Simple modification of a protein database for mass spectral identification of N-linked glycopeptides.
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.
Atwood
James A
JA
Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602-4712, USA. jatwood@chem.uga.edu
Sahoo
Satya S
SS
Alvarez-Manilla
Gerardo
G
Weatherly
Daniel B
DB
Kolli
Kumar
K
Orlando
Ron
R
York
William S
WS
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*
D006020:Glycopeptides; D001216:Asparagine