Thermo Scientific QuantStudio 1 Quick start guide

For Research Use Only. Not for use in diagnostic procedures.
QuantStudio™1 Real-Time PCR System
INSTALLATION, USE, AND MAINTENANCE
Firmware v1.0.x
Publication Number MAN0017853
Revision A.0

Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256
For descriptions of symbols on product labels or product documents, go to thermofisher.com/symbols-definition.
The information in this guide is subject to change without notice.
DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL,
INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT,
INCLUDING YOUR USE OF IT.
Revision history: Pub. No. MAN0017853 (English)
Revision Date Description
A.0 10 October 2018 New document.
Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these products, you accept
the terms and conditions of all applicable Limited Use Label Licenses.
Trademarks: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. TaqMan is a registered
trademark of Roche Molecular Systems, Inc., used under permission and license. Cy is a registered trademark of GE Healthcare. Microsoft and
Windows are trademarks of Microsoft Corporation. Pentium is a trademark of Intel Corporation. Google and Chrome are trademarks of Google, Inc.
©2018 Thermo Fisher Scientific Inc. All rights reserved.

Contents
About this guide ............................................................ 8
■CHAPTER 1 Product information ....................................... 9
Instrument hardware description ................................................. 9
Instrument overview ........................................................ 9
Parts of the instrument ..................................................... 11
Parts of the home screen ................................................... 12
Software description ........................................................... 14
Instrument, desktop, and cloud software features ............................. 14
Folders, templates, experiments, and projects ................................ 15
Third-party software ....................................................... 16
Supported options for instrument and computer connections ........................ 16
Experiment types .............................................................. 18
■CHAPTER 2 General procedures to operate the instrument ........ 20
Precautions for use ............................................................ 20
Power on the instrument ........................................................ 21
Power off the instrument ....................................................... 21
Sign in ........................................................................ 21
Sign out ....................................................................... 21
Load and unload a plate in the QuantStudio™1 Real-Time PCR Instrument ............ 22
Transfer, view, or manage files and results ........................................ 23
Transfer EDS files from the instrument home screen ........................... 23
View run history and delete or transfer files from the instrument ................ 23
Manage templates (EDT files) ............................................... 23
■CHAPTER 3 Configure the instrument and manage
instrument profiles ....................................................... 25
Initial start‑up ................................................................. 25
Installation and instrument verification ........................................... 26
Use the instrument without signing in ............................................ 26
Create an administrator instrument profile during initial start-up .................... 27
Create a new instrument profile ................................................. 27
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Overview of Settings ............................................................ 28
Manage instrument settings ..................................................... 30
Manage the instrument name (Administrator only) ............................. 31
Enable Sleep Mode ........................................................ 31
Set the idling temperature for the heated cover ................................ 31
Configure the network drive ................................................. 31
OEM connection only (Administrator only) ..................................... 31
Select a Cloud region (Administrator only) .................................... 32
Set the date and time (Administrator only) .................................... 32
Configure the network ...................................................... 32
Restore factory defaults .................................................... 34
Select a language .......................................................... 34
Learn about the instrument ..................................................... 34
View instrument specifications .............................................. 34
View and export the License Agreement ...................................... 35
Manage home screen notifications ............................................... 35
Manage maintenance, service, and calibrations .................................... 35
Update instrument software (Administrator only) .............................. 35
Enable remote instrument monitoring (Administrator only) ..................... 36
View instrument statistics .................................................. 36
View instrument logs ....................................................... 36
Manage Users ................................................................. 36
Require instrument profile sign-in (Administrator only) ......................... 37
Manage the Sign Out Timer (Administrator only) ............................... 37
Manage instrument profiles ................................................. 37
Link an instrument profile with the Thermo Fisher Cloud ........................... 38
Link an existing instrument profile with the Thermo Fisher Cloud ................ 38
Create a new instrument profile and link with the Thermo Fisher Cloud .......... 38
■CHAPTER 4 Create and run experiments on the instrument ....... 39
Workflow ..................................................................... 39
Run an experiment ............................................................. 40
Create and run an experiment from a template ................................ 40
Run an experiment from a saved file ......................................... 40
Repeat the last instrument run .............................................. 41
Edit an experiment before starting a run .......................................... 41
Enter or edit template properties ............................................ 41
Edit the run method ........................................................ 43
Define, assign, and view well details ......................................... 45
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View, pause, or stop a run ....................................................... 46
View real-time data and plots on the instrument touchscreen ................... 46
Adjust the display of real-time plots on the instrument touchscreen .............. 47
Pause or stop an instrument run ............................................. 47
