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protein-inference

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Groups proteins from peptide identifications and controls protein-level FDR, framing inference as a chosen explanation (parsimony or a probability model) of underdetermined peptide evidence rather than a measurement. Reports protein GROUPS (proteins indistinguishable by observed peptides) with a leading protein, not flat lists. Covers shared-vs-unique peptides, indistinguishable/subsumable proteins, parsimony vs probabilistic (ProteinProphet, EPIFANY) vs razor inference, picked-protein and picked-group FDR, and why the two-peptide rule is wrong. Use when resolving which proteins are present from a peptide list, building protein groups, or estimating protein-level FDR. PSM/peptide FDR and search engines are peptide-identification; razor-vs-unique quant consequences are quantification; isoform/proteoform resolution is top-down and out of scope.

When to use

• resolving which proteins are present from a peptide list
• building protein groups
• estimating protein-level FDR
• parsimony vs probabilistic inference
• picked-protein and picked-group FDR
• shared-vs-unique peptides
• indistinguishable/subsumable proteins

When not to use

• PSM/peptide FDR
• search engines
• razor-vs-unique quant consequences
• isoform/proteoform resolution
• top-down proteomics

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