title: Simple modification of a protein database for mass spectral identification of N-linked glycopeptides.
abstract: We describe an algorithm which modifies a protein database such that during a database search deamidation is limited to asparagines strictly contained within the N-glycosylation consensus sequence. The modified database was evaluated using a dataset created from the shotgun proteomic analysis of N-linked glycopeptides from human blood serum. We demonstrate that the application of the modified database eliminates incorrect glycopeptide assignments, reduces the peptide false-discovery rate, and eliminates the need for manual validation of glycopeptide identifications.
authors.affiliation: Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602-4712, USA. jatwood@chem.uga.edu
authors.forename: James A
authors.initials: JA
authors.lastname: Atwood
authors.forename: Satya S
authors.initials: SS
authors.lastname: Sahoo
authors.forename: Gerardo
authors.initials: G
authors.lastname: Alvarez-Manilla
authors.forename: Daniel B
authors.initials: DB
authors.lastname: Weatherly
authors.forename: Kumar
authors.initials: K
authors.lastname: Kolli
authors.forename: Ron
authors.initials: R
authors.lastname: Orlando
authors.forename: William S
authors.initials: WS
authors.lastname: York
mesh_terms: D000465:Algorithms; D001216:Asparagine / Q000032:analysis; D030562:Databases, Protein; D006020:Glycopeptides / Q000032:analysis* / Q000737:chemistry; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D010449:Peptide Mapping / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D006020:Glycopeptides; D001216:Asparagine