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

Rapid Commun Mass Spectrom. 2005;19(21):3002-6. doi: 10.1002/rcm.2162.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Asparagine / analysis
  • Databases, Protein*
  • Glycopeptides / analysis*
  • Glycopeptides / chemistry
  • Humans
  • Mass Spectrometry / methods*
  • Peptide Mapping / methods
  • Sequence Analysis, Protein / methods*


  • Glycopeptides
  • Asparagine