Thermo Scientific Ion 520 User Manual

For Research Use Only. Not for use in diagnostic procedures.
Ion 520
™
& Ion 530
™
ExT Kit – Chef
USER GUIDE
for use with:
Ion Chef
™
System
Ion S5
™
System
Ion S5
™
XL System
Ion GeneStudio
™
S5 System
Ion GeneStudio
™
S5 Plus System
Ion GeneStudio
™
S5 Prime System
Catalog Number A30670
Publication Number MAN0015805
Revision F.0

Thermo Scientific Ion 520 Specifications

General

Brand	Thermo Scientific
Model	Ion 520
Category	Laboratory Equipment
Language	English

Summary

CHAPTER 1 Product information

Product description

Details the contents and capabilities of the Ion 520 & Ion 530 ExT Kit – Chef.

Ion GeneStudio™ S5 Series instrument reference

Specifies the Ion GeneStudio™ S5 Series Sequencer models covered in the document.

Software compatibility

Lists the compatible Torrent Suite™ Software versions for the kit.

Kit contents and storage

Details the components included in the kit and recommended storage conditions.

Kit summary

Provides a summary of kit components, part numbers, and quantities.

Kit components

Lists the individual components within the Ion S5™ ExT Chef Supplies.

Related products

Lists compatible Ion Chip™ kits and the Ion S5™ ExT Calibration Standard.

Required materials not supplied

Lists essential materials and equipment not included with the kit.

About the Ion Chef™ System

Overview of the Ion Chef™ System, its function, and components.

Workflow

Illustrates the high-level steps for preparing and loading a sample.

CHAPTER 2 Before you begin

Precautions

Highlights essential safety and handling precautions before starting.

Guidelines for using Ion Chef™ consumables and reagents

Provides best practices for handling consumables and reagents for optimal performance.

Prepare the Ion Chef™ Instrument for use

Details steps to ensure the instrument is ready before loading consumables.

CHAPTER 3 Create a Planned Run

About Planned Runs

Explains what Planned Runs are and their role in controlling instruments.

Create a Planned Run

Step-by-step guide for creating a Planned Run in Torrent Suite™ Software.

Planned Run workflow key fields

Defines the purpose and use of key fields in the Planned Run setup.

CHAPTER 4 Start the Ion Chef™ run

Materials required

Lists all necessary materials for starting an Ion Chef™ run.

Dilute the library

Provides guidelines for diluting sample and control libraries.

Prepare the consumables

Instructions for preparing reagents and consumables before loading.

Add the diluted libraries to the Ion Chef™ Library Sample Tube

Details how to add prepared libraries to the sample tube.

Load the Ion Chef™ System

Guides users through loading all components onto the Ion Chef™ instrument.

Start the Ion Chef™ run

Procedures for initiating and managing an Ion Chef™ run.

Unload the chip for sequencing

Steps for safely removing the chip after the preparation run.

CHAPTER 5 Initialize the sequencer

Ion S5™/Ion GeneStudio™ S5 Systems component positions

Identifies key components and their locations on the sequencer.

Before you begin

Pre-initialization checks and considerations for sequencer compatibility.

When a manual cleaning of the sequencer is required

Conditions requiring manual cleaning before initialization.

Initialize the sequencer

Step-by-step instructions for initializing the sequencer.

CHAPTER 6 Start the sequencing run

Chip handling guidelines

Procedures for correctly placing a chip into the chip clamp.

Start the sequencing run

Guides on starting the sequencing run and confirming settings.

Maintain the sequencer

Information on cleaning and decontaminating the sequencer.

Reagent consumables disposal

Guidelines for proper disposal of reagent consumables.

CHAPTER 7 Clean the Ion Chef™ System

About the cleaning protocol

Explanation of the automated cleaning function and its purpose.

Materials required

Lists necessary materials for cleaning the instrument.

Clean the Ion Chef™ Instrument

Detailed procedures for cleaning the Ion Chef™ instrument after each run.

APPENDIX A Troubleshooting

Ion Chef™ System setup and operation

Troubleshooting common issues related to instrument setup and operation.

Ion S5™/Ion GeneStudio™ S5 Systems setup and operation

Troubleshooting alerts, events, and general errors for S5 systems.

APPENDIX B Supplemental procedures

Perform a manual cleaning of the sequencer

Instructions for performing a manual cleaning cycle on the sequencer.

Perform an instrument reset run with an initialized sequencer that is loaded with an unused Reagents cartridge

Procedure for resetting the instrument under specific error conditions.

Quality control of Ion Sphere™ Particles

Methods for assessing the quality of prepared Ion Sphere™ Particles.

Maintain the Ion Chef™ System

References for advanced maintenance procedures for the Ion Chef™ System.

APPENDIX C Safety

Symbols on this instrument

Explanation of hazard and safety symbols found on the instrument.

Location of safety labels on this instrument

Illustrates the placement of safety labels on the instrument.

Safety information for instruments not manufactured by Thermo Fisher Scientific

Guidance for safe use of accessories not made by Thermo Fisher Scientific.

Instrument safety

General safety warnings related to instrument operation and physical hazards.

Electrical safety

Essential safety precautions regarding electrical connections and power.

Cleaning and decontamination

Safety guidelines for cleaning and decontaminating the instrument.

Ultraviolet (UV) Safety

Information on safety precautions related to the instrument's UV lamp.

Safety and electromagnetic compatibility (EMC) standards

Details on safety compliance and EMC standards met by the instrument.

Instrument safety — Ion S5™/Ion GeneStudio™ S5 Systems

Specific safety information for Ion S5™/Ion GeneStudio™ S5 Systems.

Chemical safety

Guidelines for safe handling, storage, and disposal of chemicals.

Biological hazard safety

Precautions and guidelines for working with biological samples.

Documentation and support

Related documentation

Lists other relevant user guides and bulletins for the system.

Customer and technical support

Information on how to obtain customer and technical support.

Limited product warranty

Overview of the product's limited warranty terms.