Thermo Fisher Scientific Ion 510 and Ion 520 and Ion 530 Food Protection Kit-Chef User guide

For testing of Food and Environmental samples only.

Ion 510™ & Ion 520™ & Ion 530™ Food

Protection Kit–Chef

USER GUIDE

Instructions for automated template preparation, chip loading,

and sequencing for the Thermo Scientiﬁc™ Next Generation

Sequencing Food Authenticity Workﬂow

for use with:

Ion GeneStudio™ S5 Food Protection System

Ion Chef™ Food Protection Instrument

Ion 510™ Food Protection Chip Kit

Ion 520™ Food Protection Chip Kit

Ion S5™ Food Protection Controls Kit Plus

Catalog Numbers A39476 and A39477

Publication Number MAN0017967

Revision A.0

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. MAN0017967

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. SGS DNA is a registered

trademark of Scandinavian Gene Synthesis.

Contents

■CHAPTER 1 Product information ....................................... 6

Product description ............................................................. 6

Library compatibility ........................................................ 6

Software compatibility ....................................................... 6

Kit contents and storage ......................................................... 7

Kit summary ............................................................... 7

Ion Chef™ reagents and materials ............................................. 7

Ion S5™ reagents ........................................................... 8

Related products ................................................................ 8

Instruments ................................................................ 8

Compatible Ion Chip™ kits .................................................... 8

Ion S5™ Food Protection Controls Kit Plus ...................................... 9

Compatible library preparation kits ........................................... 9

Required materials not supplied .................................................. 9

About the Ion Chef™ Food Protection System ...................................... 10

Ion Chef™ Food Protection Instrument components ............................ 10

Interior hardware and consumables .......................................... 11

About the Ion Chef™ System touchscreen interface ............................. 12

Workﬂow ..................................................................... 13

■CHAPTER 2 Before you begin .......................................... 14

Precautions ................................................................... 14

Avoid nucleic acid contamination ............................................. 14

Avoid chip damage ......................................................... 14

Protection by equipment .................................................... 14

Guidelines for using Ion Chef™ reagents and consumables .......................... 14

Prepare the instrument for use .................................................. 15

■CHAPTER 3 Create a Planned Run .................................... 16

About Planned Runs ............................................................ 16

Create an NGS Food Authenticity template ........................................ 16

Plan an NGS Food Authenticity run using the template .............................. 19

Planned Run wizard key ﬁelds ................................................... 21

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

3

■CHAPTER 4 Run the Ion Chef™ Food Protection System ............ 22

Materials required ............................................................. 22

Dilute the library pools ......................................................... 23

Dilute the sample library pool ............................................... 23

Dilute the control library (if used) ............................................ 23

Prepare the consumables ....................................................... 23

Add the diluted library pools to the Ion Chef™ Library Sample Tube ................... 24

Load the Ion Chef™ Food Protection System ....................................... 24

Load the pipette tip racks and PCR Plate ...................................... 26

Load the Reagents and Solutions cartridges .................................. 28

Load the Recovery Tubes and Enrichment Cartridge v2 ......................... 29

Load the Chip-loading centrifuge ............................................ 31

Conﬁrm that consumables are correctly installed .............................. 33

Single chip loading workﬂow ................................................ 33

Ion Chef™ pre-run checklist ................................................. 35

Start the Ion Chef™ Food Protection Instrument run ................................ 36

Unload the chips for sequencing ................................................. 39

■CHAPTER 5 Initialize the instrument ................................. 42

Ion GeneStudio™ S5 Food Protection System component positions .................... 42

Before you begin .............................................................. 43

When a manual cleaning of the instrument is required .............................. 43

Initialize the instrument ........................................................ 44

■CHAPTER 6 Start the sequencing run ................................ 46

Chip handling guidelines ........................................................ 46

Start the sequencing run ....................................................... 47

Maintain the instrument ........................................................ 48

Materials required ......................................................... 48

Clean or decontaminate the instrument ...................................... 48

Reagent consumables disposal .................................................. 48

