WEBVTT

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Launch with: fun_proteomics setup --project /path/to/my-study. One folder holds settings and results.

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Choose DIA-PASEF and scan your raw-data folder. This demo contains synthetic acquisition metadata only.

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Drag acquisition cards into Control or Treatment. Each card also has a condition dropdown.

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Move a card back to Unassigned to exclude it. Here we put it back into Control before saving.

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Confirm independent biological replicates. Choose the matching target-only FASTA with gene annotations.

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Check inputs before running. Two conditions give one comparison at protein and available gene levels.

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The saved configuration and CSV/TSV assignment audit preserve these groups. With real spectra and installed tools, Run / continue starts the Nextflow workflow.

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This recording stops after setup. No spectrum search or biological result is claimed for synthetic acquisitions.