Extended Data Fig. 2: Benchmarking Scout against other XL-MS search engines for intra-link identifications.
Number of identified intra-linked CSMs, ResPairs and intra-linked proteins and the empirical FDR using a small (540 proteins, upper panel) or large database (4,000 proteins, lower panel). Framed bars mark post-hoc aggregated results, that is when CSMs were aggregated to unique ResPairs or unique ResPairs to unique intra-linked proteins, in case these levels were not directly reported by the software. XlinkX results were obtained with default settings (see Methods) and no further post-processing. The blue bar shows true positive, the yellow bar false positive identifications from which the empirical FDR (shown above the bars) was calculated.
