
Software description ........................................................... 14
Instrument, desktop, and cloud software features ............................. 14
Folders, templates, experiments, and projects ................................ 15
Third-party software installation ............................................ 16
Network connection options ..................................................... 16
Experiment types .............................................................. 17
■CHAPTER 2 Start, sign on, and configure the instrument .......... 19
Installation and instrument verification ........................................... 19
Precautions for use ............................................................ 20
Power on the instrument ........................................................ 20
Parts of the home screen ....................................................... 21
Use the instrument without signing in ............................................ 23
Create a new instrument profile ................................................. 23
Sign In ........................................................................ 23
Sign out ....................................................................... 24
Link your instrument profile to your Thermo Fisher Cloud account ................... 24
Link your instrument profile to Thermo Fisher Cloud ........................... 24
Create an instrument profile and link to Thermo Fisher Cloud ................... 24
Configure instrument settings ................................................... 25
QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide 3

■CHAPTER 3 Create and run experiments on the instrument ....... 28
Workflow ..................................................................... 28
Options for running an experiment ............................................... 29
Create and run an experiment from a template ................................ 29
Run an experiment from a saved file ......................................... 29
Repeat your last experiment run ............................................. 30
Edit an experiment before starting a run .......................................... 31
Define experiment properties ............................................... 31
Edit a method ............................................................. 32
Define plate wells .......................................................... 35
Load and unload a plate in the instrument ......................................... 36
View, pause, or stop a run ....................................................... 37
View well details ........................................................... 37
Pause or stop a run ........................................................ 37
Adjust the graphical view of an experiment ................................... 37
Lock the touchscreen during a run ........................................... 38
Transfer, view, or manage files and results ........................................ 38
Transfer experiment results ................................................ 38
View run history ........................................................... 38
Manage template (.edt) files ................................................. 39
■CHAPTER 4 Calibrate and verify instrument performance ......... 40
Calibration and verification schedule ............................................. 40
Calibration descriptions ........................................................ 41
View the calibration status and set reminders ..................................... 41
View calibration status and set reminders in the instrument .................... 41
View calibration status and set reminders in the Cloud ......................... 42
Perform ROI/Uniformity, Background, and Dye calibrations .......................... 42
Workflow: Calibration ...................................................... 42
Prepare a calibration plate .................................................. 43
Perform calibrations ....................................................... 44
View calibration images and transfer results to USB ........................... 46
Troubleshoot calibration failure ............................................. 47
Identify contamination ...................................................... 47
Create a background plate (optional) ......................................... 48
Perform instrument verification using RNase P plates .............................. 49
Instrument verification description and schedule .............................. 49
RNase P Instrument Verification Plates ....................................... 49
Analytical performance ..................................................... 50
Installation specification .................................................... 50
Prepare an RNase P plate ................................................... 50
Perform RNase P verification ............................................... 51
Troubleshoot verification failure ............................................. 53
Contents
4 QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide

Calibrate custom dyes .......................................................... 54
Custom dyes overview ...................................................... 54
Dilute the custom dye to an optimal concentration ............................. 54
Calibrate the custom dye ................................................... 57
Calibrate for a custom melt curve experiment ..................................... 60
■CHAPTER 5 Maintain the instrument ................................. 62
Backup or restore the instrument ................................................ 62
Decontaminate the sample block ................................................. 63
Materials required ......................................................... 63
Clean the sample block ..................................................... 63
Solvents for cleaning the sample block ....................................... 65
Replace the instrument fuses .................................................... 65
Materials required ......................................................... 65
Replace the fuses .......................................................... 66
Power on or off, store, and move ................................................. 66
Enable sleep mode ......................................................... 66
Power on the instrument ................................................... 67
Power off the instrument ................................................... 67
Prepare the instrument to ship, move, or store ................................ 67
Move the instrument ....................................................... 68
Return the instrument for service ............................................ 68
■CHAPTER 6 Profile and instrument configuration tasks ............ 70
Initial start up ................................................................. 70
Manage profiles ............................................................... 71
Create an administrator profile .............................................. 71
View all user profiles (Administrator only) .................................... 71
Manage all instrument profiles (Administrator only) ........................... 71
Edit a user profile .......................................................... 72
Enable SAE mode (Administrator only) ............................................ 72
Require sign-in (Administrator only) .............................................. 73
Enable remote instrument monitoring (Administrator only) .......................... 73
Update instrument software (Administrator only) .................................. 73
Restore factory defaults ........................................................ 74
Configure the network .......................................................... 74
Set up a wired connection ................................................... 74
Set up a wireless connection ................................................ 75
Select a Cloud region (Administrator only) ......................................... 75
Manage the instrument name (Administrator only) ................................. 75
Set the date and time ........................................................... 76
Manage the Sign Out Timer (Administrator only) ................................... 76
Contents
QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide 5