CO2 scrubber removal and disposal .......................................... 49

Recycle Ion S5™ Wash Solution and Ion S5™ Cleaning Solution bottles ............ 49

■CHAPTER 7 Clean the Ion Chef™ Food Protection System .......... 50

About the cleaning protocol ..................................................... 50

Materials required ............................................................. 50

Clean the Ion Chef™ Food Protection Instrument ................................... 51

Remove and discard used consumables ...................................... 52

Inspect and clean the Recovery centrifuges and buckets ........................ 53

Start the cleaning ......................................................... 54

Contents

4

Ion 510

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& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

■APPENDIX A Troubleshooting ......................................... 56

Ion Chef™ Food Protection System setup and operation ............................. 56

Ion GeneStudio™ S5 Food Protection System setup and operation .................... 59

Instrument alarms and events ............................................... 59

■APPENDIX B Supplemental procedures .............................. 60

Perform a manual cleaning of the instrument ...................................... 60

Perform an instrument reset run with an initialized, unused Ion S5™ Sequencing

Reagents cartridge ............................................................. 61

Maintain the Ion Chef™ Food Protection System .................................... 62

Install a ﬁrmware update ................................................... 62

Change the instrument name ............................................... 63

■APPENDIX C Safety ..................................................... 64

Symbols on this instrument ..................................................... 65

Conformity symbols ........................................................ 65

Location of safety labels on this instrument ....................................... 66

Safety information for instruments not manufactured by Thermo Fisher Scientiﬁc ..... 66

Instrument safety .............................................................. 66

General .................................................................. 66

Physical injury ............................................................ 66

Electrical safety ........................................................... 67

Cleaning and decontamination ............................................... 67

Ultraviolet (UV) Safety ...................................................... 67

Safety and electromagnetic compatibility (EMC) standards .......................... 67

Safety compliance ......................................................... 68

EMC ...................................................................... 68

Environmental design ...................................................... 68

Instrument safety — Ion GeneStudio™ S5 Food Protection Instrument ................ 69

Chemical safety ................................................................ 69

Biological hazard safety ......................................................... 70

■APPENDIX D Documentation and support ............................ 71

Food Safety support ............................................................ 71

Contents

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

5

Product information

■Product description ................................................... 6

■Kit contents and storage ................................................ 7

■Related products ...................................................... 8

■Required materials not supplied ......................................... 9

■About the Ion Chef™ Food Protection System ............................ 10

■Workow ........................................................... 13

IMPORTANT! Before using this product, read and understand the information in the

“Safety” appendix in this document.

Product description

The Ion 510™ & Ion 520™ & Ion 530™ Food Protection Kit–Chef (Cat. Nos. A39476 and

A39477) includes reagents and materials to:

• Use the Ion Chef™ Food Protection Instrument to prepare template-positive Ion

Sphere™ Particles.

• Load them onto the Ion 510™ Food Protection Chip or Ion 520™ Food Protection

Chip.

• Sequence the loaded chips using the Ion GeneStudio™ S5 Food Protection

Instrument.

Library kit

Cat. No. A39476

(1 run per

initialization)

Cat. No. A39477

(2 runs per

initialization)

SGS All Species ID Meat DNA Analyser I ✓ ✓

SGS All Species ID Meat DNA Analyser II ✓ ✓

SGS All Species ID Fish DNA Analyser I ✓ ✓

SGS All Species ID Fish DNA Analyser II ✓ ✓

SGS All Species ID Plant DNA Analyser I ✓

SGS All Species ID Plant DNA Analyser II ✓

The Ion 510™ & Ion 520™ & Ion 530™ Food Protection Kit–Chef is compatible with

Torrent Suite™ Software 10 and later. Be sure to update your Torrent Server to the

latest available version of Torrent Suite™ Software before using this kit.

1

Library

compatibility

Software

compatibility

6

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

Kit contents and storage

IMPORTANT! Do not substitute components from any other Ion sequencing kits. This

protocol has been veried using these specic materials. Substitution can adversely

aect system performance.

