title: Classification of Tandem Mass Spectra for Identification of N- and O-linked Glycopeptides.
abstract: Analysis of intact glycopeptides by mass spectrometry is essential to determining the microheterogeneity of protein glycosylation. Higher-energy collisional dissociation (HCD) fragmentation of glycopeptides generates mono- or disaccharide ions called oxonium ions that carry information about the structure of the fragmented glycans. Here, we investigated the link between glycan structures and the intensity of oxonium ions in the spectra of glycopeptides and utilized this information to improve the identification of glycopeptides in biological samples. Tandem spectra of glycopeptides from fetuin, glycophorin A, ovalbumin and gp120 tryptic digests were used to build a spectral database of N- and O-linked glycopeptides. Logistic regression was applied to this database to develop model to distinguish between the spectra of N- and O-linked glycopeptides. Remarkably, the developed model was found to reliably distinguish between the N- and O-linked glycopeptides using the spectral features of the oxonium ions using verification spectral set. Finally, the performance of the developed predictive model was evaluated in HILIC enriched glycopeptides extracted from human serum. The results showed that pre-classification of tandem spectra based on their glycosylation type improved the identification of N-linked glycopeptides. The developed model facilitates interpretation of tandem mass spectrometry data for assignment of glycopeptides.
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.
authors.forename: Shadi
authors.initials: S
authors.lastname: Toghi Eshghi
authors.affiliation: Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA.
authors.forename: Weiming
authors.initials: W
authors.lastname: Yang
authors.affiliation: Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA.
authors.forename: Yingwei
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA.
authors.forename: Punit
authors.initials: P
authors.lastname: Shah
authors.affiliation: Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA.
authors.forename: Shisheng
authors.initials: S
authors.lastname: Sun
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.
authors.forename: Xingde
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D002236:Carbohydrate Conformation; D016208:Databases, Factual; D006020:Glycopeptides / Q000032:analysis* / Q000737:chemistry*; D006021:Glycophorins / Q000032:analysis / Q000737:chemistry; D006031:Glycosylation; D006801:Humans; D016015:Logistic Models; D011134:Polysaccharides / Q000032:analysis / Q000737:chemistry; D044967:Serum / Q000737:chemistry; D013237:Stereoisomerism; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D006020:Glycopeptides; D006021:Glycophorins; D011134:Polysaccharides