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Ion GeneStudio
Instrument
USER GUIDE
for use with:
Ion GeneStudio
S5 Food Protection Instrument
™
Ion GeneStudio
S5 Plus Food Protection Instrument
™
Ion GeneStudio
S5 Prime Food Protection Instrument
™
Catalog Numbers A39513, A44648, A44649
Publication Number MAN0017965
Revision B.0
For testing of Food and Environmental samples only.
™
S5 Food Protection
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Table of Contents
Troubleshooting
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Related Manuals for ThermoFisher Scientific A39513
Summary of Contents for ThermoFisher Scientific A39513
- Page 1 Ion GeneStudio S5 Food Protection Instrument ™ Ion GeneStudio S5 Plus Food Protection Instrument ™ Ion GeneStudio S5 Prime Food Protection Instrument ™ Catalog Numbers A39513, A44648, A44649 Publication Number MAN0017965 Revision B.0 For testing of Food and Environmental samples only.
- Page 2 Life Technologies Corporation | 5781 Van Allen Way | Carlsbad, CA 92008 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.
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Page 3: Table Of Contents
Contents About this guide ............5 Purpose of the guide . - Page 4 Contents ■ APPENDIX A Touchscreen reference ....... . . 19 Clean, Initialize, and Run .
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Page 5: About This Guide
S5 Food Protection Instrument User Guide (Pub. No. MAN0017965) provides reference information for using and maintaining the Ion GeneStudio ™ ™ Food Protection System (Cat. No. A39513), Ion GeneStudio S5 Plus Food Protection ™ System (Cat. No. A44648), and Ion GeneStudio S5 Prime Food Protection System (Cat. -
Page 6: Chapter 1 Product Information
Product information Contents ™ The Ion GeneStudio S5 Food Protection System contains the following boxes and components. Ion GeneStudio ™ S5 Food Protection System (Cat. No. A39513) Components Part No. Ion GeneStudio ™ S5 Food Protection A37904 Instrument Ion S5 ™... -
Page 7: Required Materials And Equipment Not Supplied
Chapter 1 Product information Required materials and equipment not supplied Required materials and equipment not supplied Unless otherwise indicated, all materials are available through thermofisher.com. MLS: Fisher Scientific (fisherscientific.com) or other major laboratory supplier. Item Source Ion Chip ™ Minifuge (120V or 230V) 4479672 (120V) 4479673 (230V) Ion Chip... -
Page 8: Instrument Installation By Trained Personnel Only
Chapter 1 Product information Instrument installation by trained personnel only Instrument installation by trained personnel only IMPORTANT! The Ion GeneStudio ™ S5 Food Protection System is installed by trained service personnel and must not be relocated without assistance from trained service personnel. -
Page 9: Chapter 2 System Components
System components ™ Ion GeneStudio S5 Food Protection System component configuration and layout The Ion GeneStudio ™ S5 Food Protection Instrument uses a virtual server, and the Ion GeneStudio ™ S5 Plus Food Protection Instrument is equipped with an internal Ion Torrent ™... - Page 10 Chapter 2 System components Ion GeneStudio S5 Food Protection System component configuration and layout ™ Ion GeneStudio S5 Prime Food Protection System configuration ™ Ion GeneStudio S5 Prime Food Ion Torrent Server ™ ™ Protection Instrument Local area network Ion template preparation instrument Internet (Ion Chef Instrument (shown) or...
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Page 11: Internet Connectivity
Chapter 2 System components Internet connectivity 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. -
Page 12: Ion Genestudio ™ S5 Food Protection System Component Positions
Chapter 2 System components Ion GeneStudio S5 Food Protection System component positions ™ ™ Ion GeneStudio S5 Food Protection System component positions Ion GeneStudio S5 Ion GeneStudio S5 Ion GeneStudio S5 Touchscreen Power button Ion S5 Sequencing Reagents cartridge ™ Chip clamp Ion S5 Wash Solution bottle. -
Page 13: Ion Genestudio ™ S5 Food Protection Instrument Input And Output Connections
Chapter 2 System components Ion GeneStudio S5 Food Protection Instrument input and output connections ™ ™ Ion GeneStudio S5 Food Protection Instrument input and output connections USB ports–Connects a USB device to the instrument. Ethernet port—An RJ45 port that provides Ethernet (gigabit) communication between the instrument and a local area network. -
Page 14: Chapter 3 Instrument Operation
Instrument operation ™ 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 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. -
Page 15: Instrument Run Times
Chapter 3 Instrument operation Instrument run times 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 file (1 run/initialization). -
Page 16: Maintain The Ion Genestudio
Chapter 3 Instrument operation Maintain the Ion GeneStudio S5 Food Protection Instrument ™ ™ Maintain the Ion GeneStudio S5 Food Protection Instrument Materials required • Lint-free wipes • 70% isopropanol • (Optional) 10% bleach solution ™ Clean or In the event of a spill or leak on or inside the Ion GeneStudio S5 Food Protection Instrument, perform the following steps. - Page 17 Chapter 3 Instrument operation Maintain the Ion GeneStudio S5 Food Protection Instrument ™ 1. On the home screen, press Settings4Clean Instrument. The instrument door unlocks allowing access to the consumables. 2. Remove the Ion S5 ™ Wash Solution bottle to access the waste reservoir, then remove and empty the waste reservoir.
