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Summary of Contents for ThermoFisher Scientific iontorrent Ion Chef Instrument 4484177
- Page 1 Ion Chef Instrument ™ USER GUIDE Maintenance, calibration, and troubleshooting Catalog Number 4484177 Publication Number MAN0018668 Revision B.0 For Research Use Only. Not for use in diagnostic procedures.
- Page 2 Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256 For descriptions of symbols on product labels or product documents, go to thermofisher.com/symbols-definition. Revision history: MAN0018668 B.0 (English) Revision Date Description 5 October 2023 Updated instruction to contact field service for replacement of UV light bulb.
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Page 3: Table Of Contents
Contents About this guide ............5 ■... - Page 4 Contents ■ APPENDIX A Troubleshooting ........... . 33 Setup and operation of the Ion Chef System .
- Page 5 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.
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Page 6: Chapter 1 Product Information
Product information Product description The Ion Chef System (Cat. No. 4484177) provides automated, high-throughput template preparation ™ and chip loading for use with an Ion PGM Sequencer, Ion Proton Sequencer, Ion S5 Sequencer, ™ ™ ™ Ion S5 XL Sequencer, or Ion GeneStudio S5 Series Sequencer. -
Page 7: Reagent Kits
Chapter 1 Product information Ion Chef reagent kits ™ Ion Chef reagent kits ™ The following table lists the reagent kits that are available from Thermo Fisher Scientific for use with the Ion Chef System. The template preparation kits include reagents and supplies for both template ™... -
Page 8: Compatible Ion Torrent ™ Sequencing Chips
Chapter 1 Product information Compatible Ion Torrent sequencing chips ™ Compatible Ion Torrent sequencing chips ™ The following table lists the sequencing chip kits available from Thermo Fisher Scientific that are compatible with the Ion Chef System. Store all chips at 15°C−30°C. ™ Sequencing platform Quantity Cat. -
Page 9: Calibration Supplies Kit
Chapter 1 Product information Ion Chef Calibration Supplies Kit ™ Ion Chef Calibration Supplies Kit ™ The Ion Chef Calibration Supplies Kit (Cat. No. A34301) has enough components to perform ten XYƟ ™ calibrations and ten Z calibrations (reuse of the Ion Chef Tip Cartridge required). ™ Callout # Description Part No. -
Page 10: Instrument Components
Chapter 1 Product information Ion Chef Instrument components ™ Ion Chef Instrument components ™ The following figure illustrates the major external and internal features of the Ion Chef Instrument. ™ Door – Provides access to the interior of the Power button – Power switch for the Ion Chef ™... -
Page 11: Interior Hardware And Consumables
Chapter 1 Product information Interior hardware and consumables Interior hardware and consumables The following figure illustrates the interior of the Ion Chef Instrument and describes the stations ™ involved in the preparation of sequencing chips. Waste pipette tip rack – The position of the rack containing waste (used) pipette tips. Automated heated cover –... -
Page 12: Instrument
Maintain and calibrate the Ion Chef ™ Instrument ■ ™ About the Ion Chef System touchscreen interface ........13 ■... -
Page 13: System Touchscreen Interface
Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ About the Ion Chef System touchscreen interface ™ About the Ion Chef System touchscreen interface ™ The Ion Chef System features a simple interface for loading chips, cleaning the instrument, and ™ performing system maintenance and configuration tasks. Set up run button –... - Page 14 Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Settings screen Screen When/How to use Notifications View notifications about instrument status during and between runs. Note: The Notifications screen is the same screen that opens after clicking Notifications in the lower left corner of the home screen.
- Page 15 Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Settings screen (continued) Screen When/How to use Torrent server Add and manage Ion Torrent Server connections. ™ For more information on configuring Ion Chef ™ Ion Torrent Server connections, see the Ion Chef ™ ™ Instrument Network Connection User Guide (Pub.
