title: Automated N-glycopeptide identification using a combination of single- and tandem-MS.
abstract: We describe Peptoonist, a program that can automatically identify the glycans (sugars) present at each N-glycosylation site of a protein. The input to Peptoonist is a series of mass spectra, both MS and MS/MS, obtained from a liquid chromatography (LC) run of proteolytically digested purified glycoproteins. The program uses MS/MS to identify glycosylated peptides and single-MS to identify the N-glycans present on each of these peptides, at least to the level of monosaccharide composition. We validate the program on an LC run of mouse zona pellucida proteins that had been intensively hand annotated by a human expert. Our program doubled the number of glycopeptide identifications, and also found several possible errors in the hand annotation. In addition, it automatically made most of the same glycan isomer identifications as the expert annotator.
authors.affiliation: Palo Alto Research Center, Palo Alto, California 94301, USA. goldberg@parc.com
authors.forename: David
authors.initials: D
authors.lastname: Goldberg
authors.forename: Marshall
authors.initials: M
authors.lastname: Bern
authors.forename: Simon
authors.initials: S
authors.lastname: Parry
authors.forename: Mark
authors.initials: M
authors.lastname: Sutton-Smith
authors.forename: Maria
authors.initials: M
authors.lastname: Panico
authors.forename: Howard R
authors.initials: HR
authors.lastname: Morris
authors.forename: Anne
authors.initials: A
authors.lastname: Dell
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001322:Autoanalysis; D004527:Egg Proteins / Q000032:analysis; D006020:Glycopeptides / Q000032:analysis*; D006031:Glycosylation; D006801:Humans; D007536:Isomerism; D013058:Mass Spectrometry / Q000379:methods*; D008562:Membrane Glycoproteins / Q000032:analysis; D051379:Mice; D008969:Molecular Sequence Data; D011956:Receptors, Cell Surface / Q000032:analysis; D012984:Software; D053719:Tandem Mass Spectrometry; D000072216:Zona Pellucida Glycoproteins
chemical_list: D004527:Egg Proteins; D006020:Glycopeptides; D008562:Membrane Glycoproteins; D011956:Receptors, Cell Surface; D000072216:Zona Pellucida Glycoproteins