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. Author manuscript; available in PMC: 2015 Dec 14.
Published in final edited form as: Nat Protoc. 2011 Feb 10;6(3):253–269. doi: 10.1038/nprot.2010.176

Figure 7.

Figure 7

Glycopeptide MS/MS ions search process. (a) y-ion series and X0,2 (squares with diagonal lines) of N-glycan with intact peptide backbones (peptide sequence NEEYNK) are calculated. (b) Both b-ions (b1–b5) and y-ions (y1–y5) series of N-peptide (peptide NEEYNK) along with an attached GlcNAc (N-acetylglucosamine; shown as white squares) at the glycosylation site are calculated. (c) The ions are merged to generate the theoretical spectrum. (d) Experimental spectrum is cumulative intensity–normalized and matched with the theoretical spectrum. Each match produces a paired metric of score and probability of random match for both glycan moiety (ions in a) and glycopeptide (ions from both a and b).