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Page 16: Change The Instrument Name
Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Change the instrument name Change the instrument name The following procedure describes how to change the name that is used to identify the Ion Chef ™ Instrument both on the network and in the data that it generates. 1. -
Page 17: Run The Xyɵ Calibration
Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Run the XYƟ calibration Run the XYƟ calibration The XYƟ calibration finds the precise location of the Z pump head (tip mandrel) relative to each consumable cartridge and a home position for the three centrifuges. To complete these tasks, the XYƟ calibration routine performs a series of X and Y position measurements, and it performs visual checks using the camera and the black dots. -
Page 18: Set Up The Instrument
Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Run the XYƟ calibration Set up the instrument 1. Power on the instrument, then wait for it to come to idle. 2. Open the instrument door. 3. Remove any consumables that may be loaded in the instrument. 4. - Page 19 Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Run the XYƟ calibration Ion Chef Tip Cartridge with Pierce tool in position A1 ™ Ion Chef PCR Plate ™ Empty Ion Chef Tip Cartridge ™ IMPORTANT! Ensure that the Chip-loading centrifuge is in the locked position with the bucket 2 position oriented toward the front of the deck.
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Page 20: Run The Xyɵ Calibration
Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Run the XYƟ calibration Run the XYƟ calibration 1. In the main menu, tap Settings4Service tools4Calibrate. 2. Tap XYƟ Calibration, then tap Start to start the calibration. 3. Follow the screen instructions to complete the calibration. The calibration takes approximately 20–25 minutes to complete. -
Page 21: Run The Z Calibration
Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Run the Z calibration 6. Remove, then discard the Pierce tool. Note: Reuse the tip cartridges and PCR plate in the Z calibration. 7. Reinstall the deck plate and PCR lid cover. • If the calibration fails, follow the error message instructions to correct the problem, then run the calibration again. -
Page 22: Set Up The Instrument
Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Run the Z calibration Ion Chef PCR Plates Pierce tools ™ 1‑mL black tips Ion Chef Tip Cartridge ™ Ion Chef Recovery Tubes ™ Set up the instrument IMPORTANT! Before you run the Z calibration, note the following: ·... - Page 23 Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Run the Z calibration 3. Load the deck: Callout # Deck position Item New pipette tips (left rear) Ion Chef Tip Cartridge with 8 NEW UNUSED 1‑mL black tips ™ loaded in the left column (A1 to H1) Thermal cycler sample block Ion Chef PCR Plate ™...
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Page 24: Run The Z Calibration
Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Run the Z calibration Run the Z calibration 1. In the main menu, tap Settings4Service Tools4Calibrate. 2. Tap Z calibration, then tap Start to start the calibration. 3. Follow the screen instructions to complete the calibration. 4. -
Page 25: System
Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Clean the Ion Chef System ™ Clean the Ion Chef System ™ About the cleaning protocol The Ion Chef System has an automated cleaning function that must be performed after every run. ™ The cleaning routine is started from the instrument touchscreen and is designed to minimize potential contamination. - Page 26 Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Clean the Ion Chef System ™ Ion Chef Instrument stations ™ Waste pipette tip position Solutions station Empty Tip Cartridge v2: move to waste pipette tip Recovery centrifuges station Enrichment station Thermal cycler sample block Chip-loading centrifuge Reagents station Remove and dispose of used consumables...
- Page 27 Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Clean the Ion Chef System ™ 4. Remove, then discard the box of used pipette tips from the waste tip position. IMPORTANT! Handle the disposable reservoir in the waste tip position with care. During the run, liquid waste collects in the reservoir.
- Page 28 Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Clean the Ion Chef System ™ 2. Remove the buckets from the Recovery centrifuges. Clean the inside and outside of each bucket using a lint-free wipe, then place the buckets on a clean, dry surface while you clean the centrifuge.
- Page 29 Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Clean the Ion Chef System ™ 6. Install the centrifuge buckets, then close the Recovery centrifuge cover. Buckets (cleaned and installed) Start the cleaning 1. Close the instrument door by first lifting it up slightly to disengage the locking mechanism, then pushing down on the door until the locks engage.
- Page 30 Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Clean the Ion Chef System ™ 3. Confirm that you have removed all consumables from the Ion Chef Instrument, except the empty ™ pipette tip rack in the waste tip position, then tap Next. 4. With the door closed, tap Start. The instrument performs a Deck Scan before starting the cleaning routine.