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Page 18: Perform An Instrument Reset Run With An Initialized, Unused Ion S5
Chapter 3 Instrument operation Maintain the Ion GeneStudio S5 Food Protection Instrument ™ Perform an Cleaning is normally performed automatically at completion of a sequencing run. instrument reset ™ If the Ion GeneStudio S5 Food Protection Instrument is initialized and run with an •... -
Page 19: Appendix A Touchscreen Reference
Touchscreen reference Clean, Initialize, and Run Ion GeneStudio S5 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. -
Page 20: Settings
Appendix A Touchscreen reference Settings Settings In the Settings menu, users can view and/or change instrument settings, manage data and network configurations, and update the installed software. Note: The Service tools option is for use by trained service personnel only. ™... - Page 21 Appendix A Touchscreen reference Settings Item Description When/How to use IP Address Set or change the IP configuration (DHCP or Static IP). 1. Select either the DHCP or Configuration Static IP option. 2. Touch the screen in the field you want to edit to activate the field.
- Page 22 Appendix A Touchscreen reference Settings Item Description When/How to use FTP Server Change the FTP Server IP address and user information. When a change to the FTP Server IP Configuration address or user information is required. Enter the IP address in the FTPserver field. Update Server Update the software update server.
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Page 23: System Tools
Appendix A Touchscreen reference Settings System Tools The System Tools menu enables you to upload instrument diagnostics, manage data, and shut down or reboot the instrument. Item Description When/How to use RFID Lists the product, product expiration date, and remaining To determine if reagents that were left uses of the product. - Page 24 Appendix A Touchscreen reference Settings Item Description When/How to use Noise Test Provides real-time measurement of electrical noise For troubleshooting if directed to do so readings on the chip. by Technical Support. Chip Calibration Checks the status of a chip. 1.
- Page 25 Appendix A Touchscreen reference Settings Item Description When/How to use Reagent Check Reagent Check, performed by the instrument as part of If directed to do so by Technical initialization, confirms that initialization passes by testing Support as part of a troubleshooting reagent flow and signal detection.
- Page 26 Appendix A Touchscreen reference Settings Item Description When/How to use Filesystems Provides real-time drive activity status and disk space Use if directed to do so as part of a and disks used. troubleshooting procedure: 1. In the System Tools menu, press Disk Drives.
- Page 27 Appendix A Touchscreen reference Settings Item Description When/How to use Pulse clean Provides step by step instruction to perform a pulse clean Use if directed to do so by Technical of the instrument if a solid‑state buffer leak occurs. Support as part of a troubleshooting procedure: 1.
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Page 28: Check For Software Updates
Appendix A Touchscreen reference Settings Item Description When/How to use Shut Down Access to "Shut Down" and "Reboot" commands. If directed to do so by Technical Support as part of a troubleshooting procedure. Note: It is not necessary/recommended to shut down the instrument overnight or over the weekend. -
Page 29: Data Management
Appendix A Touchscreen reference Settings Data management The Data management function allows users to delete run data manually, analyze the ™ data, or transfer the data to the Ion Torrent Server. Under normal conditions, run data are automatically transferred to the server, then deleted from the instrument hard drive. - Page 30 Appendix A Touchscreen reference Settings Item Description When/How to use Ion GeneStudio S5 Food Protection Instrument User Guide ™...