IMPORTANT! Store all consumables and cartridges under the recommended

conditions and in an upright position. Do NOT store the Ion S5™ Sequencing Reagents

(Cat. No. A27768) on dry ice or in a closed environment where dry ice is present.

The Ion 510™ & Ion 520™ & Ion 530™ Food Protection Kit–Chef (Cat. No. A39476)

contains all materials that are required to prepare and sequence 8 chips. The kit

supports 4 Ion Chef™ runs and 8 sequencer initializations, as required for

400-base-read libraries.

Cat. No. A39477 supports 4 Ion Chef™ runs and 4 sequencer initializations. Use

Cat. No. A39477 if you are preparing a single chip per Ion Chef™ run or when

performing two sequencing runs per initialization (for 200-base-read libraries).

On arrival, inspect all consumables and contact Technical Support if any of the

products have been damaged during shipping.

Component

Cat. No. A39476

(1 run per initialization)

Cat. No. A39477

(2 runs per initialization)

Part No. Quantity per

kit Part No. Quantity per

kit

Ion S5™ Chef Supplies A27755 4 boxes A27755 4 boxes

Ion S5™ Chef Solutions A27754 1 box A27754 1 box

Ion 510™ & Ion 520™ &

Ion 530™ Chef

Reagents

A34018 1 box A34018 1 box

Ion S5™ Sequencing

Solutions

A27767 2 boxes A27767 1 box

Ion S5™ Sequencing

Reagents

A27768 2 boxes A27768 1 box

Contents Amount / box Storage

Ion S5™ Chef Supplies (Part No. A27755)

Chip Adapter 2 15°C to 30°C

Enrichment Cartridge v2 1

Tip Cartridge v2 1

PCR Plate 1

Kit summary

Ion Chef™

reagents and

materials

Chapter 1 Product information

Kit contents and storage

1

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

7

Contents Amount / box Storage

Frame Seal v2 15°C to 30°C1

Recovery Station Disposable Lid v2 2

Recovery Tube v2 12

Ion S5™ Chef Solutions (Part No. A27754)

Ion S5™ Chef Solutions 4 cartridges 15°C to 30°C

Ion 510™ & Ion 520™ & Ion 530™ Chef Reagents (Part No. A34018)

Ion 510™ & Ion 520™ & Ion 530™ Chef

Reagents

4 cartridges –30°C to –10°C

IMPORTANT! Do not store the Ion S5™ Sequencing Reagents (Part No. A27768) on

dry ice or in a closed environment containing dry ice.

Contents Amount / box Storage

Ion S5™ Sequencing Solutions (Part No. A27767)

Ion S5™ Wash Solution 4 × 1.5 L 15°C to 30°C

Ion S5™ Cleaning Solution 250 mL

Ion S5™ Sequencing Reagents (Part No. A27768)

Ion S5™ Sequencing Reagents

(Cartridges ship at 2°C to 8°C. Store as

indicated.)

4 cartridges –30°C to –10°C

do not store on dry ice

Related products

1

8

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

The Ion S5™ Food Protection Controls Kit Plus (Cat. No. A39478) is ordered

separately. See the Ion S5™ Food Protection Controls Kit Plus Product Information Sheet

(Pub. No. MAN0017993) for details.

Contents Amount Storage

Human CEPH Genomic DNA Control (red cap) 30 µL −30°C to −10°C

Human CEPH Control 200 Library (yellow cap) 12 µL

E. coli

DH10B Control 400 Library (orange cap) 16 µL

Library kit Cat. No. Source

SGS All Species ID Meat DNA Analyser I A38452 Thermo Fisher

Scientiﬁc

microbiology

ordering process

SGS All Species ID Meat DNA Analyser II A38453

SGS All Species ID Fish DNA Analyser I A38454

SGS All Species ID Fish DNA Analyser II A38455

SGS All Species ID Plant DNA Analyser I A38456

SGS All Species ID Plant DNA Analyser II A38457

Required materials not supplied

Unless otherwise indicated, all materials are available through thermosher.com.

