ThermoFisher Scientific QuantStudio 5 Real-Time PCR User manual

For Research, Forensic, or Paternity Use Only. For licensing and limited use restrictions
visit thermofisher.com/HIDlicensing.
QuantStudio™5 Real-Time PCR Instrument
(for Human Identification)
USER GUIDE
Installation, maintenance, and administration
for use with:
HID Real‑Time PCR Analysis Software v1.3
Publication Number MAN0017162
Revision A.0

Manufacturer: Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256
The information in this guide is subject to change without notice.
DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, LIFE TECHNOLOGIES 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. MAN0017162
Revision Date Description
A.0 15 June 2017 New document for Human Identification workflows using instrument firmware v1.3.1.
Important Licensing Information: This product may be covered by one or more Limited Use Label Licenses. By use of this product, 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. Microsoft and Windows are
trademarks of Microsoft Corporation. Pentium is a trademark of Intel Corporation.
©2017 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 Product information ....................................... 7
Instrument overview ............................................................. 7
Installation, verification, and calibration ........................................... 8
Instrument filters and supported dyes ............................................. 9
System dyes ............................................................... 9
Custom dyes .............................................................. 10
Parts of the instrument ......................................................... 10
Parts of the home screen ....................................................... 11
Comparison of features in desktop software and the instrument ..................... 13
■CHAPTER 2 Install the instrument .................................... 14
Workflow: Install the instrument ................................................. 14
Before you begin installation .................................................... 14
Unpack and install the instrument ............................................... 15
Power on and follow the startup wizard ........................................... 15
Instrument and computer connections ............................................ 16
Computer-to-instrument configuration ........................................... 17
Firewall ports that must be open ............................................ 17
■CHAPTER 3 General procedures to use the instrument ............. 18
Precautions for use ............................................................ 18
Power on the instrument ........................................................ 19
Power off the instrument ....................................................... 19
Sign in ........................................................................ 20
Sign out ....................................................................... 20
Load and unload plate in the instrument .......................................... 21
View real-time data and plots on the instrument touchscreen ........................ 22
Adjust the display of real-time plots on the instrument touchscreen .............. 22
Transfer EDS files from the instrument home screen ............................... 22
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■CHAPTER 4 Configure the instrument and manage
instrument profiles ....................................................... 23
Initial start up ................................................................. 23
Overview of instrument settings (Administrator) ................................... 24
Overview of instrument settings (Standard or Guest) ............................... 26
Manage instrument profiles ..................................................... 27
Instrument profiles and signed-in users ...................................... 27
Create an administrator instrument profile during initial start-up ................ 27
Create a new instrument profile ............................................. 28
Edit an instrument profile ................................................... 28
Manage all instrument profiles .............................................. 28
Require instrument profile sign-in ............................................... 29
Manage the sign out timer ...................................................... 29
Manage the instrument name .................................................... 29
Enable sleep mode ............................................................. 30
Set the idling temperature for the heated cover .................................... 30
Set the date and time ........................................................... 30
Restore factory defaults ........................................................ 31
Enable Remote Monitoring Service ............................................... 31
Update instrument software ..................................................... 32
■CHAPTER 5 Calibrate and verify instrument performance ......... 33
Calibration and verification schedule ............................................. 34
Calibration descriptions ........................................................ 35
View calibration status and set reminders in the instrument ......................... 36
Perform ROI/uniformity, background, and dye calibrations .......................... 36
Workflow: Calibration ...................................................... 36
Prepare a calibration plate .................................................. 37
Perform calibrations ....................................................... 38
View calibration images .................................................... 39
Identify contamination ...................................................... 40
Create a background plate (optional) ......................................... 40
Contents
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Calibrate dyes for HID‑validated workflows ........................................ 41
Workflow: Calibrate dyes for HID‑validated workflows .......................... 41
Prepare a calibration plate for HID‑validated workflows ........................ 41
Add custom dyes to the instrument for HID‑validated workflows ................. 42
Perform a custom dye calibration for HID‑validated workflows .................. 42
Perform instrument verification using RNase P plates .............................. 44
Instrument verification description .......................................... 44
RNase P instrument verification plate ........................................ 45
Performance specifications pass criteria ..................................... 45
Prepare an RNase P plate ................................................... 46
Perform RNase P verification ............................................... 47
■CHAPTER 6 Maintain the instrument ................................. 48
Backup or restore the instrument ................................................ 48
Decontaminate the sample block ................................................. 49
Materials required ......................................................... 49
Clean the sample block ..................................................... 49
Detailed procedures for cleaning the sample block ............................. 51
Replace the instrument fuses .................................................... 52
Materials required ......................................................... 52
Replace the fuses .......................................................... 52
