# 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](https://help.connected.illumina.com/illumina-connected-analytics) or [Base Space Sequence Hub](https://help.connected.illumina.com/basespace-sequence-hub), or executed locally using a phase 4 [DRAGEN Server](https://help.connected.illumina.com/dragen).

## Sample Sheet Fields

This is a non comprehensive list of fields.

<table><thead><tr><th width="260">Section</th><th>Field</th><th>Value</th></tr></thead><tbody><tr><td>Header</td><td>FileFormatVersion</td><td>Must be "2"</td></tr><tr><td>Header</td><td>InstrumentPlatform</td><td>Must be "NovaSeqXSeries" or "NovaSeq"</td></tr><tr><td>Header</td><td>RunName</td><td>User-provided value</td></tr><tr><td>Header</td><td>RunDescription</td><td>User-provided value (optional)</td></tr><tr><td>Reads</td><td>Read1Cycle</td><td>15</td></tr><tr><td>Reads</td><td>Index1Cycle</td><td>10</td></tr><tr><td>Reads</td><td>Index2Cycle</td><td>10</td></tr><tr><td>Sequencing_Settings</td><td>LibraryPrepKits</td><td>Must be "IlluminaProteinPrep9.5k"</td></tr><tr><td>BCLConvert_Data</td><td>Sample_ID</td><td>Alphanumeric name up to 100 characters. Letters, numbers, dashes only (or any combination of letters, numbers, and dashes)</td></tr><tr><td>BCLConvert_Data</td><td>Index</td><td>i7 index sequence, including A, C, T or G letters, 10 nucleotides long</td></tr><tr><td>BCLConvert_Data</td><td>Index2</td><td>i5 index sequence, including A, C, T or G letters, 10 nucleotides long</td></tr><tr><td>BCLConvert_Data</td><td>Lane</td><td>Lane value (shall be a number between 1 and 8 inclusive) (optional if instrument is NovaSeq 6k, required if instrument is NovaSeq X)</td></tr><tr><td>Cloud_Proteomics_Settings (Cloud Analysis) or Proteomics_Settings (Local Analysis)</td><td>SoftwareVersion</td><td>Three-digit version of SW used in secondary analysis. For example, "2.3.0"</td></tr><tr><td>Cloud_Proteomics_Settings (Cloud Analysis) or Proteomics_Settings (Local Analysis)</td><td>StartsFromFastq</td><td>Must be "false"</td></tr><tr><td>Cloud_Proteomics_Settings (Cloud Analysis) or Proteomics_Settings (Local Analysis)</td><td>output_file_prefix</td><td>User-provided prefix</td></tr><tr><td>Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)</td><td>Sample_ID</td><td>Alphanumeric name up to 100 characters. Letters, numbers, dashes only (or any combination of letters, numbers, and dashes)</td></tr><tr><td>Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)</td><td>PlateBarcode</td><td>For each plate, associated plate barcode</td></tr><tr><td>Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)</td><td>MatrixTubeBarcode</td><td>For each plate, associated matrix tube barcode</td></tr><tr><td>Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)</td><td>BatchID</td><td>For each plate, user-provided batchID</td></tr><tr><td>Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)</td><td>InputType</td><td>For each sample, associated input type.<br>Examples: Plasma_Calibrator, Plasma_QC, Plasma, Serum_Calibrator, Serum_ QC, Serum, Blank</td></tr><tr><td>Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)</td><td>ControlID</td><td>ID of the calibrator, QC, and blank lot (applied to controls only).</td></tr><tr><td>Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)</td><td>ProbePlate</td><td>For each plate, probe plate lot number, from library prep</td></tr><tr><td>Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)</td><td>SOMAmerBeadPlate</td><td>For each plate, SOMAmer Bead Plate lot number, from library prep</td></tr><tr><td>Cloud_Proteomics_Data (Cloud Analysis) or Proteomics_Data (Local Analysis)</td><td>WellPosition</td><td>For each sample, well position (A1-H12)</td></tr><tr><td>Cloud_Settings</td><td>GeneratedVersion</td><td>Software version of the BSSH Run Planner tool that generated the sample sheet</td></tr><tr><td>Cloud_Settings</td><td>Cloud_Proteomics_Pipeline (Cloud Only)</td><td><p>ICA Path to the proteomics pipeline.<br>For example:</p><pre class="language-shell"><code class="lang-shell">urn:ilmn:ica:pipeline:896aa1df-0412-45db-814e-4683b3215203#DRAGEN_Protein_Quantification_2-2-2
</code></pre></td></tr><tr><td>Cloud_Data</td><td>Sample_ID</td><td>Alphanumeric name up to 100 characters. Letters, numbers, dashes only (or any combination of letters, numbers, and dashes)</td></tr><tr><td>Cloud_Data</td><td>ProjectName</td><td>(optional) user-provided plate-specific project</td></tr><tr><td>Cloud_Data</td><td>LibraryName</td><td>For each sample, must be &#x3C;Sample_ID>_&#x3C;index><em>_</em>&#x3C;index2></td></tr><tr><td>Cloud_Data</td><td>LibraryPrepKitName</td><td>Must be "IlluminaProteinPrep9.5k"</td></tr><tr><td>Cloud_Data</td><td>IndexAdapterKitName</td><td>Must be "IlluminaDNARNAUDISetABCDTagmentation_Proteomics"</td></tr></tbody></table>

## Samplesheet Examples

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

### Local

{% file src="<https://958780164-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FnyQb4WG1K4VQZKovLv5v%2Fuploads%2Fgit-blob-7858adc2d7ff6c6beb82a2eddc0ee79e4ad203c7%2FSampleSheet_NVSQ6000_local_v2.3.0.csv?alt=media>" %}
Example NovaSeq 6000 samplesheet for local analysis
{% endfile %}

{% file src="<https://958780164-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FnyQb4WG1K4VQZKovLv5v%2Fuploads%2Fgit-blob-f725fee78f1ccd6963d7d72bbc3c6742aea0b0b1%2FSampleSheet_NVSQX_local_v2.3.0.csv?alt=media>" %}
Example NovaSeq X samplesheet for local analysis
{% endfile %}

### Cloud

{% file src="<https://958780164-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FnyQb4WG1K4VQZKovLv5v%2Fuploads%2Fgit-blob-f3ef1f27e73d77e524cbe4b1dd597febc0ed0b7a%2FSampleSheet_NVSQ6000_autolaunch_v2.3.0.csv?alt=media>" %}
Example NovaSeq 6000 samplesheet for autolaunch analysis
{% endfile %}

{% file src="<https://958780164-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FnyQb4WG1K4VQZKovLv5v%2Fuploads%2Fgit-blob-b0e175f7aad5293a88aef6709e36cb4e3df73845%2FSampleSheet_NVSQX_autolaunch_v2.3.0.csv?alt=media>" %}
Example NovaSeq X samplesheet for autolaunch analysis
{% endfile %}

For additional information, refer to the ICS [Samplesheet documentation](https://help.connected.illumina.com/run-set-up/overview).