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Page 31: Install A Firmware Update
Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Install a firmware update Install a firmware update To ensure proper operation of the Ion Chef Instrument, we recommend periodically confirming ™ that your instrument is running the most current firmware. We occasionally release updates to the instrument firmware, which can include important changes to the Ion Chef System operation. -
Page 32: Replace The Ultraviolet Bulb
Chapter 2 Maintain and calibrate the Ion Chef Instrument ™ Replace the ultraviolet bulb Replace the ultraviolet bulb Replace the ultraviolet (UV) bulb after about 500 hours of use. Contact your local field service engineer to schedule a bulb replacement. Ion Chef Instrument User Guide ™... -
Page 33: Appendix A Troubleshooting
Troubleshooting Setup and operation of the Ion Chef System ™ Observation Possible cause Recommended action Instrument does not display 1. Power off the instrument, wait Multiple causes are possible. the home screen when 30 seconds, then power on the powered on instrument. 2. - Page 34 Appendix A Troubleshooting Setup and operation of the Ion Chef System ™ Observation Possible cause Recommended action Instrument will not begin a run The instrument has 1. Confirm that the touchscreen does encountered a Deck Scan error not display any Deck Scan warnings. (one or more consumables are If alarms are present, note the absent or loaded improperly).
- Page 35 Appendix A Troubleshooting Setup and operation of the Ion Chef System ™ Observation Possible cause Recommended action Instrument displays one or • Network connection to the 1. Tap the Instrument status button to view more alerts during a run server was interrupted. the alert(s). (continued) 2.
- Page 36 Appendix A Troubleshooting Setup and operation of the Ion Chef System ™ Observation Possible cause Recommended action Sequencing results are variable The Ion Chef Instrument If you see systematic variation that is ™ between samples in a run needs deck calibration. unrelated to library input, perform the XYƟ and Z calibration routines (see “Run the XYƟ...
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Page 37: Expected Throughput For Ion Torrent ™ Chips
Appendix A Troubleshooting Expected throughput for Ion Torrent chips ™ Expected throughput for Ion Torrent chips ™ The following table provides expected sequencing throughput specifications per chip type. For further information, see the specification sheets available at thermofisher.com at the web addresses listed after the table. -
Page 38: Loading Images For Normal Runs
Appendix A Troubleshooting Loading images for normal runs Loading images for normal runs The following table shows loading images that depict typical loading phenotypes for normal runs. For each image type, causes and best practices are listed. Description Run details Causes and best practices •... -
Page 39: Troubleshoot Common Loading Failure Types With Chip Image Phenotypes
Appendix A Troubleshooting Troubleshoot common loading failure types with chip image phenotypes Troubleshoot common loading failure types with chip image phenotypes The following tables show loading images for commonly seen failure types. For each type, a description and possible causes and recommended actions are listed. This information is intended to help focus troubleshooting efforts based on the loading image from the sequencing run report. - Page 40 Appendix A Troubleshooting Troubleshoot common loading failure types with chip image phenotypes Observation Possible cause Recommended action Punctate yellow or blue dots, No or insufficient polymerase 1. Repeat the Ion Chef templating run to ™ or uniform teal loading or primer was added to the rule out user error, or a consumable or sample.
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Page 41: Ion Proton ™ , Ion S5 ™ /Ion S5 ™ Xl, And Ion Genestudio ™ S5 Chef Runs
Appendix A Troubleshooting Troubleshoot common loading failure types with chip image phenotypes Observation Possible cause Recommended action Bubbles • The Wash 2 Bottle had a Contact Technical Support for service on the leaky seal. Ion PGM Sequencer. ™ • The sequencer waste line was clogged. - Page 42 Appendix A Troubleshooting Troubleshoot common loading failure types with chip image phenotypes Observation Possible cause Recommended action Low loading • The Chip Adapter was 1. Review Test Fragment (TF) metrics. improperly installed. • If TFs are missing, or count or signal • The Chip Adapter was is low, there may be a problem defective.
- Page 43 Appendix A Troubleshooting Troubleshoot common loading failure types with chip image phenotypes Observation Possible cause Recommended action Poor loading on the left side of The sample volume that was Contact Technical Support to report the the chip loaded in the chip was low. problem and for further assistance.
