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peptide-identification

separate

Peptide-spectrum matching from MS/MS with target-decoy FDR control, framing identification confidence as a property of a ranked list (q-value/PEP) rather than a raw engine score (XCorr, hyperscore, Andromeda, SpecEValue). Covers sequence-database search engines (Comet, MS-GF+, MSFragger, Sage, MaxQuant, MetaMorpheus), concatenated vs separate target-decoy competition, PEP vs q-value, the multi-level FDR cascade, open/mass-tolerant search, rescoring (Percolator, mokapot, MS2Rescore), and pyOpenMS SimpleSearchEngineAlgorithm + FalseDiscoveryRate. Use when identifying peptides from tandem mass spectra and deciding what FDR threshold to act on. Protein grouping and protein-level FDR are protein-inference; PTM site localization is ptm-analysis; DIA peptide-centric scoring is dia-analysis; intensity quant is quantification.

When to use

• spectrum-to-peptide matching
• PSM/peptide-level FDR
• target-decoy competition
• q-value and PEP calculation
• open/mass-tolerant search
• rescoring with Percolator or mokapot
• sequence-database search engines

When not to use

• protein grouping
• protein-level FDR
• PTM site localization
• DIA peptide-centric scoring
• intensity quantification
• mzML/raw loading

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