Fig. 2.

Search score distributions for the variant (red) and wildtype (green) peptides identified with FDR < 0. 05 in the SW480 data set. A, Under regular FDR estimation, an apparent shift to the low-score end was observed in the distribution for variant identifications as compared with that for the wild-type identifications. B, Naïve separate estimation reduced the bias to a certain degree. C,The new refined separate FDR estimation approach proposed in this study further improved the quality of variant peptide identifications.