Fig. 4.

XL plug-in performance. A, Total processing time to generate a set of crosslinked peptide candidates is measured as a function of increasing the number of proteins in the root library, using an E-score threshold of 0.3. in the library prefiltering. B, Total processing time as a function of E-score threshold, with a database size of 51 proteins (BSA + 50 random E. coli proteins). C, The number of total results (identified peptides of all types) as a function of E-score threshold for search configuration as in (B). D, The same data as in (C), with the application of results filters: a threshold for crosslink score (-ln transformed E′ score of 13) and a threshold for component linear peptide score (-ln transformed E′ score of 10).