title: A review of methods for interpretation of glycopeptide tandem mass spectral data.
abstract: Despite the publication of several software tools for analysis of glycopeptide tandem mass spectra, there remains a lack of consensus regarding the most effective and appropriate methods. In part, this reflects problems with applying standard methods for proteomics database searching and false discovery rate calculation. While the analysis of small post-translational modifications (PTMs) may be regarded as an extension of proteomics database searching, glycosylation requires specialized approaches. This is because glycans are large and heterogeneous by nature, causing glycopeptides to exist as multiple glycosylated variants. Thus, the mass of the peptide cannot be calculated directly from that of the intact glycopeptide. In addition, the chemical nature of the glycan strongly influences product ion patterns observed for glycopeptides. As a result, glycopeptidomics requires specialized bioinformatics methods. We summarize the recent progress towards a consensus for effective glycopeptide tandem mass spectrometric analysis.
authors.affiliation: Center for Biomedical Mass Spectrometry, Boston University, Boston, MA, USA.|Bioinformatics Program, Boston University, Boston, MA, USA.
authors.forename: Han
authors.initials: H
authors.lastname: Hu
authors.affiliation: Department of Biochemistry, Boston University, Medical Campus, 670 Albany St., Rm. 509, Boston, MA, 02118, USA.|Center for Biomedical Mass Spectrometry, Boston University, Boston, MA, USA.
authors.forename: Kshitij
authors.initials: K
authors.lastname: Khatri
authors.affiliation: Center for Biomedical Mass Spectrometry, Boston University, Boston, MA, USA.|Bioinformatics Program, Boston University, Boston, MA, USA.
authors.forename: Joshua
authors.initials: J
authors.lastname: Klein
authors.affiliation: Department of Biochemistry, Boston University, Medical Campus, 670 Albany St., Rm. 509, Boston, MA, 02118, USA.|Center for Biomedical Mass Spectrometry, Boston University, Boston, MA, USA.
authors.forename: Nancy
authors.initials: N
authors.lastname: Leymarie
authors.affiliation: Department of Biochemistry, Boston University, Medical Campus, 670 Albany St., Rm. 509, Boston, MA, 02118, USA. jzaia@bu.edu.|Center for Biomedical Mass Spectrometry, Boston University, Boston, MA, USA. jzaia@bu.edu.|Bioinformatics Program, Boston University, Boston, MA, USA. jzaia@bu.edu.
authors.forename: Joseph
authors.initials: J
authors.lastname: Zaia
mesh_terms: D019295:Computational Biology / Q000379:methods*; D006023:Glycoproteins / Q000737:chemistry*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D006023:Glycoproteins
keywords: Bioinformatics; Collisional activated dissociation; Electron transfer dissociation; Glycopeptide; Glycoprotein; Mass spectrometry; Software tool; Tandem mass spectrometry