WEBVTT

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Choose your output folder. For raw BAF, first install the reader with fun_proteomics install --baf.

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Drag acquisitions into conditions or use each card’s dropdown. Give technical injections the same biological sample ID so they are quantified together.

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Select paired comparisons when each donor contributes multiple conditions. Four conditions produce six comparisons.

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Enter the donor ID on every card. Technical injections do not increase the number of biological replicates.

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Choose a target/decoy FASTA with gene annotations and your registered search tools. Add a service matrix to benchmark detections.

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Check: sixteen technical injections become eight biological samples. Donor pairing is preserved for all six contrasts.

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Settings are saved. With real acquisitions, Run / continue starts conversion, search, LFQ and reporting. Later use --continue with this folder.

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This is a setup demonstration only. Placeholder files contain no spectra and are never searched.