Sample Sheet Fields

A sample sheet is required to kick off secondary analysis. It can be made either using the BSSH Run Planner Tool (recommended), Excel Sample Sheet Generator, or manually. The following table describes the sample sheet fields and its values depending on the environment used to execute the DRAGEN Protein Quantification application. The pipeline can be executed via cloud using either Illumina Connected Analytics or Base Space Sequence Hub, or executed locally using a phase 4 DRAGEN Server.

Sample Sheet Fields

This is a non comprehensive list of fields.

Section
Field
Value

Header

FileFormatVersion

Must be "2"

Header

InstrumentPlatform

Must be "NovaSeqXSeries" or "NovaSeq"

Header

RunName

User-provided value

Header

RunDescription

User-provided value (optional)

Reads

Read1Cycle

15

Reads

Index1Cycle

10

Reads

Index2Cycle

10

Sequencing_Settings

LibraryPrepKits

Must be "IlluminaProteinPrep9k"

BCLConvert_Data

Sample_ID

Alphanumeric name up to 100 characters. Letters, numbers, dashes only (or any combination of letters, numbers, and dashes)

BCLConvert_Data

Index

i7 index sequence, including A, C, T or G letters, 10 nucleotides long

BCLConvert_Data

Index2

i5 index sequence, including A, C, T or G letters, 10 nucleotides long

BCLConvert_Data

Lane

Lane value (shall be a number between 1 and 8 inclusive) (optional if instrument is NovaSeq 6k, required if instrument is NovaSeq X)

Cloud_Proteomics_Settings (Cloud Analysis) or Proteomics_Settings (Local Analysis)

SoftwareVersion

Three-digit version of SW used in secondary analysis. For example, "2.0.0"

Cloud_Proteomics_Settings (Cloud Analysis) or Proteomics_Settings (Local Analysis)

StartsFromFastq

Must be "false"

Cloud_Proteomics_Settings (Cloud Analysis) or Proteomics_Settings (Local Analysis)

output_file_prefix

User-provided prefix

Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)

Sample_ID

Alphanumeric name up to 100 characters. Letters, numbers, dashes only (or any combination of letters, numbers, and dashes)

Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)

PlateBarcode

For each plate, associated plate barcode

Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)

MatrixTubeBarcode

For each plate, associated matrix tube barcode

Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)

BatchID

For each plate, user-provided batchID

Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)

InputType

For each sample, associated input type. Examples: Plasma_Calibrator, Plasma_QC, Plasma, Serum_Calibrator, Serum_ QC, Serum, Blank

Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)

ControlID

ID of the calibrator, QC, and blank lot (applied to controls only).

Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)

ProbePlate

For each plate, probe plate lot number, from library prep

Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)

SOMAmerBeadPlate

For each plate, SOMAmer Bead Plate lot number, from library prep

Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)

WellPosition

For each sample, well position (A1-H12)

Cloud_Settings

GeneratedVersion

Software version of the BSSH Run Planner tool that generated the sample sheet

Cloud_Settings

Cloud_Proteomics_Pipeline (Cloud Only)

ICA Path to the proteomics pipeline. For example: urn:ilmn:ica:pipeline:6475f989-f9fc-4874-9ff6-10ac23d11681#DRAGEN_Protein_Quantification_2-0-0

Cloud_Data

Sample_ID

Alphanumeric name up to 100 characters. Letters, numbers, dashes only (or any combination of letters, numbers, and dashes)

Cloud_Data

ProjectName

(optional) user-provided plate-specific project

Cloud_Data

LibraryName

For each sample, must be <Sample_ID>_<index>_<index2>

Cloud_Data

LibraryPrepKitName

Must be "IlluminaProteinPrep9k"

Cloud_Data

IndexAdapterKitName

Must be "IlluminaDNARNAUDISetABCDTagmentation_Proteomics"

Samplesheet Examples

Examples of local and cloud sample sheets for NovaSeq 6000 and NovaSeq X are attached to this page.

Local

Example NovaSeq 6000 samplesheet for local analysis
Example NovaSeq X samplesheet for local analysis

Cloud

Example NovaSeq X samplesheet for autolaunch analysis
Example NovaSeq 6000 samplesheet for autolaunch analysis

For additional information, refer to the ICS Samplesheet documentation.

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