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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Browse files on the computer running the analysis. Select your protein quantification table.

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Discover samples from the matrix. Cards start in Unassigned; a sample table can optionally prefill conditions.

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Drag cards into your conditions. Add or rename columns, or use the dropdown on each card.

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Unassigned cards are excluded. Drag the sample back into Control to include it in this analysis.

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Keep all-versus-all comparisons and confirm independent samples. An optional service matrix adds detection gains and losses.

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The check finds six samples, three condition pairs, ten protein groups and ten unambiguous genes.

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Save configuration and check writes config/run.json. Now start the saved analysis.

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The real synthetic analysis is complete. Open results for comparisons, QC and the service benchmark.

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The matrix catalogue links directly to CSV and TSV files for proteins, genes and transformed quantities.

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Run / continue verifies completed outputs. Unchanged results are reused without repeating the analysis.