Thermo Scientific Ion Torrent S5 User manual

USER GUIDE
For Research Use Only. Not for use in diagnostic procedures.
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.
Ion Torrent S5™and Ion Torrent S5™XL
Sequencer
Catalog Numbers A27211, A27213
Publication Number MAN0010811
Revision A.0

The information in this guide is subject to change without notice.
DISCLAIMER
LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) DISCLAIM ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT. TO
THE EXTENT ALLOWED BY LAW, IN NO EVENT SHALL LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) BE LIABLE, WHETHER IN CONTRACT, TORT,
WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL
DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF.
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.
©2015 Thermo Fisher Scientific Inc. All rights reserved.

Contents
About this guide ............................................................ 5
Revision history ................................................................. 5
Purpose of the guide ............................................................ 5
■CHAPTER 1 Product information ....................................... 6
Contents ....................................................................... 6
Required materials and equipment ................................................ 7
Update the software ............................................................. 8
Instrument installation by trained personnel only ................................... 8
Nucleic acid contamination ....................................................... 8
Instrument vibration and clearances .............................................. 8
Static electricity ................................................................ 8
■CHAPTER 2 System components ....................................... 9
Internet connectivity ............................................................ 10
Ion Torrent S5™System component positions ...................................... 11
Ion Torrent S5™and Ion Torrent S5™XL Sequencer input and output connections ...... 12
■CHAPTER 3 Create a Planned Run .................................... 13
About planned runs ............................................................ 13
Create a planned run ........................................................... 13
Planned run wizard: key fields ................................................... 14
■CHAPTER 4 Instrument operation .................................... 16
Power the Ion Torrent S5™or Ion Torrent S5™XL Sequencer on or off ................. 16
Power on ................................................................. 16
Power off ................................................................. 16
Chip handling guidelines ........................................................ 16
Select the planned run and perform the run ....................................... 17
Update the Ion Torrent S5™System software ...................................... 18
Clean the instrument ........................................................... 19
Ion Torrent S5™andIon Torrent S5™XL Instrument User Guide
3
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.

■APPENDIX A Touchscreen reference ................................. 20
Clean, Initialize, and Run ........................................................ 20
Options and Tools .............................................................. 21
Touchscreen gauges ........................................................... 22
Chip status icon ................................................................ 23
Alarms/events pop-up .......................................................... 23
■APPENDIX B Troubleshooting ......................................... 26
Ion Torrent S5™Sequencer alarms and events ..................................... 26
Chip Check .................................................................... 27
Chip calibration (before loading sample) .......................................... 28
Chip calibration (after loading sample) ........................................... 29
Initialization—General errors ................................................... 30
Troubleshooting using the controls ............................................... 30
■APPENDIX C Supplemental procedures .............................. 31
Set up and test the Ion Chip™Minifuge ............................................ 31
Install the Ion Proton™Rotor and Buckets ..................................... 31
Test the minifuge .......................................................... 32
■APPENDIX D Safety ..................................................... 34
Symbols on this instrument ..................................................... 34
Conformity symbols on this instrument ....................................... 35
Safety alerts on this instrument .................................................. 36
Location of safety labels on this instrument ................................... 36
Safety information for instruments not manufactured by Thermo Fisher Scientific ..... 37
Instrument safety .............................................................. 37
General .................................................................. 37
Electrical ................................................................. 37
Cleaning and decontamination .............................................. 38
Safety and electromagnetic compatibility (EMC) standards .......................... 39
Safety .................................................................... 39
EMC ...................................................................... 39
Environmental design ...................................................... 39
Chemical safety ................................................................ 41
■Documentation and support ............................................. 43
Placeholder for related documentation ........................................... 43
Customer and technical support ................................................. 43
Limited product warranty ....................................................... 43
Contents
4 Ion Torrent S5™andIon Torrent S5™XL Instrument User Guide
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.

