Fig. 7: Assessment of algorithms for the identification of peptides crosslinked with cleavable reagents DSBU and DSSO. | Nature Communications

Fig. 7: Assessment of algorithms for the identification of peptides crosslinked with cleavable reagents DSBU and DSSO.

From: A synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes

Fig. 7

a, b Data were collected using MS2 method with stepped collision energy, analysed using MeroX (in Rise and RiseUP mode) and XlinkX, with data filtered to an estimated 5% FDR (a) and 1% FDR (b), with no additional score cut-off values employed. c Data for DSSO-crosslinked peptides were collected using HCD-, MS3- and ETD-based methods, and analysed using XlinkX with the recommended score cut-off values of 45 and 4 for crosslink score and Δcrosslink score, respectively. Values are given in Supplementary Tables 810.

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