Fig. 2
From: ECL 3.0: a sensitive peptide identification tool for cross-linking mass spectrometry data analysis
Performance comparison results. a, b The performance of ECL 3.0, Kojak, and pLink 2 in non-cleavable data analysis using three technical replicates (R1, R2, and R3) of a synthetic peptide sample (PXD014337) [15], which uses disuccinimidyl suberate (DSS) as the cross-linker. The number of cross-linked peptide spectrum matches (CSMs), the number of unique cross-linked peptides and precision (TP/TP+FP) were calculated for each software tool. ECL 3.0 identified over twice as many results as other tools in the CSMs number and similar results in the unique cross-linked peptides. Using the (one-sided) Fisher’s exact test, the p-value indicated that ECL 3.0 has significantly better precision than Kojak and has similar precision as pLink 2. c, d Identification results of ECL 3.0, MaxLynx, and MeroX using cleavable data. Results using two different cross-linkers (disuccinimidyl sulfoxide (DSSO) and disuccinimidyl dibutyric urea (DSBU)) are shown. ECL 3.0 identified over twice as many results as other tools in CSMs numbers and similar results in the unique cross-linked peptides. The precision of these three tools does not have a significant difference according to the (one-sided) Fisher’s exact test (p-value)