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 BioInsight Platform Core or BaseSpace 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 "IlluminaProteinPrep9.5k"
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, "2.3.0"
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 (optional)
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. Permitted values: Blank, Plasma, Serum, CSF, or MultiMatrix-<tissuetype>
Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)	Control	For each sample, the control type. Permitted values: Blank, Calibrator, QC, or empty (for non-control samples)
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)	KitType	The kit type for the plate. Permitted values: Plasma, Serum, CSF, or MultiMatrix
Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)	ProbePlate	For each plate, probe plate barcode from library prep
Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)	SOMAmerBeadPlate	For each plate, SOMAmer Bead Plate barcode from library prep. SBP1 format for Plasma/Serum/CSF, MBP format for MultiMatrix.
Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)	WellPosition	For each sample, well position with UDI set prefix (e.g., A-A01 through D-H12)
Cloud_Settings	GeneratedVersion	Software version of the BSSH Run Planner tool that generated the sample sheet
Cloud_Settings	Cloud_Proteomics_Pipeline (Cloud Only)	Platform Core Path to the proteomics pipeline. For example: urn:ilmn:ica:pipeline:896aa1df-0412-45db-814e-4683b3215203#DRAGEN_Protein_Quantification_2-2-2
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 project. Multiple values are allowed across samples.
Cloud_Data	LibraryName	For each sample, must be <Sample_ID>_<index>_<index2>
Cloud_Data	LibraryPrepKitName	Must be "IlluminaProteinPrep9.5k"
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 (Plasma/Serum)

Cloud (Plasma/Serum)

CSF

MultiMatrix

For additional information, refer to the Illumina BioInsight Platform Sample Sheet documentation.