Fig. 2.

Characteristics of conflicting matches. A, Fraction of conflicting (deamidation: D, methylation: M, carbamylation: C) PSMs among all decoy database hits from a standard search at PSM FDR 0.01. Decoy database hits that were explained by conflicting peptides in more than one of the searches are denoted as “mu” (multiple matches). Cumulative LScore (B) and intensity (C) distribution of decoy database hits from a standard search at no PSM FDR threshold. The population of decoy database hits was split into hits that were caused by conflicting peptides and other hits. p values were derived from the Kolmogorov-Smirnov test.