Fig. 2.

Overview of protein group-level FDR estimation methods, its constituent stages, and the available options at each stage.A, a protein group-level FDR estimation method takes a list of PSMs and chooses one of the available options at each of the three stages: protein grouping, handling of shared peptides, and target-decoy strategy. B, subset grouping combines proteins into groups if the peptides of one protein (ProteinA) form a subset of the peptides of another protein (ProteinB). C, the razor peptide approach assigns a shared peptide to the protein group with the most unique identifications. D, the picked target-decoy strategy performs a target-decoy competition on protein level, retaining only the best scoring protein out of each target-decoy pair. FDR, false discovery rate; PSM, peptide-spectrum match.