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
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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
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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
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Parts of the home screen
2
4
5
6
1
3
9
8
7
1Avatar and Instrument name
2Eject instrument drawer icon
3Help system icon
4Status dial
5Instrument profile name;
instrument block type
6Settings button
7Access templates buttons (not applicable
for HID‑validated workflows)
8Connectivity icons
9Sign In (or My Profile) button
Table 1 Parts of the home screen
Element of the home screen Function
Avatar and Instrument name Set by the administrator to uniquely identify the instrument.
Eject instrument drawer icon Touch to open or close the instrument drawer.
Help icon Touch to launch the touchscreen Help system to access step-by-step
instructions.
Status dial When the instrument is not in use – Displays Set up run.
Note: Instrument runs must be set up and started from the desktop software.
When the instrument is in use – Displays the sample block temperature, the
elapsed run time, and the run status.
Note: Swipe the dial to the left or touch to access real-time views of the run.
Instrument profile username
and block type
Displays the username of a signed-in user and the instrument block type.
Note: If no user is signed in, the instrument defaults to the Guest profile.
Chapter 1 Product information
Parts of the home screen
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Element of the home screen Function
Settings button Touch Settings to configure, calibrate, or learn about the instrument.
Connectivity icons • – The instrument is connected via a wired configuration.
• – A USB drive is plugged into the instrument.
Sign In button
(My Profile button when a user
is signed in)
• Touch Sign In to sign into an instrument profile.
• Touch My Profile to change instrument profile settings.
Chapter 1 Product information
Parts of the home screen
1
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Comparison of features in desktop software and the instrument
To run experiments using HID assays, the instrument must be integrated with the
HID Real-Time PCR Analysis Software v1.3.
Actions Desktop software Instrument
Enter or edit properties [1]
Edit experiment name; enter user name ✓—
Select instrument, experiment type, chemistry, run mode ✓—
Edit method [1]
Edit the thermal protocol, reaction volume, optical filter selection ✓—
Set up plate and well details [1]
Define samples ✓—
Assign samples to wells ✓—
Define targets ✓—
Assign targets to wells ✓—
Instrument run
Start an instrument run [1] ✓—
Monitor a run in progress ✓ ✓
View time remaining ✓ ✓
View real-time plots — ✓
Run results
Review run results (analyzed run data) ✓—
Configure analysis settings ✓—
Export
Select export options for run data and run results (analyzed run data) ✓—
Export run data ✓ ✓
Export template settings ✓—
[1] Feature is available in the instrument touchscreen, but it is not validated for the HID assay workflow.
Chapter 1 Product information
Comparison of features in desktop software and the instrument
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Install the instrument
■Workow: 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 conguration .................................. 17
Workflow: Install the instrument
Perform all steps in “Before you begin installation“ on page 14
▼
“Unpack and install the instrument“ on page 15
▼
“Power on and follow the startup wizard“ on page 15
▼
“Perform instrument verification using RNase P plates“ on page 44
▼
“Calibrate dyes for HID‑validated workflows“ on page 41
Before you begin installation
A Thermo Fisher Scientic service representative will contact you to schedule an
installation. However, you do have the option to install the instrument yourself.
Before starting the installation:
• Review the site requirements in the QuantStudio™ 5 Real-Time PCR Instrument Site
Preparation Guide (for Human Identication) (Pub. No. MAN0016701).
• Review the HID-validated computer-to-instrument conguration (page 16).
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Unpack and install the instrument
1. Prepare the installation site as described in the QuantStudio™ 5 Real-Time PCR
Instrument Site Preparation Guide (for Human Identication) (Pub.
No. MAN0016701).
2. Follow the pre-printed instructions on the instrument box to unpack the
instrument, accessories, and reference documentation. Save the packing material
for future use or recycle it.
The instrument box contains:
• Reference documentation: Welcome note, unpacking and set up instructions
card, system documentation insert
• One instrument
• Accessories: power cable, Ethernet cable, USB drive, reaction tube retainer
• Shipping plate
Note: Save the shipping plate but do not use it to operate the instrument.
• Spectral calibration plates for HID-validated workows.
Note: Store these plates at –20°C (–15°C to –25°C).
3. Place the instrument on the bench.
4. Plug the power cable into the power port on the back panel of the instrument,
then plug the cable into an electrical receptacle.
5. Connect an Ethernet cable to the Ethernet port on the back panel of the
instrument, then connect the cable to the computer.
Power on and follow the startup wizard
1. Power on the instrument.
2. Follow the startup wizard through the following tasks:
• Accept the license agreement
•Congure the instrument date and time.
•Create an administrator instrument prole
Note: You can perform any of the steps above at a later time if you do not have
the information needed to complete the startup screens. See page 23.
IMPORTANT! Before using the instrument for the rst time, we recommend that you
“Perform instrument verication using RNase P plates“ on page 44.
Chapter 2 Install the instrument
Unpack and install the instrument
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Instrument and computer connections
1
7
66
5
4
2
3
Figure 1 Instrument back panel
1USB ports
2WiFi USB port—Not applicable
3Ethernet Port—RJ45 port for
100/1,000 Mbps Ethernet communication
with the instrument
4RS232 Port—For service use only
5Fuse Cover
6Power Switch
7Power Port—100 to 240 VAC
3
1 1
2
4
Figure 2 Instrument‑to‑computer connections (minitower configuration)
1Detachable power supply cord compatible with local power supply receptacle.
2Connection between the computer and the instrument.
3Connection between the computer and the monitor, keyboard, and mouse.
4Connection between the computer and the
(optional) handheld barcode scanner.
Chapter 2 Install the instrument
Instrument and computer connections
2
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Computer-to-instrument configuration
IMPORTANT! For HID use, the QuantStudio™ 5 Real-Time PCR System has been
validated for a direct (computer-to-instrument) conguration. During installation, a
Thermo Fisher Scientic service representative can set up only a direct conguration.
Direct configuration
• A computer provided by Thermo Fisher Scientific with the HID Real‑Time PCR Analysis Software v1.3
• Computer‑to‑instrument connection:
– Direct, wired connection between the computer and the instrument
using an Ethernet cable
Ports Condition
mDNS, 7000 Instrument-to-computer connection
mDNS, 5353 Instrument discovery
Firewall ports that
must be open
Chapter 2 Install the instrument
Computer-to-instrument configuration
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General procedures
to use the instrument
■Precautions for use ................................................... 18
■Power on the instrument .............................................. 19
■Power o 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
■Transfer EDS les from the instrument home screen ...................... 22
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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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.
If left unaended (for about two hours), the
instrument automatically enters sleep mode
(enabled by default) to conserve power.
Note: To customize the sleep mode seing,
touch Seings4Instrument
Seings4Sleep Mode.
Power off the instrument
The instrument operates in low-power mode when not in use. However, the
instrument can be powered o completely so that the components use no power.
Note: To power o the instrument for >1 week, see page 53 .
1. Power o the instrument using the power switch on the back of the instrument.
2. Power o the computer.
Chapter 3 General procedures to use the instrument
Power on the instrument
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Sign in
Create an instrument prole before signing into the instrument (see “Create a new
instrument prole“ on page 28).
Note: An instrument prole is a user account specically for the instrument. It is not
related to any other user account for the system or software.
In the home screen:
1. Touch Sign In.
2. Touch Sign In, then select your username.
3. Enter your PIN, then touch Enter.
Sign out
In the home screen:
1. Touch My Prole.
2. Touch Sign Out.
Chapter 3 General procedures to use the instrument
Sign in
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