WEBVTT

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For SSH or terminal users: add --terminal and --run to the same setup command.

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Choose a quantification matrix, raw DIA, raw DDA or an existing run. Enter accepts the displayed default.

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Provide the protein matrix and sample table. The same inputs work in browser setup.

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A matching FASTA can supply missing gene symbols. This synthetic table already includes gene names.

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Optionally add service quantification to benchmark shared proteins and detection gains or losses.

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Confirm independence only when samples represent different patients or biological replicates.

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Setup saves the configuration, reports the planned comparisons, and starts the real analysis.

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Later, from any working directory, continue by supplying the same project folder.

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Setup saves the configuration, reports the planned comparisons, and starts the real analysis.

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Checksums and recorded inputs match. Completed results are reused without recomputation.

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Open START_HERE.html for results and MATRICES.html for clear CSV and TSV links.