About this guide
CAUTION! ABBREVIATED SAFETY ALERTS. Hazard symbols and hazard
types specified in procedures may be abbreviated in this document. For the
complete safety information, see the “Safety” appendix in this document.
IMPORTANT! Before using this product, read and understand the information in the
“Safety” appendix in this document.
Revision history
Revision Date Description
A.0 November 2014 Ion Torrent S5
™and Ion Torrent S5 ™XL Instrument
User Guide for compliance testing.
Purpose of the guide
The Ion Torrent S5™ and Ion Torrent S5™ XL Instrument User Guide (Pub. no.
MAN0010811) provides reference information for using the
Ion Torrent S5™ or Ion Torrent S5™ XL Sequencer's (Cat. nos. A27211 and A27213).
Ion Torrent S5™andIon Torrent S5™XL Instrument User Guide
5
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.

Product information
Contents
The Ion Torrent S5™ and Ion Torrent S5™ XL Systems (Catalog nos. A27212, or
A27214) contain the following boxes and components.
Ion Torrent S5™System (Catalog no. A27212)
Components Catalog no.
Ion Torrent S5™Sequencer A27211
Ion S5™Installation Kit A27215
Ion Torrent S5™XL System (Catalog no. A27214)
Components Catalog no.
Ion Torrent S5™XL Sequencer A27213
Ion S5™Installation Kit A27215
Ion S5™Installation Kit (Catalog no. A27215)
Components Color Quantity Volume Storage
Ion 520™& 530™OT2 Kit — 4 — 2°C to 8°C
Ion 540™Chip Kit — 4 — 15°C to 30°C
Ion Torrent S5™Sequencing Kit — 4 — 2°C to 8°C
Ion S5™Controls Kit — 1 — 2°C to 8°C
1
6 Ion Torrent S5™andIon Torrent S5™XL Instrument User Guide
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.

Required materials and equipment
The following tables list required materials and equipment that are not provided with
the Ion Torrent S5™ Systems.
Table 1 Required materials and equipment for sequencing
3Description[1] Supplier Catalog no. Quantity
Ion Chip™Minifuge (120 V or 230 V) Life
Technologies 4479672 (120V) or
4479673 (230V)
1
Ion Proton™Rotor and Buckets Kit Life
Technologies 4482578 1
Uninterruptable Power Supply (UPS) [2] MLS — 1
Isopropanol (100%) MLS — —
Nuclease-free water molecular biology grade MLS — —
Microcentrifuge[3] MLS — 1
P2, P10, P20, P200, P1000 µL pipette set and filtered tips MLS — 1 set
Rainin®Pipet-Lite®XLS with RFID LTS 2 µL to 20 µL Rainin L-20XLS 1
Rainin®Pipet-Lite®XLS with RFID LTS 10 µL to 100 µL Rainin L-100XLS 1
Rainin®StableRak™LTS tips 2-20 µL Rainin SR-L20F —
Rainin®StableRak™LTS tips 200 µL Rainin SR-L200F —
0.2-mL MAXYMum Recovery®Thin Wall PCR Tubes, Flat
Cap (do not use polystyrene tubes) Axygen PCR-02-L-C Varies
1.5-mL or 1.7-mL microcentrifuge tubes MLS — Varies
Ice buckets and ice — — —
Aluminum heat block, capable of maintaining 50°C MLS — —
Vortex mixer with a rubber platform MLS — 1
Thermal cycler with a heated lid MLS — 1
Standard laboratory vacuum line or vacuum pump MLS — 1
Liquid trap MLS — 1
Tygon®tubing [4] MLS — 1
[1] Thermo Fisher Scientific has validated this protocol using these specific materials. Substitution may adversely affect system performance.
[2] For laboratories that experience frequent power outages or line voltage fluctuations, we recommend that you use an uninterruptable power
supply that is compatible with 2500 W output or higher.
[3] Must fit standard 1.5- and 0.2-mL microcentrifuge tubes and generate 15,500 ×
g .
[4] As needed to connect laboratory vacuum to liquid trap and liquid trap to P200 pipette tip.
Chapter 1 Product information
Required materials and equipment
1
Ion Torrent S5™andIon Torrent S5™XL Instrument User Guide 7
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.

