Thermo Scientific Ion GeneStudio S5 User Manual
Ion GeneStudio™ S5 Food Protection
Instrument
USER GUIDE
Catalog Numbers A39513
Publication Number MAN0017965
Revision A.0
For testing of Food and Environmental samples only.
Manufacturer: Life Technologies Corporation | 5781 Van Allen Way | Carlsbad, CA 92008
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. MAN0017965
Revision Date Description
A.0 18 October 2018 New document.
Trademarks: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.
©2018 Thermo Fisher Scientific Inc. All rights reserved.
Contents
About this guide ............................................................ 5
Purpose of the guide ............................................................ 5
■
CHAPTER 1 Product information ....................................... 6
Contents ....................................................................... 6
Optional materials and equipment ................................................ 6
Instrument installation by trained personnel only ................................... 7
Nucleic acid contamination ....................................................... 7
Instrument vibration and clearances ............................................... 7
■
CHAPTER 2 System components ....................................... 8
Network configuration .......................................................... 8
Internet connectivity ............................................................. 9
Ion GeneStudio™ S5 Food Protection System component positions .................... 10
Ion GeneStudio™ S5 Food Protection Instrument input and output connections ......... 11
■
CHAPTER 3 Instrument operation .................................... 12
Power the Ion GeneStudio™ S5 Food Protection Instrument on or off .................. 12
Power on ................................................................. 12
Power off ................................................................. 12
Update the Ion GeneStudio™ S5 Food Protection System software .................... 12
Instrument run times ........................................................... 13
Maintain the Ion GeneStudio™ S5 Food Protection Instrument ........................ 14
Materials required ......................................................... 14
Clean or decontaminate the instrument ...................................... 14
Manually clean the instrument .............................................. 14
Perform an instrument reset run with an initialized, unused Ion S5™ Wash
Solution cartridge ......................................................... 16
Ion GeneStudio™ S5 Food Protection Instrument User Guide
3
Contents
■
APPENDIX A Touchscreen reference ................................. 17
Clean, Initialize, and Run ........................................................ 17
Settings ....................................................................... 18
Network Settings .......................................................... 18
System Tools .............................................................. 21
Check for software updates ................................................. 26
Data Management ......................................................... 27
Manually delete run data ................................................... 29
Perform the instrument Clean operation ...................................... 30
Instrument settings ........................................................ 31
Touchscreen icons ............................................................. 33
Alarms, Notifications, and Events ................................................ 35
■
APPENDIX B Troubleshooting ......................................... 38
Instrument alarms and events ................................................... 38
Initialization fails ............................................................... 39
Troubleshooting using control libraries ........................................... 41
Solid-state buffer leak .......................................................... 41
Pulse clean the Ion GeneStudio™ S5 Food Protection Instrument ................. 42
■
APPENDIX C Instrument warranty .................................... 43
■
APPENDIX D Safety ..................................................... 45
Safety alerts on this instrument .................................................. 45
Location of safety labels on the instrument ................................... 46
Safety information for instruments not manufactured by Thermo Fisher Scientific ..... 46
Instrument safety .............................................................. 47
General .................................................................. 47
Cleaning and decontamination ............................................... 47
Electrical safety ........................................................... 48
Safety and electromagnetic compatibility (EMC) standards .......................... 49
Safety .................................................................... 49
EMC ...................................................................... 49
Environmental design ...................................................... 50
Chemical safety ................................................................ 51
■
Documentation and support ............................................. 53
Related documentation ......................................................... 53
Food Safety support ............................................................ 53
4
Ion GeneStudio™ S5 Food Protection Instrument User Guide
IMPORTANT! Before using this product, read and understand the information in the
“Safety” appendix in this document.
Purpose of the guide
This Ion GeneStudio™ S5 Food Protection Instrument User Guide (Pub. No. MAN0017965)
provides reference information for using and maintaining the Ion GeneStudio™ S5
Food Protection System (Cat. No. A39513).