MLS: Fisher Scientic (sherscientic.com) or other major laboratory supplier.

Item Source

P2, P10, P20, P200, P1000 pipettor set and ﬁltered tips MLS

Gloves, powder-free nitrile MLS

Ice buckets and ice —

Nuclease-free water, molecular biology grade MLS

Isopropanol, 70% solution MLS

Wipes, disposable lint-free MLS

(Optional)

Non-interruptible Power Supply (UPS) [1] MLS

[1] 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.

Ion S5™ Food

Protection

Controls Kit Plus

Compatible library

preparation kits

Chapter 1 Product information

Required materials not supplied

1

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

9

About the Ion Chef™ Food Protection System

The Ion Chef™ Food Protection System provides automated, high-throughput

template preparation and chip loading for use with the Ion GeneStudio™ S5 Food

Protection Instrument. The system includes a complete set of cartridge-based

consumables and reagents that enable you to load two Ion 510™ Food Protection

Chips or Ion 520™ Food Protection Chips in approximately 13 hours with less than

15 minutes of hands-on time.

The Ion Chef™ Food Protection System features network integration with the Torrent

Suite™ Software to enable sample and reagent traceability throughout the chip

preparation workow.

The following gure illustrates the major external and internal features of the

Ion Chef™ Food Protection Instrument.

4

1 2 3

5 6 7

8

1Door—Provides access to the interior of

the instrument. The door is locked in the

closed position during operation.

2Micropipettor—A mechanical positive-

displacement pipettor that performs all

ﬂuid transfers during sample and chip

preparation.

3Robotic arm—Performs ﬂuid transfer

during chip loading. The arm also

contains an optical sensor that reads the

barcodes of instrument reagents and

consumables.

4Touchscreen—Provides access to all

instrument functions for operation,

maintenance, and troubleshooting.

5Power button—Power switch for the

Ion Chef™ Food Protection Instrument,

where the states are on (illuminated) and

off.

6Power port—A 100–240 VAC port that

provides power to the Ion Chef™ Food

Protection Instrument.

7Ethernet port—An RJ45 port that provides

Ethernet (100 Mbit) communication with

the Ion Chef™ Food Protection Instrument.

8USB port—Provides USB communication

with the Ion Chef™ Food Protection

Instrument. Used to update the

instrument ﬁrmware and to transfer data

during service or maintenance.

Ion Chef™ Food

Protection

Instrument

components

Chapter 1 Product information

About the Ion Chef

™

Food Protection System

1

10

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

The following gure illustrates the interior of the Ion Chef™ Food Protection

Instrument and describes the stations that are involved in the preparation of chips for

sequencing on the Ion GeneStudio™ S5 Food Protection System.

A

B

C

D

E

F

G

H

1 2 3 4 56 7 8 9 10 11 12

5

3

8

12

6

4

7

530 CCBD02226

9

1Waste pipette tip rack—The position of the rack containing waste (used) pipette tips.

2Automated heated cover—Transfers the plate cover to the PCR reaction plate within the

sample block. During thermal cycling, the heated cover applies compression to seal the

reaction plate and heats the cover to prevent condensation.

3New pipette tips—The position of the rack containing unused pipette tips.

4Thermal cycler sample block—Performs thermal cycling of the sequencing reactions on a

96-well PCR reaction plate.

5Reagents station—The position on the instrument deck of the diluted libraries, NaOH, and

the Ion 510™ & Ion 520™ & Ion 530™ Chef Reagents cartridge.

6Solutions station—The position on the instrument deck of the Ion S5™ Chef Solutions

cartridge, which is maintained at room temperature.

7Recovery centrifuges—Twin stations that perform centrifugation of the ISPs during the

recovery phase of template preparation.

8Enrichment station—The position of the rack containing consumables for the enrichment

of the template-positive ISPs.

9Chip-loading centrifuge—Performs centrifugation of sequencing chips that have been

mounted to chip-loading adapters and loaded with template-positive ISPs.

