Workflow of pMatchGlyco. (A) Deglycosylated peptide identification through other search engines, e.g., pFind. The letter ‘J’ represents Asn residue within a peptide sequence sequon of Asn-Xaa-Ser/Thr/Cys, where Xaa can be any amino acid except Pro. (B) Spectral library construction. Decoy spectra are generated for FDR estimation. (C) Glycopeptide spectrum with diagnostic peak with m/z of 138.054953 Da. The purple peaks represent oxonium ions. (D) Deletion of oxonium ions from the query spectrum in (C). (E-F) Selection of candidate library spectra for each glycopeptide spectrum. (G) Scoring the matches between query spectrum and candidate library spectra and reporting the best match.