Protocol

This section describes the Illumina Protein Prep protocol.

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Review the planned complete sequencing workflow, from sample through analysis, to ensure compatibility of products and experiment parameters.

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Before proceeding, confirm the kit contents and make sure that you have the required components, equipment, and consumables. This protocol requires library prep reagents and index adapters. Index adapter plates are ordered separately. Refer to Product Contents for details.

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If you are combining two plates for sequencing, each sample ID must be unique per sample sheet.

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[NovaSeq 6000] Index sequences must be unique within a sequencing run. Avoid combining plates that contain the same index sequences.

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[NovaSeq X Series] Index sequences can be repeated on separate lanes. Make sure that samples are designated appropriately to lanes in the sample sheet.

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The Illumina Protein Prep protocol is time sensitive. Unless a safe stopping point is specified, proceed immediately to the next step. The protocol has safe stopping points at the end of the following steps:

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Proteomics Assay (Automated)

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Proteomics Assay QC (Optional)

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Index PCR

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Pooled Library Cleanup

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Dilute Libraries to the Starting Concentration

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Follow the protocol steps in the order shown, using the specified volumes and incubation parameters. Changes in volumes, timing, or steps can result in failure of assay quality control metrics.

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Perform all steps, including centrifuge steps, at room temperature.

Illumina Lab Automation Software Solution

Run all automated assay workflows using the Illumina Lab Automation Software Solution (ILASS) touch screen or system computer peripherals, as follows.

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Follow the prompts to load consumables, confirm deck layout, and complete steps. To proceed, select Next.

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When prompted to check the waste containers, empty the containers.

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Access the options to Abort or Pause the run from the lower-right corner of the screen.

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Abort Setup terminates the run setup process.

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Abort Batch terminates a run that is in progress.

The ILASS requires confirmation of the request to abort the run before initiating termination.

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Only select Continue when prompted to do so by the main ILASS window.

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You must select Execute Run to initiate the automation scripts.

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The ILASS automatically closes login sessions that have been idle for 10 minutes. You must log in again to resume the workflow or to pause or abort a workflow step.