title: GlycoPep grader: a web-based utility for assigning the composition of N-linked glycopeptides.
abstract: GlycoPep grader (GPG) is a freely available software tool designed to accelerate the process of accurately determining glycopeptide composition from tandem mass spectrometric data. GPG relies on the identification of unique dissociation patterns shown for high mannose, hybrid, and complex N-linked glycoprotein types, including patterns specific to those structures containing fucose or sialic acid residues. The novel GPG scoring algorithm scores potential candidate compositions of the same nominal mass against MS/MS data through evaluation of the Y(1) ion and other peptide-containing product ions, across multiple charge states, when applicable. In addition to evaluating the peptide portion of a given glycopeptide, the GPG algorithm predicts and scores product ions that result from unique neutral losses of terminal glycans. GPG has been applied to a variety of glycoproteins, including RNase B, asialofetuin, and transferrin, and the HIV envelope glycoprotein, CON-S gp140ΔCFI. The GPG software is implemented predominantly in PostgreSQL, with PHP as the presentation tier, and is publicly accessible online. Thus far, the algorithm has identified the correct compositional assignment from multiple candidate N-glycopeptides in all tests performed.
authors.affiliation: Department of Chemistry, University of Kansas, Lawrence, Kansas 66047, United States.
authors.forename: Carrie L
authors.initials: CL
authors.lastname: Woodin
authors.forename: David
authors.initials: D
authors.lastname: Hua
authors.forename: Morgan
authors.initials: M
authors.lastname: Maxon
authors.forename: Kathryn R
authors.initials: KR
authors.lastname: Rebecchi
authors.forename: Eden P
authors.initials: EP
authors.lastname: Go
authors.forename: Heather
authors.initials: H
authors.lastname: Desaire
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D006020:Glycopeptides / Q000032:analysis* / Q000737:chemistry; D006031:Glycosylation; D006801:Humans; D020407:Internet; D008969:Molecular Sequence Data; D008970:Molecular Weight; D011134:Polysaccharides / Q000032:analysis*; D012794:Sialic Acids / Q000032:analysis*; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D006020:Glycopeptides; D011134:Polysaccharides; D012794:Sialic Acids