Fig. 2: Analyzing N-glycopeptides using pGlyco3.
From: Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3
a, Accuracy comparison using 15N-/13C-labeled fission yeast data (PXD005565). The element-level error rate (incorrect number of N or C elements) of the identified glycopeptides was tested via the 15N-/13C-labeled precursor signals. The potential glycan-level error rate was tested by the percentage of NeuAc-containing GPSMs and the potential peptide-level error rate was tested via GPSMs with mouse peptides. pGlyco3 shows the best accuracies at all three levels. b, Search speed comparison under N-glycopeptide data of five mouse tissues (Liu et al.8, 30 RAW files in total). The algorithm part (searching mascot generic format (MGF) files) of pGlyco3 is 5-40 times faster than that of the other tools, even when using larger glycan databases. MSFragger kernel takes only 106 min, but its postprocessing modules use too much time. c, Validation of pGlycoSite using the PRM of the synthetic double-site N-glycopeptide ‘NVN[H(5)N(4)]ISYTVN[H(5)N(4)]DSFFPQRPQK.’ d, Validation of pGlycoSite using double-site N-glycopeptides ‘K.THTN(272)ISESHPN(279)ATF.S’ of IGHM digested with chymotrypsin and trypsin. The SSGL results were validated using Glu-C and trypsin digestion with PRM. The example spectra are annotated in Supplementary Fig. 10. All annotated GPSMs for these 12 localized glycans are shown in Supplementary Data.
