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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QuantStudio
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1 Real-Time PCR System Installation, Use, and Maintenance Guide