Interior hardware

and consumables

Chapter 1 Product information

About the Ion Chef

™

Food Protection System

1

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

11

The Ion Chef™ Food Protection System features a simple interface for loading chips,

cleaning the instrument, and performing system maintenance and conguration tasks.

2

1

3 4 5

1Set up run button – Set up the Ion Chef™ template preparation and chip-loading routine.

Choose Step by Step to have the instrument lead you stepwise through installation of

reagents and consumables, or choose Quick Start to proceed if you have already installed

the consumables.

2Open Door button.

3Notiﬁcations button – View notiﬁcations about instrument status during and between runs.

4Quick Start button – Proceed directly to the Quick Start instrument setup mode. User

veriﬁes the loading of a new pipette tip cartridge and an empty pipette tip rack to hold

waste tips generated during the run, before proceeding to Deck Scan.

5Settings button – Advance to a screen providing the following options:

•Notiﬁcations: view notiﬁcations about instrument status during and between runs

•Instrument Settings: view current settings and network conﬁguration, set instrument

name, adjust time zone

•Service tools: access screens for service-related maintenance and instrument

diagnostics

•Torrent Server: add and manage Torrent Server connections

•Clean Ion Chef: proceed directly to the instrument cleaning routine

•Check for updates: check availability of system software updates

About the Ion

Chef™ System

touchscreen

interface

Chapter 1 Product information

About the Ion Chef

™

Food Protection System

1

12

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

Workﬂow

The following workow illustrates how to prepare and load samples using the Ion

510™ & Ion 520™ & Ion 530™ Food Protection Kit–Chef and Ion Chef™ Food Protection

System for sequencing on an Ion GeneStudio™ S5 Food Protection Instrument.

Create a Planned Run in Torrent Suite™ Software.

q

Dilute the library samples, and thaw the reagents.

q

Load the Ion Chef™ Food Protection Instrument.

q

Start the Ion Chef™ Food Protection Instrument.

q

Unload the Ion Chef™ Food Protection Instrument.

q

Load the prepared chip into the sequencer, then begin the sequencing

run.

Chapter 1 Product information

Workﬂow

1

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

13

Before you begin

■Precautions .......................................................... 14

■Guidelines for using Ion Chef™ reagents and consumables ................ 14

■Prepare the instrument for use ......................................... 15

Precautions

IMPORTANT! A primary source of contamination is spurious DNA fragments from

previous sample processing steps. Do not introduce amplied DNA into the library

preparation laboratory or work area.

IMPORTANT! To avoid possible damage to the chip due to electrostatic discharge,

ground yourself before picking up a chip or placing a chip on a surface such as a lab

bench. For example, touch the metal trim on the chip compartment before inserting or

removing a chip from the chip clamp.

WARNING! The protection that is provided by the equipment can be impaired

if the instrument is operated outside the environment and use specications,

the user provides inadequate maintenance, or the equipment is used in a

manner that is not specied by the manufacturer (Thermo Fisher Scientic).

Guidelines for using Ion Chef™ reagents and consumables

To ensure the proper function of the Ion Chef™ Food Protection System, handle the

associated consumables and reagents according to the following guidelines:

• Store all consumables and cartridges under the recommended conditions and in

an upright position.

• Inspect all consumables and cartridges for damage on arrival and again before

use.

• Hold sequencing chips by gently gripping them by their edges.

• When the instrument is not in use, remove all consumables and reagents from the

deck and close the instrument door.

• Do not reuse any consumables or reagents. All components are single-use only.

Note: Each new Tip Cartridge v2 is used by the instrument for multiple

pipeing steps, but after each run, the empty Tip Cartridge v2 is transferred to

the waste tip station.

2

Avoid nucleic acid

contamination

Avoid chip damage

Protection by

equipment

14

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

• Use only specied kits and supplies with the Ion Chef™ Food Protection

Instrument. The use of third-party reagents and supplies can adversely aect the

performance of the instrument and chips.

• Remove and sequence chips within 1 hour after the instrument nishes loading

them. If you cannot sequence a loaded chip immediately, store it in a chip storage

container at 4°C until you are ready to run it (up to 6–8 hours maximum).

