title: Identification of Glycopeptides with Multiple Hydroxylysine O-Glycosylation Sites by Tandem Mass Spectrometry.
abstract: Glycosylation is one of the most common post-translational modifications in proteins, existing in ~50% of mammalian proteins. Several research groups have demonstrated that mass spectrometry is an efficient technique for glycopeptide identification; however, this problem is still challenging because of the enormous diversity of glycan structures and the microheterogeneity of glycans. In addition, a glycopeptide may contain multiple glycosylation sites, making the problem complex. Current software tools often fail to identify glycopeptides with multiple glycosylation sites, and hence we present GlycoMID, a graph-based spectral alignment algorithm that can identify glycopeptides with multiple hydroxylysine O-glycosylation sites by tandem mass spectra. GlycoMID was tested on mass spectrometry data sets of the bovine collagen α-(II) chain protein, and experimental results showed that it identified more glycopeptide-spectrum matches than other existing tools, including many glycopeptides with two glycosylation sites.
authors.affiliation: Department of Computer Science, City University of Hong Kong , Kowloon, Hong Kong.|Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis , Indianapolis, Indiana 46202, United States.
authors.forename: Yanlin
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: School of Informatics and Computing, Indiana University Bloomington , Bloomington, Indiana 47405, United States.
authors.forename: Chuan-Yih
authors.initials: CY
authors.lastname: Yu
authors.affiliation: Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409, United States.
authors.forename: Ehwang
authors.initials: E
authors.lastname: Song
authors.affiliation: Department of Computer Science, City University of Hong Kong , Kowloon, Hong Kong.
authors.forename: Shuai Cheng
authors.initials: SC
authors.lastname: Li
authors.affiliation: Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409, United States.
authors.forename: Yehia
authors.initials: Y
authors.lastname: Mechref
authors.affiliation: School of Informatics and Computing, Indiana University Bloomington , Bloomington, Indiana 47405, United States.
authors.forename: Haixu
authors.initials: H
authors.lastname: Tang
authors.affiliation: Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis , Indianapolis, Indiana 46202, United States.|Center for Computational Biology and Bioinformatics, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D000818:Animals; D002356:Cartilage / Q000737:chemistry; D002417:Cattle; D024043:Collagen Type II / Q000378:metabolism; D006020:Glycopeptides / Q000032:analysis* / Q000378:metabolism*; D006031:Glycosylation; D006901:Hydroxylysine / Q000378:metabolism*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D024043:Collagen Type II; D006020:Glycopeptides; D006901:Hydroxylysine
keywords: Alignment algorithm; MS/MS spectra; O-linked glycosylation; collagen α-(II) chain; glycopeptide identification