Lock the touchscreen during a run ........................................... 47
Transfer EDS files from the instrument home screen ............................... 48
■CHAPTER 5 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 the Cloud ......................... 51
Perform ROI/uniformity, background, and dye calibrations .......................... 52
Workflow: Calibration ...................................................... 52
Prepare a calibration plate .................................................. 52
Perform calibrations ....................................................... 53
View calibration images and transfer results to USB ........................... 54
Troubleshoot calibration failure ............................................. 55
Identify contamination ...................................................... 56
Create a background plate
(optional) ......................................... 56
Perform instrument verification using RNase P plates .............................. 57
Instrument verification description .......................................... 57
RNase P instrument verification plate ........................................ 58
Performance specifications pass criteria ..................................... 58
Prepare an RNase P plate ................................................... 58
Perform RNase P verification ............................................... 59
Troubleshoot verification failure ............................................. 61
Calibrate custom dyes .......................................................... 62
Custom dyes overview ...................................................... 62
Use a dilution series to determine an optimal custom dye concentration .......... 62
Calibrate the custom dye ................................................... 65
Calibrate for a custom melt curve experiment ..................................... 68
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■CHAPTER 6 Maintain the instrument ................................. 70
Backup or restore the instrument ................................................ 70
Decontaminate the sample block ................................................. 71
Materials required ......................................................... 71
Clean the sample block ..................................................... 71
Detailed procedures for cleaning the sample block ............................. 73
Replace the instrument fuses .................................................... 73
Materials required ......................................................... 73
Replace the fuses .......................................................... 74
Prepare the instrument to store, move, or ship .................................... 74
Move the instrument ....................................................... 75
Return the instrument for service ............................................ 75
■APPENDIX A Install and connect the instrument to a network ..... 77
Workflow: Install and connect to a network ........................................ 77
Before you begin ............................................................... 78
Instrument and computer connections ............................................ 78
Unpack and install the instrument ............................................... 79
Power on and follow the startup wizard ........................................... 80
Connect the instrument and the computer directly or to a LAN ....................... 80
Networking ................................................................... 81
Supported options for instrument and computer connections .................... 81
Control and monitor networked instruments .................................. 82
Ethernet port overview ..................................................... 83
Firewall ports that must be open ............................................ 83
Networking guidelines and best practices ..................................... 83
■APPENDIX B Troubleshooting ......................................... 84
■APPENDIX C Instrument specification and layout ................... 86
Configured system dimensions .................................................. 87
Instrument clearances ..................................................... 88
Electrical requirements ......................................................... 88
Environmental requirements .................................................... 89
Network requirements .......................................................... 90
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■APPENDIX D Parts and materials ..................................... 91
Kits, consumables, accessories, and reagents ..................................... 91
Consumables (96‑well, 0.2‑mL format) ............................................ 91
Accessories ................................................................... 92
General-use materials and consumables ......................................... 92
■APPENDIX E Safety ..................................................... 93
Symbols on this instrument ..................................................... 94
Conformity symbols ........................................................ 95
Safety alerts on this instrument .................................................. 96
Location of safety labels on the instrument ................................... 97
Safety information for instruments not manufactured by Thermo Fisher Scientific ..... 97
Instrument safety .............................................................. 97
General .................................................................. 97
Physical injury ............................................................ 98
Electrical safety ........................................................... 98
Cleaning and decontamination ............................................... 98
Safety and electromagnetic compatibility (EMC) standards .......................... 98
Safety compliance ......................................................... 99
EMC ...................................................................... 99
Environmental design ..................................................... 100
Chemical safety ............................................................... 100
Biological hazard safety ........................................................ 101
■Documentation and support ........................................... 102
Related documentation ........................................................ 102
Obtain information from the Help system ........................................ 102
Customer and technical support ................................................ 102
Limited product warranty ...................................................... 103
Index ..................................................................... 104
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About this guide
This guide provides information about installing, using, and maintaining the
QuantStudio™ 1 Real-Time PCR System. For information and instructions on
performing experiments on this system, refer to QuantStudio™ Design and Analysis
Desktop Software User Guide (Pub. No. MAN0010408).