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Page 31: Manually Delete Run Data
Appendix A Touchscreen reference Settings Manually delete To troubleshoot data management problems the Data Management function allows users to delete run data manually, or transfer the data to the server. Under normal run data ™ conditions, run data are automatically transferred to the Ion Torrent Server, then deleted from the instrument hard drive. -
Page 32: Perform The Instrument Clean Operation
Appendix A Touchscreen reference Settings Perform the The Clean operation is normally performed automatically at the completion of the previous sequencing run. Manually run the Clean operation under any of the instrument Clean following conditions: operation • The sequencing run was aborted or there was a power failure during the second of two runs started after a single initialization. -
Page 33: Instrument Settings
Appendix A Touchscreen reference Settings Instrument The Instrument Settings menu provides information about the instrument and allows you to set the instrument name and calibrate the touchscreen. settings Ion GeneStudio S5 Food Protection Instrument User Guide ™... - Page 34 Appendix A Touchscreen reference Settings Item Description When/How to use About Provides instrument details. To view instrument reference information or access regulatory information. Regulatory Info Lists instrument-specific regulatory information. To view instrument regulatory information. Instrument To change the instrument name. Name Ion GeneStudio S5 Food Protection Instrument User Guide...
- Page 35 Appendix A Touchscreen reference Settings Item Description When/How to use Screen For troubleshooting if directed to do so Calibration by Technical Support. Touch the red cross with your finger or a stylus each time it appears. In total, you will touch the screen 4 times, one time in each corner.
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Page 36: Touchscreen Icons
Appendix A Touchscreen reference Touchscreen icons Touchscreen icons Number Icon Description Network connectivity – connected Network connectivity – not connected Instrument idle Sequencing in progress Instrument ready Error Chip status – Absent Chip status – Standby Chip status – Connecting Chip status –... - Page 37 Appendix A Touchscreen reference Touchscreen icons Number Icon Description Manifold air pressure – Bad. If the icon reads "0" and there is an alarm, contact Technical Support. Regulator air pressure – Good Regulator air pressure – Bad. If the icon reads "0" and there is an alarm, contact Technical Support.
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Page 38: Alarms, Notifications, And Events
Appendix A Touchscreen reference Alarms, Notifications, and Events Alarms, Notifications, and Events If the Alarms/Notifications indicator appears, press the indicator to open the Notifications screen, then press Alarms or Events to see detailed messages. Ion GeneStudio S5 Ion GeneStudio S5 Alarms and Notifications indicator. - Page 39 Appendix A Touchscreen reference Alarms, Notifications, and Events Alarm Description Recommended Action Front/Rear FanX speed below Where X is the fan number and YYYY Contact Technical Support. threshold YYYY. is the low threshold speed for the system fan. FPGA failed to connect in emulate Internal error.
- Page 40 Appendix A Touchscreen reference Alarms, Notifications, and Events Alarm Description Recommended Action Network Manager not connected. Check that the Ethernet cable If the problem persists, contact connecting the instrument to the Technical Support. local area network is properly connected. See “Ion GeneStudio ™...
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Page 41: Appendix B Troubleshooting
Troubleshooting Instrument alarms and events Observation Possible cause Recommended action Red "Alarms" and/or "Events" message in Main • Available Press the red Alarms icon to see Menu software detailed messages. updates were • If a message states "Newer detected. Ion GeneStudio S5 Software Available": •... -
Page 42: Initialization Fails
Appendix B Troubleshooting Initialization fails Initialization fails Observation Possible cause Recommended action Chip Check fails • The chip clamp was not 1. Open the chip clamp, closed. remove the chip, and look for signs of water • The chip was not outside the flow cell. - Page 43 Appendix B Troubleshooting Initialization fails Observation Possible cause Recommended action Reagent Check fails A chip failure was detected. 1. Replace the used sequencing chip used during initialization with a different used chip. 2. Press Retry. 3. If the initialization completes without failure, touch Home, then continue with your sequencing run.