About this guide
CAUTION! ABBREVIATED SAFETY ALERTS. Hazard symbols and hazard
types specied in procedures may be abbreviated in this document. For the
complete safety information, see the “Safety” appendix in this document.
Ion GeneStudio™ S5 Food Protection Instrument User Guide
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1
Contents
Product information
The Ion GeneStudio™ S5 Food Protection System (Cat. No. A39513) contains the
following boxes and components.
Ion GeneStudio™ S5 Food Protection System (Cat. No. A39513)
Components
Ion GeneStudio™ S5 Food Protection
Instrument
Ion S5™ Installation Kit A27215
Ion S5™ Installation Kit (Part No. A27215; Not available for separate purchase.)
Contents
Ion 540™ Chip Kit A27766 4 pack 15°C to 30°C
Ion S5™ Sequencing Solutions A27767 1
Ion S5™ Sequencing Reagents A27768 1 –30°C to –10°C
Ion 540™ Control Ion Spheres A28195 1
Ion 540™ Loading Reagents OT2 A27897 1
Ion S5™ Cartridge Tool A28308 2 15°C to 30°C
Ion Chef™ S5 Series Chip Balance A29022 1
Part No. Quantity Storage
Part No.
A37904
Optional materials and equipment
Unless otherwise indicated, all materials are available through thermosher.com.
MLS: Fisher Scientic (sherscientic.com) or other major laboratory supplier.
(
Optional
[1]
[2]
) Non-interruptible Power Supply (UPS)
IMPORTANT! Thermo Fisher Scientific has verified the procedures in this user guide using these specific materials. Substitution may adversely
affect system performance.
For laboratories that experience frequent power outages or line voltage fluctuations, we recommend that you use a non-interruptible power
supply that is compatible with 2500 W output or higher.
6
Item
[1]
[2]
Source
MLS
Ion GeneStudio™ S5 Food Protection Instrument User Guide
Instrument installation by trained personnel only
Chapter 1 Product information
Instrument installation by trained personnel only
1
IMPORTANT! The Ion GeneStudio
service personnel and must not be relocated without assistance from trained service
personnel. See “Food Safety support“ on page 53.
Nucleic acid contamination
IMPORTANT! A primary source of contamination is DNA fragments from previously
processed samples. Do not introduce amplied DNA into the library preparation
laboratory or work area.
Instrument vibration and clearances
IMPORTANT! Signicant vibration during sequencing may add noise and reduce the
quality of the measurements. The Ion GeneStudio™ S5 Food Protection System must
be installed on a bench that is free from vibrations or in contact with equipment that
can cause vibrations to the bench (freezers, pumps, and other similar equipment).
IMPORTANT! Place the instrument at least 40 in. (1 meter) away from major sources
of electronic noise such as refrigerators or microwaves.
™
S5 Food Protection System is installed by trained
Ion GeneStudio™ S5 Food Protection Instrument User Guide
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5
3
4
1
2
2
Network configuration
The Ion GeneStudio™ S5 Food Protection Instrument is not connected to an external
Torrent Server and requires connection only to a local area network (see gure).
System components
Figure 1 Network configuration
1
Ion GeneStudio™ S5 Food Protection Instrument
2
Ion Chef™ Food Protection Instrument
3
Local area network
4
Internet
5
Client computer
Note: The Ion Chef™ Food Protection Instrument must be connected to the Torrent
Server either directly using a category 6 Ethernet cable, or indirectly through a local
area network that has been congured to allow HTTP-443, SSH-22, and FTP-20/21
trac.
8
Ion GeneStudio™ S5 Food Protection Instrument User Guide
Internet connectivity
The Ion GeneStudio™ S5 Food Protection Instrument should be connected to a
network with Internet access. Connecting to the Internet allows you to update your
software and access remote system support easily. Software updates through the
network/Internet are free. If you do not connect your instrument or server to a
network, software updates must be manually installed via USB.
IMPORTANT! Thermo Fisher Scientic does not support the USB method for
updating software.