Note: If you choose to store a loaded chip, remove the chip from 4°C storage (but

keep it in the chip storage container) at least 20 minutes before running it,

allowing the chip to warm to room temperature.

Prepare the instrument for use

Before you use the Ion Chef™ Food Protection Instrument:

• Ensure that the instrument has been cleaned following the previous run. If not,

clean the instrument before loading it with consumables.

Note: For more information on the cleaning procedure, see Chapter 7, “Clean the

Ion Chef™ Food Protection System“.

• Inspect the empty compartments of the Reagents and Solutions stations for

condensation. Condensate can collect in these compartments, depending on

temperature and humidity conditions. Before loading consumables into the

instrument, wipe the compartments dry with a laboratory wipe or absorbent

cloth, if needed.

• Thaw the Ion 510™ & Ion 520™ & Ion 530™ Chef Reagents cartridge at room

temperature for 45 minutes before use.

• Ensure that the instrument has a connection to the Torrent Server. On the

instrument home touchscreen, touch Seings, then Torrent Server to view the

connection status.

Note: If the instrument is not connected, see Ion Chef™ and Torrent Server Network

Setup User Guide (MAN0013444) for instructions on how to congure a direct or

indirect network connection.

Chapter 2 Before you begin

Prepare the instrument for use

2

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

15

Create a Planned Run

■About Planned Runs .................................................. 16

■Create an NGS Food Authenticity template .............................. 16

■Plan an NGS Food Authenticity run using the template ................... 19

■Planned Run wizard key elds ......................................... 21

About Planned Runs

Planned Runs are digital instructions that are created in Torrent Suite™ Software for

controlling the template preparation and sequencing instruments. Planned Runs

contain seings such as number of ows, kit types, barcodes, sample information, and

reference les (if any). Planned Runs are also used to track samples, chips, and

reagents throughout the workow, from template preparation on the Ion Chef™ Food

Protection Instrument through sequencing on an Ion GeneStudio™ S5 Food Protection

Instrument and subsequent data analysis. Each chip that is prepared in an Ion Chef™

run requires its own Planned Run.

IMPORTANT! For more information on creating a Planned Run in Torrent Suite™

Software, including a complete description of each eld in the Create Plan workow

bar, see the Torrent Suite™ Software Help, available by clicking the Help buon in the

software.

Create an NGS Food Authenticity template

Create one or more NGS Food Authenticity templates for your Planned Runs.

Detailed information on creating Planned Run templates is provided in the Torrent

Suite™ Software Help.

Dierent SGS All Species ID DNA Analyser library preparation kits require dierent

numbers of ows during sequencing, and the number of ows is controlled by the

Planned Run. Therefore, you may have to create dierent Planned Run templates,

depending on the library kits you are using. A single Planned Run template

containing 600 ows can be used for all SGS All Species ID DNA Analyser library

preparation kits. However, if using only the SGS All Species ID DNA Analyser library

3

16

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

preparation kit for meat or for sh, an alternative Planned Run containing 500 ows

can be used to reduce the run time and enable two sequencing runs per initialization.

1. Sign in to Torrent Suite™ Software on the Torrent Server that is connected to your

Ion Chef™ Food Protection Instrument and Ion GeneStudio™ S5 Food Protection

Instrument.

Note: Your software account is set up on Torrent Server during system

installation.

2. Click the Plan tab, then click Templates.

3. Select Generic Sequencing4Add New Template

4. Select parameters for the template based on the types of samples to be analyzed.

Meat and/or ﬁsh

analysis parameter Selection

Ion Reporter

Account

None

Sample Grouping Other

Research Application

Research

Application

DNA

Target Technique Other

Kits

Instrument Select Ion GeneStudio™ S5 Food Protection Instrument

Sample

Preparation Kit

Library Kit Type

Template Kit Select Ion 510™ & Ion 520™ & Ion 530™ Food Protection Kit–

Chef

Advanced settings Use recommended defaults for meat or ﬁsh samples

Sequencing Kit Select Ion S5 Sequencing Kit

Note: The sequencing kit name is generic for this application.