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Product information
■Instrument hardware description ........................................ 9
■Software description .................................................. 14
■Supported options for instrument and computer connections .............. 16
■Experiment types ..................................................... 18
Instrument hardware description
The QuantStudio™ 1 Real-Time PCR System uses uorescence-based polymerase
chain reaction (PCR) reagents to perform the following types of experiments.
• Quantitative detection of target nucleic acid sequences (targets).
• Qualitative detection of targets.
• Qualitative analysis of the PCR product.
For more information, see “Experiment types“ on page 18.
The instrument is congured with a 96-well 0.2-mL xed block and a 3-color coupled
lter set.
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 ordered separately.
1
Instrument
overview
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Instrument filters and supported dyes
System dyes
The instrument use a coupled three-color lter set that supports the dyes shown in the
following table and gure. 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 ± 15 520 ± 15 FAM™,
SYBR™Green SYT09
x2-m2 Green 520 ± 10 558 ± 12 VIC™JOE™,
HEX™, TET™[2]
x4-m4 Orange 580 ± 10 623 ± 14 ROX™, JUN™Texas Red™
[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.
Filters
Wavelength
(nm)
123
x1-m1 x2-m2 x4-m4
Emission
Spectra
1x1-m1 — FAM™, SYBR™Green
2x2-m2 — VIC™
3x4-m4 — JUN™, ROX™, Texas Red™
Custom dyes
The instrument can run assays designed with custom dyes. Custom dyes include the
following:
• Dyes that are not supplied by Thermo Fisher Scientic.
• 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 62).
• Ensure that the custom dye excites and emits within the wavelength range of the
lters (see the lter-wavelength table in “System dyes“).
• Select a custom dye that does not overlap with other dyes used in the run (see the
lter-wavelength table in “System dyes“).
Chapter 1 Product information
Instrument hardware description
1
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1
2
3
1Touchscreen – Controls the instrument.
2USB port – For connection to an external network drive or external data storage device.
3Instrument 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.
Parts of the
instrument
Chapter 1 Product information
Instrument hardware description
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4
3
9
1
5
6
8 7
2
1Avatar and Instrument name
2Help icon
3Drawer status
4Status dial
5Current user name; instrument block type
6Settings button
7Buttons for accessing Experiment
Template files (EDT)
8Connectivity icons
9Sign In (or My Profile) button
Table 2 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 31.
Help icon Touch to launch the touchscreen Help system to access
step-by-step instructions.
—
Drawer status • — The drawer is locked. The drawer locks during
experiment runs, calibration runs, and self
verification test runs. The drawer automatically
unlocks when a run is complete.
• — The drawer is unlocked.
•Drawer is open — The drawer is open. No message
displays when the drawer is closed.
—
Parts of the home
screen
Chapter 1 Product information
Instrument hardware description
1
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Element of the
home screen Function For more information, see...
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.
—
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.
Chapter 3, “Configure the instrument
and manage instrument profiles“.
Buttons for
accessing
experiment and
template files
Load Experiment — Touch to open a user-created EDT
file from a Cloud account, USB, instrument folder, or
network drive.
“Run an experiment from a saved
file“ on page 40 .
Open Template — Touch to open a system EDT template
file.
“Create and run an experiment from
a template“ on page 40“Run an
experiment from a saved file“ on
page 40 .
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 41.
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 Cloud account.
—
Sign In button
(My Profile button
when a user is
signed in)
• Touch Sign In to sign into an instrument profile
and link to a Cloud account.