Store, move, or ship the instrument .............................................. 53
Prepare the instrument to store, move, or ship ................................ 53
Move the instrument ....................................................... 53
Return the instrument for service ............................................ 54
■APPENDIX A Troubleshooting ......................................... 55
Instrument troubleshooting ..................................................... 55
Troubleshoot calibration failure .................................................. 56
Troubleshoot verification failure ................................................. 57
■APPENDIX B Parts and materials ..................................... 58
Kits, consumables, accessories, and reagents ..................................... 58
Consumables (96‑well, 0.2‑mL format) ............................................ 59
Accessories ................................................................... 60
General-use materials and consumables ......................................... 60
Contents
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■APPENDIX C Instrument specification and layout ................... 61
Configured system dimensions .................................................. 62
Instrument and computer connections ............................................ 63
Instrument clearances .......................................................... 64
Electrical requirements ......................................................... 64
Environmental requirements .................................................... 65
■APPENDIX D Safety ..................................................... 66
Symbols on this instrument ..................................................... 67
Conformity symbols ........................................................ 68
Safety alerts on this instrument .................................................. 69
Location of safety labels on the instrument ................................... 69
Safety information for instruments not manufactured by Thermo Fisher Scientific ..... 70
Instrument safety .............................................................. 70
General .................................................................. 70
Physical injury ............................................................ 71
Electrical ................................................................. 72
Cleaning and decontamination ............................................... 72
Safety and electromagnetic compatibility (EMC) standards .......................... 72
Safety compliance ......................................................... 73
EMC ...................................................................... 73
Environmental design ...................................................... 74
Chemical safety ................................................................ 74
Biological hazard safety ......................................................... 75
■Documentation and support ............................................. 76
Related documentation ......................................................... 76
Obtain information from the Help system ......................................... 76
Customer and technical support ................................................. 76
Limited product warranty ....................................................... 76
Index ....................................................................... 77
Contents
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Product information
■Instrument overview .................................................. 7
■Installation, verication, and calibration .................................. 8
■Instrument lters and supported dyes .................................... 9
■Parts of the instrument ................................................ 10
■Parts of the home screen ............................................... 11
■Comparison of features in desktop software and the instrument ............ 13
Instrument overview
The QuantStudio™ 5 Real-Time PCR Instrument uses uorescence-based polymerase
chain reaction (PCR) reagents to perform:
• Quantitative detection of target nucleic acid sequences (targets).
• Qualitative detection of targets (endpoint analysis, genotyping, and
presence/absence).
The instrument is congured with a 96-well 0.2-mL xed block (6 color de-coupled).
To run experiments using HID assays, the instrument must be integrated with the
HID Real-Time PCR Analysis Software v1.3.
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Installation, verification, and calibration
Your HID Support Representative will contact you to schedule the installation. During
instrument installation, the service representative will perform the initial instrument
verication using an RNase P plate and calibrate the instrument for the versions of
ABY™ and JUN™ dye used by HID-validated workows.
Instruments are factory calibrated, so ROI, uniformity, background, and system dye
calibrations are not necessary at installation.
You do have the option to install the instrument yourself. Before rst use of the
instrument, complete the following tasks:
• Install the instrument (see page 14).
• Verify instrument performance (see page 44).
• Perform custom dye calibrations for ABY™ and JUN™ dyes (see page 41).
After installation, perform regular calibration and verication according to the
“Calibration and verication schedule“ on page 34.
Chapter 1 Product information
Installation, verification, and calibration
1
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Instrument filters and supported dyes
The instrument uses a de-coupled six-color optical 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 instrument, contact your HID Support
Representative.
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]
x3-m3 Yellow 550 ± 10 587 ± 10 NED™, TAMRA™,
ABY™[3] Cy®3
x4-m4 Orange 580 ± 10 623 ± 14 ROX™, JUN™[3] Texas Red™
x5-m5 Red 640 ± 10 682 ± 14 MUSTANG
PURPLE™, Cy®5LIZ™
x6-m6 Deep-
Red 662 ± 10 711 ± 12 None [4] Cy®5.5
[1] The central wavelengths are the optimized wavelengths.
[2] The HEX™and TET™dyes from Thermo Fisher Scientific fall within the emission wavelength range of the
system, therefore they can be added and adapted for use on the instrument.
[3] HID-validated workflows use versions of ABY™and JUN™dyes that are considered custom dyes.
[4] This filter set currently does not support any dyes supplied by Thermo Fisher Scientific.
Filters
Wavelength
(nm)
1 2 345
x1-m1 x2-m2 x3-m3 x4-m4 x5-m5 x6-m6
Emission
Spectra
1x1-m1 — FAM™, SYBR™Green
2x2-m2 — VIC™
3x3-m3 — ABY™, NED™, Cy®3, TAMRA™
4x4-m4 — JUN™, ROX™, Texas Red™
5x5-m5 — Cy®5, MUSTANG PURPLE™
System dyes
Chapter 1 Product information
Instrument filters and supported dyes
1
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The instrument can run assays designed with custom dyes. Custom dyes include:
•Dyes that are not supplied by Thermo Fisher Scientic.
• Dyes or versions of dyes that are not factory-calibrated on the instrument.
Note: HID-validated workows use versions of ABY™ and JUN™ dyes that are
considered custom dyes for the instrument. To calibrate these ABY™ and JUN™
dyes, see page 41. To calibrate any other custom dye, contact your HID Support
Representative.
Parts of the instrument
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.
Custom dyes
Chapter 1 Product information
Parts of the instrument
1
10
QuantStudio
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5 Real-Time PCR Instrument User Guide (for Human Identification) | MAN0017162 A.0