Update the software
IMPORTANT! Before proceeding, make sure that you have updated the Torrent
Suite™ and Ion Torrent S5™ System software to Version 4.4 or later. See “Update the
Ion Torrent S5™ System software“ on page 18.
Instrument installation by trained personnel only
IMPORTANT! The Ion Torrent S5™ System is installed by trained service personnel
and must not be relocated without assistance from trained service personnel. See
“Customer and technical support“ on page 43.
Nucleic acid contamination
IMPORTANT! A primary source of contamination is DNA fragments from previously
processed samples. Do not introduce amplified DNA into the library preparation
laboratory or work area.
Instrument vibration and clearances
IMPORTANT! Significant vibration during sequencing may add noise and reduce the
quality of the measurements. The Ion Torrent S5™ 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.
Static electricity
IMPORTANT! To avoid possible damage to the chip from static electricity, you must
ground yourself on the grounding plate (located next to the chip clamp) prior to
handling chips, and do not place chips on non-grounded surfaces such as a bench.
Always use the grounding plate to hold chips that are not in the package or inserted
in the chip clamp or the Ion PGM™ Chip Minifuge bucket.
Chapter 1 Product information
Update the software
1
8 Ion Torrent S5™andIon Torrent S5™XL Instrument User Guide
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.

System components
We support the layout in which the Ion Torrent™ Server is directly connected to the
Ion Torrent S5™ XL Sequencer, rather than through the local area network from a
remote location such as a server room. Data are most robustly transferred from the
Ion Torrent S5™ XL Sequencer to the Ion Torrent™ Server when they are directly
connected by a standard Category 6 Ethernet cable provided with the installation
materials.
IMPORTANT! The Ion Torrent S5™ System must be connected to the Ion Torrent™
Server by a standard Category 6 Ethernet cable. We do not troubleshoot data transfer
issues associated with an indirect connection between the Ion Torrent S5™ XL
Sequencer and the Ion Torrent™ Server.
Torrent Browser
3
4
5
6
2
1
Figure 1 Ion Torrent S5™XL Sequencer configuration
1Ion Torrent S5™XL Sequencer
2Ion template preparation instrument (Ion
Chef™Instrument (shown) or Ion
OneTouch™2 System)
3Ion Torrent™Server
4Local area network
5Internet
6Client computer
2
Ion Torrent S5™andIon Torrent S5™XL Instrument User Guide 9
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.

Torrent Browser
3
4
5
2
1
Figure 2 Ion Torrent S5™Sequencer configuration
1Ion Torrent S5™Sequencer
2Ion template preparation instrument (Ion
Chef™Instrument (shown) or Ion
OneTouch™2 System)
3Local area network
4Internet
5Client computer
Internet connectivity
The Ion Torrent S5™ Sequencer or the Ion Torrent™ Server should be connected to a
network with internet access. Connecting to the internet provides you the ability to
easily update your software and access remote system support. Software updates
through the network/internet are free. If you choose not to connect your instrument or
server to a network, software updates will need to be manually installed via USB.
IMPORTANT! The USB method for updating is not supported by Thermo Fisher
Scientific.
Any issues (file corruption, incomplete updates, etc.) updating the sequencer or server
in this manner requiring correction of the faulty update is not covered by your Ion
Torrent S5™ or Ion Torrent S5™ XL Sequencer warranty or any service contract you
may have purchased. You will be required to schedule an on-site Time and Materials
visit by a Thermo Fisher Scientific field service engineer to correct the problem at your
own expense.
In providing outbound access to the internet from the server, you enable the Thermo
Fisher Scientific support team to provide inbound support. Both the Ion Torrent S5™
Sequencer and the Ion Torrent™ Server run 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 remotely log into the Ion Torrent S5™ Sequencer and the Ion Torrent™ Server, which
is required for system support. Without remote access, service personnel cannot
access, view, and troubleshoot issues regarding machine performance.
To enable full support, the Ion Torrent™ Server must have outbound internet access
(ports 22, 80, and 443) and be behind an appropriately configured firewall. While not
recommended, you can enable access to the Ion Torrent™ Browser (the web server
running on the Ion Torrent™ Server from the Internet). If you provide such access, you
must restrict access to the server using HTTP and AUTH firewall rules, or a
Chapter 2 System components
Internet connectivity
2
10 Ion Torrent S5™andIon Torrent S5™XL Instrument User Guide
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.