PSM Desk — is this proteomics ID list reportable?

Paste the identification export of one finished LC-MS/MS proteomics run - a PSM, peptide or protein table from MaxQuant, FragPipe, Proteome Discoverer, DIA-NN or any other search engine - together with the search parameters, and find out whether the identifications can be reported. A free in-browser read does the arithmetic first: it counts your own decoys and recomputes the false-discovery rate both ways (D/T and 2D/(T+D)), checks it against the threshold you claimed, applies the enzyme rule with its proline exception to every peptide, takes the median precursor mass error, counts the protein groups resting on a single peptide, matches the contaminant classes, measures each quantitation column's missingness, and answers a thirty-item reporting checklist in three states. Then three lanes work the run: the identification review, the quantification review, and the methods and reporting pack. Derived from the SkillSafe skill @k-dense-ai/pyopenms (mass spectrometry analysis: feature detection, peptide identification, protein quantification, LC-MS/MS pipelines) - a derived work, not a republication of that skill.

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