Any problems (for example, le corruption, incomplete updates) resulting from
update of the instrument or server using a USB device that require correction of the
faulty update is not covered by your Ion GeneStudio™ S5 Food Protection System
warranty or any service contract you may have bought. You are required to schedule
an on-site Time and Materials visit by a eld service engineer to correct the problem
at your own expense.
In providing outbound access to the Internet from the server, you enable the support
team to provide inbound support. The Ion GeneStudio™ S5 Food Protection
Instrument runs a remote monitor agent that can provide service personnel with
critical system information, such as installed software versions and instrument
alarms. With your permission, the agent also allows service personnel to access
remotely the Ion GeneStudio™ S5 Food Protection Instrument, which is required for
system support. Without remote access, service personnel cannot access, view, and
troubleshoot problems regarding machine performance.
Chapter 2 System components
Internet connectivity
2
Ion GeneStudio™ S5 Food Protection Instrument User Guide
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7
2
3
5
6
4
1
Ion GeneStudio S5
Ion GeneStudio S5
Ion GeneStudio S5
Chapter 2 System components
2
Ion GeneStudio™ S5 Food Protection System component positions
Ion GeneStudio™ S5 Food Protection System component positions
1
Touchscreen
2
Power button
3
Ion S5™ Sequencing Reagents cartridge
4
Chip clamp
5
Ion S5™ Wash Solution bottle. Waste reservoir located behind the Ion S5™ Wash Solution
bottle (shown on the right).
6
Ion S5™ Cleaning Solution bottle
7
Waste reservoir
Note: The system uses RFID technology to verify that the proper reagents are loaded
in positions 3, 5, and 6. Reagents that exceed their expiration date or usage count
generate an error message prompting the user to replace the reagent before
performing the run.
Note: RFID regulatory information can be found on the main screen under
Options4Regulatory info.
10
Ion GeneStudio™ S5 Food Protection Instrument User Guide
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4
2
1
3
1
Ion GeneStudio™ S5 Food Protection Instrument input and output connections
Chapter 2 System components
Ion GeneStudio™ S5 Food Protection Instrument input and output
connections
1
USB ports–Connects a USB device to the instrument.
2
Ethernet port—An RJ45 port that provides Ethernet (gigabit) communication between the
instrument and a local area network.
3
Ethernet port—An RJ45 port that provides Ethernet (gigabit) communication with the
Ion Chef™ Food Protection Instrument.
4
On/off switch—Power switch, where the states are on ( | ) or off ( O ).
5
Power port—100–240VAC port that provides power to the instrument.
2
Ion GeneStudio™ S5 Food Protection Instrument User Guide
11
Instrument operation
3
Power the Ion GeneStudio™ S5 Food Protection Instrument on or off
Note: If the Ion GeneStudio™ S5 Food Protection Instrument is powered on, and the
touchscreen is blank, touch the screen to "wake" the touchscreen.
Power on
Power off
If the touchscreen is unresponsive, check the power switch on the back of the
instrument to ensure that the switch is in the on (|) position. If the power switch is in
the o (0) position, proceed with step 1. If the power switch is already in the on
position, proceed to step 2.
Turn the power switch on the back of the instrument to the on (|) position.
1.
Press the power buon on the left side of the instrument.
2.
The buon illuminates. When the instrument touchscreen Main Menu appears,
the instrument is ready for use.
It is not necessary to power o the instrument overnight or over the weekend. If
needed, the instrument can be powered o as follows:
In the Main Menu, press Seings4System Tools4Shut Down.
1.
Select either Shut Down or Reboot.
2.
Note: If you select Shut Down, a conrmation message appears. Select Yes to
power o the instrument.
Note: Do not press the power buon during a run. Interrupting power to the
instrument during a run may result in sequencing run failure and loss of sample.
Update the Ion GeneStudio™ S5 Food Protection System software
Note: An internet connection is required for the Ion GeneStudio™ S5 Food Protection
System to receive alerts that software updates are available.
