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. 2022 Apr 7;13:1900. doi: 10.1038/s41467-022-29530-y

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a Tandem mass spectrum example of glycopeptide “MHLNGSNVQVLHRLTIR- Hex(9)HexNAc(2)” (top) and the in silico deglycosylation result of the spectrum (bottom). Blue: b ions of peptide; red: y ions of peptide; purple: b/y ions with HexNAc residue; green: B ions; orange: Y ions of glycan with intact peptide backbone attached. b Fragmentation patterns of the peptide backbone “MHLNGSNVQVLHR” modified by different glycans and/or with different precursor charge states in six glycopeptide spectra. c Distributions of similarities between the peptide fragmentation pattern in each peptide-spectrum match (PSM) from in silico deglycosylation and the averaged pattern of the corresponding peptide backbone. The quartiles of the distributions are indicated by inner dashed lines. The medians and the spectrum numbers are labeled in the plot. The similarity value of 0.9 is indicated by an outer dashed line. Source data are provided as a Source Data file. d Distribution of matching scores for the peptide backbone “MHLNGSNVQVLHR” with glycopeptide spectra across the entire data acquisition time window. Specifically note that the score of PSM from in silico deglycosylation was re-calculated with the consideration of peptide fragmentation pattern. Inset: The score distribution of PSMs after score filtration and core structure peak matching in spectrum expansion. The dashed line indicates PSM score threshold of 52.75 derived from the e-value filtration method. Green box: target PSMs obtained by in silico deglycosylation; blue circle: target PSMs obtained in spectrum expansion; orange cross: decoy PSMs generated in spectrum expansion for quality control. e Comparison of identifications before (pale blue) and after (blue) spectrum expansion. The glycan part was matched with the GlyTouCan database to obtain glycopeptide-spectrum match (GPSM, PSM with definite glycan composition) identifications. Site-specific glycans were classified into three categories based on the glycan composition: truncated glycans (Hex(<4)HexNAc(<3)Fuc(<2)), oligo-mannose glycans (Hex(>3)HexNAc(2)Fuc(<2)) and complex/hybrid glycans. f Performance comparison between Glyco-Decipher and MSFragger (V3.1.1) in open search mode. Green: the consistently identified spectra. Orange: the spectra commonly identified, but matched to different peptides. Gray: spectra specifically matched by MSFragger.