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Page 44: Troubleshooting Using Control Libraries
Appendix B Troubleshooting Troubleshooting using control libraries Troubleshooting using control libraries Observation Possible cause Recommended action Ion Sphere Test Fragments • Chip loading was poor. 1. Confirm that the Control Ion Sphere ™ ™ are not present in the Test Particles (included in the Ion S5 ™... -
Page 45: Pulse Clean The Ion Genestudio ™ S5 Food Protection Instrument
Appendix B Troubleshooting Solid-state buffer leak ™ Pulse clean the You should pulse clean the Ion GeneStudio S5 Food Protection Instrument only if directed by Technical Support, or your Field Service Engineer (FSE), to recover Ion GeneStudio ™ instrument performance from a diagnosed solid-state buffer leak. S5 Food Protection Note: You must contact Technical Support, or your FSE, to diagnose whether a solid-... -
Page 46: Appendix C Instrument Warranty
Instrument warranty For new Ion Torrent ™ instruments, Life Technologies warrants to and only to buyer for twelve (12) months from the date of shipping, that the Ion Torrent ™ software and ™ Ion Torrent instruments are free from defects in material and workmanship and conform to Life Technologies’... - Page 47 Appendix C Instrument warranty Solid-state buffer leak A PARTICULAR PURPOSE, NON-INFRINGEMENT, OR REGARDING RESULTS OBTAINED THROUGH THE USE OF ANY PRODUCT (INCLUDING, WITHOUT LIMITATION, ANY CLAIM OF INACCURATE, INVALID OR INCOMPLETE RESULTS), WHETHER ARISING FROM A STATUTE OR OTHERWISE IN LAW OR FROM A COURSE OF PERFORMANCE, DEALING OR USAGE OF TRADE.
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Page 48: Appendix D Safety
Safety WARNING! GENERAL SAFETY. Using this product in a manner not specified in the user documentation may result in personal injury or damage to the instrument or device. Ensure that anyone using this product has received instructions in general safety practices for laboratories and the safety information provided in this document. -
Page 49: Location Of Safety Labels On The Instrument
Appendix D Safety Safety information for instruments not manufactured by Thermo Fisher Scientific Location of safety The Ion GeneStudio ™ S5 Food Protection Instrument has warnings at the location shown: labels on the instrument Safety and regulatory Ion Torrent S5™ XL Sequencer 1234987 00000000 For Research Use Only. -
Page 50: Instrument Safety
Appendix D Safety Instrument safety Instrument safety General CAUTION! Do not remove instrument protective covers. If you remove the protective instrument panels or disable interlock devices, you may be exposed to serious hazards including, but not limited to, severe electrical shock, laser exposure, crushing, or chemical exposure. -
Page 51: Electrical Safety
Appendix D Safety Instrument safety Electrical safety WARNING! Ensure appropriate electrical supply. For safe operation of the instrument: · Plug the system into a properly grounded receptacle with adequate current capacity. · Ensure the electrical supply is of suitable voltage. ·... -
Page 52: Safety And Electromagnetic Compatibility (Emc) Standards
Appendix D Safety Safety and electromagnetic compatibility (EMC) standards Safety and electromagnetic compatibility (EMC) standards The instrument design and manufacture complies with the following standards and requirements for safety and electromagnetic compatibility. Safety Reference Description EU Directive European Union “Low Voltage Directive” 2014/35/EU Safety requirements for electrical equipment for measurement, IEC 61010-1... -
Page 53: Environmental Design
Appendix D Safety Safety and electromagnetic compatibility (EMC) standards Environmental Waste and hazardous substances design Reference Description Directive 2012/19/EU European Union “WEEE Directive” – Waste electrical and electronic equipment Directive 2011/65/EU European Union “RoHS Directive” – Restriction of hazardous substances in electrical and electronic equipment Radio compliance Reference Description... -
Page 54: Chemical Safety
Appendix D Safety Chemical safety Chemical safety WARNING! GENERAL CHEMICAL HANDLING. To minimize hazards, ensure laboratory personnel read and practice the general safety guidelines for chemical usage, storage, and waste provided below. Consult the relevant SDS for specific precautions and instructions: ·... - Page 55 Appendix D Safety Chemical safety · Vérifier régulièrement l’absence de fuite ou d’écoulement des produits chimiques. En cas de fuite ou d’écoulement d’un produit, respecter les directives de nettoyage du fabricant recommandées dans la FDS. · Manipuler les déchets chimiques dans une sorbonne. ·...
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Page 56: Documentation And Support
Documentation and support Related documentation Title Pub. No. Ion 510 & Ion 520 & Ion 530 Food Protection Kit–Chef User ™ ™ ™ MAN0017967 Guide Ion GeneStudio ™ S5 Food Protection System Site Preparation MAN0017966 Guide Food Safety support Website: thermoscientific.com/foodmicro or thermofisher.com/foodsafety Support email: •... - Page 58 thermofisher.com/support | thermofisher.com/askaquestion thermofisher.com 13 September 2019...
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