■APPENDIX A Install and connect the instrument to a network ..... 77
Workflow: Install and connect to a network ........................................ 77
Before you begin ............................................................... 78
Unpack and install the instrument ............................................... 78
Power on and follow the startup wizard ........................................... 79
Connect the instrument and the computer directly or to a LAN ....................... 79
Instrument and computer connections ............................................ 81
Download and install the QuantStudio™Design and Analysis desktop Software ......... 82
Computer requirements for the desktop software .............................. 82
Download the desktop software ............................................. 82
Install the software ........................................................ 82
Networking ................................................................... 84
Supported network configuration options ..................................... 84
Control and monitor networked instruments .................................. 85
About the Ethernet port .................................................... 85
Firewall ports that must be open ............................................ 85
Networking guidelines and best practices ..................................... 85
■APPENDIX B Troubleshooting ......................................... 87
■APPENDIX C Parts and materials ..................................... 88
Kits, consumables, and accessories .............................................. 88
96-Well (0.2-mL) consumables .................................................. 88
384-well consumables .......................................................... 89
96-Well Fast (0.1-mL) consumables .............................................. 90
QuantStudio™3 and 5 Systems accessories ........................................ 91
General-use materials and consumables ......................................... 91
■APPENDIX D Instrument specification and layout ................... 92
Configured system dimensions .................................................. 93
Instrument clearances ..................................................... 94
Electrical requirements ......................................................... 94
Environmental requirements .................................................... 95
Network requirements .......................................................... 95
Contents
6 QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide

■APPENDIX E Safety ..................................................... 97
Symbols on this instrument ..................................................... 98
Conformity symbols ........................................................ 99
Safety alerts on this instrument ................................................. 100
Location of safety labels on the instrument .................................. 100
Safety information for instruments not manufactured by Thermo Fisher Scientific .... 101
Instrument safety ............................................................. 101
General ................................................................. 101
Physical injury ........................................................... 102
Electrical ................................................................ 103
Cleaning and decontamination ............................................. 103
Safety and electromagnetic compatibility (EMC) standards ......................... 103
Safety compliance ........................................................ 104
EMC .................................................................... 104
Environmental design ..................................................... 105
Chemical safety ............................................................... 105
Biological hazard safety ........................................................ 106
■Documentation and support ........................................... 107
Related documentation ........................................................ 107
Obtain information from the Help system ........................................ 108
Customer and technical support ................................................ 108
Limited product warranty ...................................................... 109
Index ..................................................................... 110
Contents
QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide 7

About this guide
Revision history
Revision Date Description
C.0 December 2015 Updates – describes new features in Firmware
v1.2.x, including:
• Updated workflow to create an instrument
profile
• Streamlined workflow for connectivity to the
Thermo Fisher Cloud
• Improved display of VeriFlex™Zones
• Plate insert reminder before starting run
• Support for 96-well Fast (0.1 mL) plates
B.0 September 2015 Updates – describes new features in Firmware
v1.1.x, including:
•Experiment runs: monitor real-time data, edit
cycle number and lock screen during a run, view
end plot, and support for 384-well plates
•File management: access Network folders,
navigate folder structures and save templates
on instrument, and perform batch actions for
file management
•Instrument configuration: support for Security,
Audit, and e-Signature (SAE), smart monitoring,
and choice of server region
Includes information on software feature
comparison, definitions of terms, parts of method,
network connection options, experiment types,
desktop software installation.
A.0 April 2015 New document. Describes installation, operation,
and maintenance of the QuantStudio™3 and 5 Real-
Time PCR Systems.
8 QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance 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,
refer to the QuantStudio™ Design and Analysis desktop Software User Guide (Pub. no.
MAN0010408).
About this guide
Purpose
QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide 9