• Touch My Profile to change instrument profile
settings, link to a Cloud account, or lock the
instrument during a run.
“Sign in“ on page 21.
Chapter 1 Product information
Instrument hardware description
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Software description
The instrument and the software (desktop and cloud) include the features described
in the following table.
Feature Instrument Desktop Cloud
Use as guest (no sign in) 3 3 —
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 )
Instrument,
desktop, and
cloud software
features
Chapter 1 Product information
Software description
1
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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 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
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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 installing third-party software on the computer running QuantStudio™ Design
and Analysis Desktop Software, conrm that the third-party software will not do the
following:
• Restrict Ethernet communication.
• Interfere with instrument or computer operation.
Supported options for instrument and computer connections
We support the following direct, networked (LAN– local area network), or Cloud
congurations. Congurations other than those listed are not recommended. Select a
conguration that meets the needs of your laboratory's instrument, software, and
workow requirements.
IMPORTANT! Do not connect both an Ethernet cable and the Wi-Fi module
(Cat. No. A26774) to the instrument. Conguring the instrument for both wired and
wireless connection can interfere with instrument operation.
Third-party
software
Chapter 1 Product information
Supported options for instrument and computer connections
1
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Note: For detailed information about networking your instrument, see the
QuantStudio™ 1 Real-Time PCR System IT Checklist (Pub. No. MAN0018164).
Direct configuration option
• A computer provided by Thermo Fisher Scientific with the QuantStudio™Design and Analysis Desktop 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 Cloud configurations.
Networked configuration option
• A computer provided by Thermo Fisher Scientific with the QuantStudio™Design and Analysis Desktop Software
• The computer and instrument must be on the same subnet mask.
• Computer‑to‑LAN connection (select an option) :
– Wired connection to the network using an Ethernet cable – or –
– Wireless connection to the network
LAN
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
Thermo Fisher Cloud configuration option
• Internet access and a computer with the Chrome™web browser to access the Cloud
• Computer‑to‑Cloud connection (select an option) :
– Wired connection to the internet using an Ethernet cable – or –
– Wireless connection to the internet
LAN
• Instrument‑to‑Cloud 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
Chapter 1 Product information
Supported options for instrument and computer connections
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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. The software uses the standard curve to interpolate 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. The software uses the standard curves to interpolate the quantities of the target of
interest and the endogenous control in each sample. The target quantity in each sample
is then normalized to the sample's endogenous control quantity.
4. To determine the relative quantity of the target in test samples, the software divides the
normalized target quantity in the sample by the normalized target quantity in the
reference sample.
Comparative Ct(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 ΔCq(ΔCtor ΔCrt) for the sample to the normalized ΔCq(ΔCtor ΔCrt) for
the reference sample.
Chapter 1 Product information
Experiment types
1
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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
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
1. The software normalizes the fluorescence of the reporter dyes to the fluorescence of
the passive reference dye in each well.
2. The software plots the normalized reporter dye signal of each sample well on an Allelic
Discrimination Plot, which contrasts the reporter dye intensities of the allele-specific
probes.
3. The software algorithmically clusters the sample data, and assigns a genotype call to
the samples of each cluster according to its position on the plot.
Presence/absence 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
that used
intercalating dyes.
In the software, melt curve analysis is included in the default run method for any experiment
type that uses intercalating dyes.
1. The software plots a melt curve based on the fluorescence of the dye with respect to
change in temperature.
2. Using the melt curve, the software calculates the melting temperature (Tm).
Chapter 1 Product information
Experiment types
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General procedures
to operate the instrument
■Precautions for use ................................................... 20
■Power on the instrument .............................................. 21
■Power o the instrument .............................................. 21
■Sign in .............................................................. 21
■Sign out ............................................................. 21
■Load and unload a plate in the QuantStudio™ 1 Real-Time PCR Instrument .. 22
■Transfer, view, or manage les and results ............................... 23
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 instrument.
CAUTION! Use at caps for tubes. Rounded caps can damage the heated cover.
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