If an update to the Ion GeneStudio™ S5 Food Protection Instrument software is
available, the Notications/Alarms buon illuminates red in the touchscreen Main
Menu. Press the red Alarms buon to see the detailed messages. If a message states
New Software Available, follow these steps to update the software:
In the Main Menu, press Seings4Check for Updates.
1.
Press Update to download and install the updates automatically.
2.
Press Done.
3.
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Ion GeneStudio™ S5 Food Protection Instrument User Guide
The instrument automatically restarts when the software update is complete.
Instrument run times
Approximate run times for the Ion GeneStudio™ S5 Food Protection Instrument for a
given chip type, read length, and number of reads are shown in the following table.
Run times indicate the typical time from run start to delivery of a BAM le
(1 run/initialization).
For the Food Authenticity application, a FASTQ le is created instead of a BAM le.
The instrument run time is shorter for this application.
Chip type Number of reads Read length/output
Chapter 3 Instrument operation
Instrument run times
Instrument run time
Ion GeneStudio™ S5 Food Protection
Instrument
3
Ion 510™ Chip 2–3 M
4–6 M
Ion 520™ Chip
3–4 M
15–20 M
Ion 530™ Chip
9–12 M
200 bases
4.5 hours
0.3–0.5 Gb
400 bases
10.5 hours
0.6–1 Gb
200 bases
7.5 hours
0.6–1 Gb
400 bases
12 hours
1.2–2 Gb
600 bases
12 hours
0.5–1.5 Gb
200 bases
10.5 hours
3–4 Gb
400 bases
21.5 hours
6–8 Gb
600 bases
21 hours
1.5–4.5 Gb
Ion 540™ Chip 60–80 M
Ion 550™ Chip 100–130 M
Ion GeneStudio™ S5 Food Protection Instrument User Guide
200 bases
19 hours
10–15 Gb
200 bases
—
20–25 Gb
13
Chapter 3 Instrument operation
3
Maintain the Ion GeneStudio™ S5 Food Protection Instrument
Maintain the Ion GeneStudio™ S5 Food Protection Instrument
Materials required
Clean or
decontaminate the
instrument
Manually clean
the instrument
• Lint-free wipes
• 70% isopropanol
• (Optional) 10% bleach solution
In the event of a spill or leak on or inside the Ion GeneStudio™ S5 Food Protection
Instrument, perform the following steps.
Note: Dispose of all waste in appropriate liquid or solid waste containers.
Remove the Ion S5™ Wash Solution bole, then remove and empty the waste
1.
reservoir.
Remove the Ion S5™ Sequencing Reagents cartridge.
2.
Inspect the waste and nucleotide reagent bays for liquid.
3.
Using absorbent paper soak up as much liquid as possible, then wash the
4.
aected area with 10% bleach solution.
Wipe the aected surfaces with 70% isopropanol, then allow to air-dry.
5.
The Ion GeneStudio™ S5 Food Protection Instrument requires cleaning before
initialization. Cleaning is normally performed automatically at the completion of the
previous sequencing run. To enable two sequencing runs on a single initialization,
you must deselect the Enable post-run clean checkbox for the rst sequencing run.
The post-run cleaning is then performed normally after the second sequencing run.
However, if the Enable post-run clean checkbox is deselected for the second run, the
cleaning is not performed after either run. If the second sequencing run is not
performed, or the cleaning is not performed automatically after the second run, the
instrument will not allow the subsequent initialization to proceed until a manual
cleaning is performed.
Do not perform a manual cleaning if the Ion GeneStudio™ S5 Food Protection
Instrument is initialized and
• a sequencing run is not started within 24 hours, or
• a run is not started or completed due to a power failure or an abort
In these cases, an instrument reset run is required before reinitialization. See “Perform
an instrument reset run with an initialized, unused Ion S5™ Wash Solution
cartridge“ on page 16 for more information.
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Ion GeneStudio™ S5 Food Protection Instrument User Guide
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2
3
Maintain the Ion GeneStudio™ S5 Food Protection Instrument
Chapter 3 Instrument operation
When a manual cleaning is necessary, use the following procedure:
On the home screen, press Seings4Clean Instrument.
