Fig. 4.

The picked group target-decoy strategy handles competition of protein groups but does not resolve the issues of the state-of-the-art methods.A, the picked group TDS extends the picked TDS to handle protein groups. Protein groups are sorted by decreasing identification score. Going down the sorted list, all groups containing ≥1 counterpart of one of the leading proteins of the current group are eliminated. B, protein group-level FDR calibration plots using entrapment searches for two methods using the picked group TDS. The region between y = 1.5× and y = 0.67× (dashed lines) was deemed well-calibrated. The Razor + Picked group method produces anticonservative FDR estimates, whereas Discard + Picked group has reduced sensitivity. C, the results in panel (B) can be explained by this example. Low-confident, incorrect peptides 2-4 prevent proteins A and B from being grouped. Razor peptides (rS) lead to anticonservative estimates due to the erroneous assignment of true positive peptide 1 to the incorrect protein B. If shared peptides are discarded (dS), the high-confident peptide 1 is discarded, leading to reduced sensitivity as neither protein is identified. D, schematic summary of the methods evaluated in panel (B). FDR, false discovery rate; TDS, target-decoy strategy.