Chip Type Select the chip type that you are using

Chapter 3 Create a Planned Run

Create an NGS Food Authenticity template

3

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

17

Meat and/or ﬁsh

analysis parameter Selection

Control sequence

Barcode Set

Flows Select 500 for meat or ﬁsh samples

Advanced settings Use the recommended defaults

Plugins

Plugins FileExporter™ plugin

Note: To conﬁgure the FileExporter™ settings, click

Settings4Plugins4FileExporter settings4Conﬁgure . In the

dialog, include FastQ ﬁles and do not include other ﬁle types,

then save the conﬁguration.

Projects

Save

Template Name Type a name for the template

Analysis

Parameters

Default

Plant analysis

parameter Selection

Ion Reporter

Account

None

Sample Grouping Other

Research Application

Research

Application

DNA

Target Technique Other

Kits

Instrument Select Ion GeneStudio™ S5 Food Protection Instrument

Sample

Preparation Kit

Library Kit Type

Template Kit Select Ion 510™ & Ion 520™ & Ion 530™ Food Protection Kit–

Chef

Advanced settings Select Customize4Chef Protocol4400 bp for plant samples,

and do not change any other settings.

Sequencing Kit Select Ion S5 Sequencing Kit

Note: The sequencing kit name is generic for this application.

Chapter 3 Create a Planned Run

Create an NGS Food Authenticity template

3

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Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

Plant analysis

parameter Selection

Chip Type Select the chip type that you are using

Control sequence

Barcode Set

Flows Select 600 for plant samples

Advanced settings Use the recommended defaults

Plugins

Plugins FileExporter™ plugin

Note: To conﬁgure the FileExporter™ settings, click

Settings4Plugins4FileExporter settings4Conﬁgure . In the

dialog, include FastQ ﬁles and do not include other ﬁle types,

then save the conﬁguration.

Projects

Save

Template Name Type a name for the template

Analysis

Parameters

Default

5. Save the template.

Plan an NGS Food Authenticity run using the template

1. Sign in to Torrent Suite™ Software on the Torrent Server that is connected to your

Ion Chef™ Food Protection Instrument and Ion GeneStudio™ S5 Food Protection

Instrument.

Note: Your software account is set up on Torrent Server during system

installation.

2. On the Plan tab, click Templates, then select Generic Sequencing.

3. For the template that you will use for the run, on the far right click the Seings

buon, then select Plan Run.

4. In the Planned Run wizard, review the tabs (IonReporter, Research Application,

Kits, Plugins, Projects) and make selections appropriate for your run (see

“Planned Run wizard key elds“ on page 21).

5. Complete the Plan tab.

a. Enter a name for the planned run.

b. For Analysis Parameters, make sure that Default (Recommended) is

selected.

Chapter 3 Create a Planned Run

Plan an NGS Food Authenticity run using the template

3

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

19

c. Enter the number of chips to create for the Planned Runs. To specify two

sample names, in Number of chips, enter 2, then click the check mark

buon on the right.

d. In the Sample elds appropriate for each plan, enter a sample name

(Library pool name).

e. In Sample Tube Label, enter or scan the barcode of the Ion Chef™ Library

Sample Tube.

IMPORTANT! You must enter or scan the barcode of each Ion Chef™ Library

Sample Tube.

f. When you have completed your selections, click Plan Run to save the run.

The run is listed on the Planned Runs page with the specied name and is

automatically used by the Ion Chef™ Food Protection Instrument when the

sample is loaded.

Chapter 3 Create a Planned Run

Plan an NGS Food Authenticity run using the template

3

20

Ion 510

™

& Ion 520

™

& Ion 530

™

Food Protection Kit–Chef User Guide

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Thermo Fisher Scientific Ion 510 and Ion 520 and Ion 530 Food Protection Kit-Chef User guide

Thermo Fisher Scientific Ion 510 and Ion 520 and Ion 530 Food Protection Kit-Chef User guide

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