1.
The instrument door unlocks allowing access to the consumables.
Remove the Ion S5™ Wash Solution bole to access the waste reservoir, then
2.
remove and empty the waste reservoir.
3
Reinstall the empty waste reservoir and a used Ion S5™ Wash Solution bole.
3.
Ensure that the Ion S5™ Sequencing Reagents cartridge and Ion S5™ Wash
4.
Solution bole are properly installed.
IMPORTANT! Perform the cleaning with a used reagent cartridge and wash
solution bole installed. The cleaning procedure pumps cleaning solution into
the wash solution bole and reagent cartridge making them unsuitable for
sequencing.
Place a used sequencing chip in the chip clamp, then push the chip clamp in all
5.
the way to engage.
Close the instrument door, then press Next.
6.
Cleaning takes ~35 minutes to complete. On completion, the instrument door
automatically unlocks and the chip and cartridge clamps disengage.
Ion GeneStudio™ S5 Food Protection Instrument User Guide
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Chapter 3 Instrument operation
3
Maintain the Ion GeneStudio™ S5 Food Protection Instrument
Perform an
instrument reset
run with an
initialized, unused
Ion S5™ Wash
Solution cartridge
Cleaning is normally performed automatically at completion of a sequencing run.
If the Ion GeneStudio™ S5 Food Protection Instrument is initialized and
• a sequencing run is not started within 24 hours after initialization, or
• a sequencing run is not completed due to a power failure or an abort, and <200
ows occurred before the stoppage
then an instrument reset run is required to ensure proper cleaning before
reinitialization
Do NOT perform a manual cleaning with an unused, initialized Ion S5™ Wash
Solution cartridge.
Note:
If a power failure or abort occurs during the second of two runs that are started
·
after a single initialization, a manual cleaning is sucient (see “Manually clean the
instrument“ on page 14).
If the number of ows that occurred before a power failure or abort is unknown,
·
perform an instrument reset run.
To perform an instrument reset run, use the following procedure before
reinitialization:
In the instrument touchscreen main menu, touch Run.
1.
The instrument door unlocks and the chip clamp disengages.
Ensure that a used sequencing chip is in the chip clamp, then push the chip
2.
clamp in all the way to engage.
Close the instrument door, then touch Next.
3.
When prompted, select Planned Run (none). Ensure that the Enable post-run
4.
clean checkbox is selected, then press Review.
In the Select Run screen, touch Edit, then in the Detail screen set the number of
5.
ows to 200. Ensure that the Post-Run/Clean checkbox is selected, then touch
Close.
Touch Start run, then touch Accept to conrm that Post-Run Clean is enabled,
6.
and to start the run.
When the instrument reset run completes, the instrument automatically performs the
cleaning procedure. After cleaning, the touchscreen returns to the main menu.
16
Ion GeneStudio™ S5 Food Protection Instrument User Guide
Ion GeneStudio S5
A
Clean, Initialize, and Run
Touchscreen reference
In the Home screen, the Clean, Initialize, and Run programs lead you through the
necessary steps to prepare the instrument for sequencing and to start a sequencing
run. Press the main dial to start a program. Simple, easy to follow instructions are
provided on the touchscreen.
• Cleaning must be performed before each initialization to ensure that the reagents
from the previous run are cleared from the uid lines. The Clean program is
normally performed automatically at the completion of the previous sequencing
run. Perform a Clean if for any reason the sequencing run was not properly
completed. Follow the instructions that are provided on the touchscreen.
• The Initialize program must be performed before each run to load and prepare
the run reagents. The Initialize program walks you through:
– Emptying the waste reservoir
– Loading the reagent cartridge, wash solution, and cleaning solution
• The Run program walks you through steps leading up to and through
sequencing, including:
– Placing a loaded chip on the instrument
– Selecting a Planned Run created in the Torrent Suite™ Software
– Performing sequencing
Ion GeneStudio™ S5 Food Protection Instrument User Guide
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