Product information
■Instrument hardware description ....................................... 10
■Software description .................................................. 14
■Network connection options ........................................... 16
■Experiment types ..................................................... 17
Instrument hardware description
The QuantStudio™ 3 and 5 Real-Time PCR Systems use uorescent-based polymerase
chain reaction (PCR) reagents to perform:
•Quantitative detection of target nucleic acid sequences (targets).
• Qualitative detection of targets (endpoint analysis).
• Qualitative analysis of the PCR product (post-PCR melt curve analysis).
The following xed-block congurations 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 QuantStudio™ Design and Analysis Software (desktop or cloud).
An optional barcode scanner and optional wireless adapter can be purchased
separately.
1
Instrument
overview
10 QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide

Instrument filters and supported dyes
System dyes
The QuantStudio™ 3 and 5 Systems use a coupled four-color, coupled ve-color, or de-
coupled six-color lter set that supports the dyes shown in the following table and
gure. For more information about the spectral dye calibration kits available for the
QuantStudio™ 3 and 5 Systems, contact Support.
Peak
channel Color
Filter wavelength
(nm)[1] Pre-calibrated
dyes
Example custom
dyes
Excitation Emission
x1-m1 Blue 470 ± 15 520 ± 15 FAM™and SYBR™
Green
SYT09
x2-m2 Green 520 ± 10 558 ± 12 VIC™HEX™, TET™, and
JOE™[2]
x3-m3 Yellow 550 ± 10 587 ± 10 ABY™, NED™, and
TAMRA™Cy®3
x4-m4 Orange 580 ± 10 623 ± 14 JUN™and ROX™Texas Red™
x5-m5 Red 640 ± 10 682 ± 14 Cy®5 and
MUSTANG
PURPLE™
LIZ™
x6-m6 Deep-
Red
662 ± 10 711 ± 12 None[3] Cy®5.5
[1] The central wavelengths are the optimized wavelengths.
[2] The HEX™and TET™dyes from Thermo Fisher Scientific fall within the emission wavelength range of the
system, therefore they can be added and adapted for use in experiments on the system. To add any of these
dyes to the Dye Library, perform a custom dye calibration.
[3] This filter set currently does not support any dyes supplied by Thermo Fisher Scientific.
Emission
Spectra
Filters
Wavelength
(nm)
1 2 345
x1-m1 x2-m2 x3-m3 x4-m4 x5-m5 x6-m6
1x1-m1 — FAM™, SYBR™Green
2x2-m2 — VIC™
3x3-m3 — ABY™, NED™, Cy®3, and TAMRA™
4x4-m4 — JUN™, ROX™, and Texas Red™
5x5-m5 — Cy®5 and MUSTANG PURPLE™
Chapter 1 Product information
Instrument hardware description
1
QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide 11

Custom dyes
The QuantStudio™ 3 and 5 Systems can run assays designed with custom dyes (dyes
not supplied by Thermo Fisher Scientic or dyes not pre-calibrated with the
instrument). Custom dyes must excite between 455 – 672 nm and emit between 505 –
723 nm. Select a custom dye that does not overlap with other dyes used in an
experiment (see the lter-wavelength table in “System dyes“ on page 11).
To use a custom dye and add it to the Dye Library, perform a custom dye calibration
(see “Calibrate custom dyes“ on page 54).
About data collection
The instrument collects raw uorescence data at dierent points during the PCR
cycle, depending on the type of run performed.
When you create an experiment template (.edt le) in the desktop or cloud software,
you can customize the optical lter channels through which the instrument collects
data. You can specify a lter channel set for all PCR thermal protocols and, optionally,
a dierent lter set for the melt curve stage(s).
Run type Experiment type Data collection point
Real-time • Standard curve
• Relative standard curve
• Comparative CT(DDCT)
• Melt curve
During the thermal cycling protocol.
Typical timing is to collect data at each cycle
of a PCR stage or continuously during a melt
stage.
Post-PCR
(endpoint)
• Genotyping
• Presence/ Absence
• After thermal cycling is completed.
For Presence/Absence and Genotyping
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.
Chapter 1 Product information
Instrument hardware description
1
12 QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide

Blocks with VeriFlex™Zones
Applied Biosystems™ VeriFlex™ technology provides independent temperature zones
that oer enhanced functionality and precise control over your qPCR runs.
QuantStudio™3 System QuantStudio™5 System
Three programmable VeriFlex™Zones. Six programmable VeriFlex™Zones.[1]
[1] Only applicable for 96-well 0.2-mL and 0.1-mL blocks.
These independent zones are ideal for qPCR 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.
2
3
1
1Touchscreen – Controls the instrument.
2USB port – For connection to an external
network drive, jump drive, or other
external data storage device.
3Instrument drawer – Contains sample
plate.
The instrument includes three additional USB ports on the back of the instrument.
The instrument recognizes only one external storage device at a time for data transfer.
Parts of the
instrument
Chapter 1 Product information
Instrument hardware description
1
QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide 13

Software description
The instrument software and the QuantStudio™ Design and Analysis Software
(desktop and cloud) include the features described below.
Feature Instrument Desktop Cloud
Use as guest (no sign in) 3 3 [1] —
Create templates (unlocked or locked) — 3 3
Edit unlocked templates 333
Edit locked templates (password
assigned by template creator required)
—3 3
Load system or user-created templates
(.edt file) to instrument
3 3 —
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
3— —
Load plate in instrument 3— —
Start run 3 3 —
View real-time data during a run 333
View instrument status (running,
calibration needed, and so on)
3—3
Analyze results — 3 3
Set calibration reminders 3—3
Review exported calibration or RNase P
verification results
—3 3
( only RNase P )
[1] Login required if the Security, Audit, and e-Signature (SAE) module is enabled (QuantStudio™5 Systems only)
Instrument,
desktop, and
cloud software
features
Chapter 1 Product information
Software description
1
14 QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide

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
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 cloud)
• User-created, accessed from Load Experiment
Instrument
Desktop
Cloud
Experiment Run
File (.eds)
Settings and data for a completed instrument run. Instrument
Desktop
Cloud
Project Function in the Cloud Data Manager that is used for
secondary analysis applications. Does not apply to
the QuantStudio™Design and Analysis cloud
Software, which is a primary analysis application.
Cloud
Template and
experiment
components
Instrument Desktop Cloud
Properties • Experiment file name
• Reagent information (Reagent
barcode, Lot#)
• Plate barcode
• Data destination (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
• ( Cloud software only ) Notifications
Method Thermal cycling conditions Thermal cycling conditions
Folders,
templates,
experiments, and
projects
Chapter 1 Product information
Software description
1
QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide 15

Template and
experiment
components
Instrument Desktop Cloud
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 Cloud
Instrument Details)
View: Time remaining and
Temperature, Method, Plots
Results Not applicable Review plots
Export Not applicable Export results
Before you install third-party software on the computer running the QuantStudio™
desktop Software, conrm that the third-party software will not:
• Restrict Ethernet communication.
• Interfere with instrument or computer operation.
Network connection options
You can connect a QuantStudio™ 3 or 5 Instrument to a network or computer in the
congurations listed below. For specic information on networking, see
“Networking“ on page 84.
Direct connection Local area network (LAN) connection Cloud connection
wired wired or wireless wired or wireless
Third-party
software
installation
Chapter 1 Product information
Network connection options
1
16 QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide

Experiment types
Purpose Description
Standard Curve experiment
Determines absolute
target quantity in
samples.
1. The software measures amplification of the target in a standard dilution series and in
test samples.
2. The software generates a standard curve using data from the standard dilution series.
3. Using the standard curve, the software interpolates the absolute quantity of target in
the test samples.
Relative Standard Curve experiment
Determines relative
target quantity in
samples.
1. 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 effects on gene expression, an untreated
control is an appropriate reference sample.
2. The software generates standard curves for the target of interest and the endogenous
control using data from the corresponding standard dilution series.
3. Using the standard curves, the software interpolates 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 endogenous control quantity in the sample.
4. To determine the relative quantity of the target in test samples, the software divides the
normalized target quantity in the sample by the normalized target quantity in the
reference sample.
Comparative CT(DDCT) experiment
Determines relative
target quantity in
samples.
1. 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 effects on gene expression, an untreated
control is an appropriate reference sample.
2. The measurements for the target of interest are normalized to the endogenous control.
3. To determine the relative quantity of the target in test samples, the software compares
the normalized CT(DCT) for the sample to the normalized CT(DCT) for the reference
sample.
Chapter 1 Product information
Experiment types
1
QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide 17

Purpose Description
Genotyping experiment
Detects single
nucleotide
polymorphism (SNP)
variants of a target
nucleic acid
sequence.
Genotyping experiments use preformulated TaqMan™SNP Genotyping Assays that include:
• Two sequence-specific primers for amplification of sequences containing the SNP of
interest.
• Two allele-specific TaqMan™probes for Allele 1 and Allele 2.
1. The software normalizes the fluorescence of the reporter dyes to the fluorescence of
the passive reference dye in each well.
2. The software plots the normalized intensities (Rn) of the reporter dyes in each sample
well on an Allelic Discrimination Plot, which contrasts the reporter dye intensities of the
allele-specific probes.
3. The software algorithmically clusters the sample data, and assigns a genotype call to
the samples of each cluster according to its position on the plot.
Presence/Absence experiment
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 different from the CTthreshold; the CTthreshold is not used
to make calls.)
Melt Curve experiment
Determines the
melting temperature
(Tm) of the
amplification
products of a PCR
reaction that used
SYBR™Green dye.
In the software, Melt Curve analysis is included in the default run method for any experiment
type that uses SYBR™Green reagents.
Chapter 1 Product information
Experiment types
1
18 QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide

Start, sign on, and configure the
instrument
■Installation and instrument verication ................................. 19
■Precautions for use ................................................... 20
■Power on the instrument .............................................. 20
■Parts of the home screen ............................................... 21
■Use the instrument without signing in .................................. 23
■Create a new instrument prole ........................................ 23
■Sign In .............................................................. 23
■Sign out ............................................................. 24
■Link your instrument prole to your Thermo Fisher Cloud account ......... 24
■Congure instrument seings .......................................... 25
Installation and instrument verification
Before the rst use of the instrument:
• Install the instrument (see “Unpack and install the instrument“ on page 78).
• Verify instrument performance (see “Perform instrument verication using
RNase P plates“ on page 49).
Note: Instruments are factory calibrated, so no calibration is necessary at
installation. However, we recommend that you verify instrument performance
before using the instrument.
Note: Regular calibration and verication should be performed according to the
“Calibration and verication schedule“ on page 40.
2
QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide 19

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 re,
replace fuses only with listed and certied 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 Scientic, conrm with Thermo Fisher
Scientic that the proposed method will not damage the equipment.
CAUTION! Use at caps for 0.2 mL tubes and 0.1 mL tubes. Rounded caps can
damage the heated cover.
Power on the instrument
To power on the instrument from a powered-o state:
1. Touch anywhere on the touchscreen to determine if the instrument is in sleep
mode. If the home screen displays, the instrument is already powered on.
2. If the home screen does not display, power on the instrument by pressing the
switch on the rear panel.
The instrument is ready to use when the home screen is displayed.
If left unaended (for about two hours), the instrument automatically enters sleep
mode (enabled by default) to conserve power. Refer to the touchscreen Help system
for step-by-step instructions for changing the sleep mode seing.
Chapter 2 Start, sign on, and configure the instrument
Precautions for use
2
20 QuantStudio™3 and 5 Real-Time PCR Systems Installation, Use, and Maintenance Guide