Simple modification of a protein database for mass spectral identification of N-linked glycopeptides

TitleSimple modification of a protein database for mass spectral identification of N-linked glycopeptides
Publication TypeJournal Article
Year of Publication2005
AuthorsJames Atwood, Satya Sahoo, Gerardo Alvarez-Manilla, D. Brent Weatherly, Kumar Kolli, Ron Orlando, William York
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.

Full Text

J.A. Atwood III, S.S. Sahoo, G. Alvarez-Manilla, D.B. Weatherly, K. Kolli, R. Orlando, and S. York, “Simple modification of a protein database for mass spectral identification of N-linked glycopeptides,” Rapid Commun Mass Spectrom, 19 (no. 21), 2005, pp. 3002–06. PMID: 16196021.

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