Fig. 2: Comparison of pLink, StavroX and Xi performance based on the crosslinked peptide library. | Nature Communications

Fig. 2: Comparison of pLink, StavroX and Xi performance based on the crosslinked peptide library.

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

Fig. 2

a number of CSMs that correspond to correct (black) and incorrect (grey) crosslinks identified by three search algorithms with incorporated FDR estimation. Results were filtered to an estimated 5% CSM-FDR, and the calculated FDR is given for each algorithm. b Agreement of correct (left) and incorrect CSMs (right) between pLink, StavroX and Xi for one technical repeat. c Number of correct unique crosslinks (black) and incorrect crosslinks (grey) identified with an estimated CSM-FDR of 5%. d Overlap of correct (left) and incorrect crosslinks (right) for one technical repeat. Values for figures a and c are given in Supplementary Tables 2 and 3, and average values ± standard deviation are shown on the stacked bar plots (rounded to the closest whole number). All results files can be found in Supplementary Data 1. Error bars correspond to the standard deviation between technical replicates (n = 3).

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