Fig. 7.

Results from the analysis of the synthetic peptides data set at a 5% FDR cutoff. All three replicates R1, R2 and R3 are shown. The blue bars show the number of valid CSMs/cross-links and the red bars on the negative y axis show the number of false-positive identifications. All data except for OpenPepXL was taken from Beveridge et al. (25). xQuest was omitted because it was not considered in that publication. A, Number of reported CSMs. The exact numbers are in supplemental Table S4. B, Number of identified URPs. The exact numbers are in supplemental Table S5.