Prerequisites

Before setting up and running the Illumina Protein Prep End-to-End (E2E) solution, ensure that the necessary software, tools, and configurations are in place. These prerequisites can vary depending on the environment used to run the secondary analysis (e.g., via cloud or locally). Follow the steps below to configure instrument and software appropriately.

Instrument Software Prerequisites

NovaSeq 6000

• Control Software (v1.8.0 or later)

• Illumina Protein Prep custom recipe XML file installed on the sequencing instrument. Illumina provides the file.

  • Illumina Protein Prep NovaSeq 6000 v1.0.xml

• Illumina Protein Prep Automation System output files, depending on the sequencing set up.

  • NovaSeq 6000 (S4 flow cell)

    • Recommended: Two IPPAS output files / 192 reactions

NovaSeq X Series

• Control Software (v1.3.0 or later)

• Illumina Protein Prep custom recipe XML file installed on the sequencing instrument. Illumina provides the file.

  • Illumina Protein Prep NovaSeq X 10B v2.0.xml

  • Illumina Protein Prep NovaSeq X 25B 100 cycle v1.0.xml

  • Illumina Protein Prep NovaSeq X 25B 200 cycle v1.0.xml (upon request only)

  • Illumina Protein Prep NovaSeq X 25B 300 cycle v1.0.xml (upon request only)

• Illumina Protein Prep Automation System output files, depending on the sequencing set up.

  • NovaSeq X (10B flow cell)

    • Recommended: Two IPPAS output files / 192 reactions

  • NovaSeq X (25B flow cell)

    • Recommended: Four IPPAS output files / 384 reactions

Cloud Secondary Analysis Prerequisites

• BaseSpace Sequence Hub (BSSH) or Illumina Connected Analytics (ICA) account.

  • All BSSH and ICA subscriptions come with access to the DRAGEN Protein Quantification application.

  • [ICA subscribers] To view results in ICA, select ICA Run Storage in BSSH Workgroup Settings.

  • For more information about which subscription is best for your use case, contact your FAS or TAM.

• For information on registering a BaseSpace Sequence Hub or Illumina Connected Analytics account, refer to the account management documentation or connect with an Illumina Account Manager.

Note: When performing analysis with more than one plate, each plate must have their own unique plate barcode value.

Local Secondary Analysis Prerequisites

• DRAGEN Phase 4 server with the following space recommendations:

  • NovaSeq6000, S4 flow cell: ≥ 10GB

  • NovaSeqX, 10B flow cell: ≥ 20 GB

  • NovaSeqX, 25B flow cell: ≥ 35 GB

• External storage drive mounted to a DRAGEN server. This drive must be mounted through a network share and support CIFS/SMB protocols. Read and write permissions are required to use this network share. For more information, please refer to the Illumina Protein Prep Product Documentation (document # 200045446).