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Page 44: Ion Chef ™ Instrument User Issues
Appendix A Troubleshooting Ion Chef Instrument user issues ™ Ion Chef Instrument user issues ™ The following is a list of common errors that are made by Ion Chef users. ™ • Tip Cartridge locking bracket is not closed securely before the start of a run. –... -
Page 45: Appendix B 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 46: Conformity Symbols
Appendix B Safety Symbols on this instrument (continued) Symbol English Français Ultraviolet light Rayonnement ultraviolet Protective conductor terminal (main Borne de conducteur de protection (mise à la terre ground) principale) Do not dispose of this product in unsorted Ne pas éliminer ce produit avec les déchets usuels municipal waste non soumis au tri sélectif. -
Page 47: Location Of Safety Labels On This Instrument
Appendix B Safety Location of safety labels on this instrument Location of safety labels on this instrument Safety information for instruments not manufactured by Thermo Fisher Scientific Some of the accessories provided as part of the instrument system are not designed or built by Thermo Fisher Scientific. -
Page 48: Physical Injury
Appendix B Safety Instrument safety Physical injury CAUTION! Moving and Lifting Injury. The instrument is to be moved and positioned only by the personnel or vendor specified in the applicable site preparation guide. Improper lifting can cause painful and permanent back injury. Things to consider before lifting or moving the instrument or accessories: ·... -
Page 49: Electrical Safety
Appendix B Safety Instrument safety Electrical safety WARNING! Fuse Installation. Before installing the instrument, verify that the fuses are properly installed and the fuse voltage matches the supply voltage. Replace fuses only with the type and rating specified for the unit. Improper fuses can damage the instrument wiring system and cause a fire. -
Page 50: Ultraviolet (Uv) Safety
Appendix B Safety Safety and electromagnetic compatibility (EMC) standards Ultraviolet (UV) Safety The Ion Chef System uses a UV lamp which emits light at 254 nm. Under normal operating conditions, ™ the UV lamp is powered on when performing the cleaning protocol. Safety interlocks are used to ensure that the UV lamp is not powered when the door is open. -
Page 51: Environmental Design
Appendix B Safety Safety and electromagnetic compatibility (EMC) standards (continued) Reference Description US FCC CFR Title 47 Part 15.225, Subpart Operation within the band 13.110−14.010 MHz. Industry Canada RSS 210, Issue 8, Annex Licence-Exempt Radio Apparatus: Category I Equipment 2 EN 302 291-1/2 V1.1.1 Environmental design Reference Description... -
Page 52: Chemical Safety
Appendix B 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: · Read and understand the Safety Data Sheets (SDSs) provided by the chemical manufacturer before you store, handle, or work with any chemicals or hazardous materials. -
Page 53: Biological Hazard Safety
Appendix B Safety Biological hazard safety Biological hazard safety WARNING! Potential Biohazard. Depending on the samples used on this instrument, the surface may be considered a biohazard. Use appropriate decontamination methods when working with biohazards. WARNING! BIOHAZARD. Biological samples such as tissues, body fluids, infectious agents, and blood of humans and other animals have the potential to transmit infectious diseases. -
Page 54: Documentation And Support
Documentation and support Related documentation The following Ion Chef reagent kit user guides and quick references, and related guides are available ™ for download on the instrument and kit product pages at thermofisher.com. Document Publication number Ion AmpliSeq Library Preparation on the Ion Chef System User Guide MAN0013432 ™... -
Page 55: Customer And Technical Support
Documentation and support Customer and technical support Customer and technical support Visit thermofisher.com/support for the latest service and support information. • Worldwide contact telephone numbers • Product support information – Product FAQs – Software, patches, and updates – Training for many applications and instruments •... - Page 56 Ion Chef System_UG_MAN0018668-v2-GUID-B1CC96F3-37AB-4D2E-86F8-D0A29FEBD83F-2023/08/16 22:11:38 en 00:31:51.826+01:00 thermofisher.com/support | thermofisher.com/askaquestion thermofisher.com 5 October 2023...
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