Fig. 5: Performance of Scout on published XL-MS benchmarking datasets from Matzinger et al. using synthetic peptides and Lenz et al. using fractionated E. coli lysate.
a, Overlap of ResPairs identified by Scout and MSAnnika and the true FDR of Scout-specific (left), shared (middle) and MSAnnika-specific (right) identifications using the DSSO main library from Matzinger et al.10 and our standard search parameters, which are similar to the ones reported in the original publication. b, Scout’s true-positive (blue) and false-positive (yellow) ResPair-level identifications from the DSSO main library spiked 1:5 into tryptic HEK peptides when searched on increasingly large databases. The software-defined FDR cutoff was set to 1%; empirical FDR and operating times are indicated above the bars. c, Overlap of PPI-level identifications from Scout (left) and xiSEARCH (right) using the PPI benchmarking dataset by Lenz et al.12 and a 1% separate software-defined FDR cutoff on the PPI level. Scout was operated with standard parameters and xiSEARCH identifications were retrieved from the original publication. Empirical FDR was determined using the procedure suggested in the original publication.12 d, Performance of Scout and xiSEARCH in identifying intra- and interprotein CSMs, interprotein CSMs only, interprotein PepPairs (peptide pairs) and PPIs when setting an all-level software-defined FDR cutoff of 1%. Scout was operated with standard parameters and xiSEARCH identifications were retrieved from the original publication. The empirical FDR was calculated as described by Lenz et al. and is indicated above the bars.
