Document Detail


GlycoPep grader: a web-based utility for assigning the composition of N-linked glycopeptides.
MedLine Citation:
PMID:  22540370     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
GlycoPep grader (GPG) is a freely available software tool designed to accelerate the process of accurately determining glycopeptide composition from tandem mass spectrometric data. GPG relies on the identification of unique dissociation patterns shown for high mannose, hybrid, and complex N-linked glycoprotein types, including patterns specific to those structures containing fucose or sialic acid residues. The novel GPG scoring algorithm scores potential candidate compositions of the same nominal mass against MS/MS data through evaluation of the Y(1) ion and other peptide-containing product ions, across multiple charge states, when applicable. In addition to evaluating the peptide portion of a given glycopeptide, the GPG algorithm predicts and scores product ions that result from unique neutral losses of terminal glycans. GPG has been applied to a variety of glycoproteins, including RNase B, asialofetuin, and transferrin, and the HIV envelope glycoprotein, CON-S gp140ΔCFI. The GPG software is implemented predominantly in PostgreSQL, with PHP as the presentation tier, and is publicly accessible online. Thus far, the algorithm has identified the correct compositional assignment from multiple candidate N-glycopeptides in all tests performed.
Authors:
Carrie L Woodin; David Hua; Morgan Maxon; Kathryn R Rebecchi; Eden P Go; Heather Desaire
Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2012-05-21
Journal Detail:
Title:  Analytical chemistry     Volume:  84     ISSN:  1520-6882     ISO Abbreviation:  Anal. Chem.     Publication Date:  2012 Jun 
Date Detail:
Created Date:  2012-07-03     Completed Date:  2012-10-23     Revised Date:  2013-06-25    
Medline Journal Info:
Nlm Unique ID:  0370536     Medline TA:  Anal Chem     Country:  United States    
Other Details:
Languages:  eng     Pagination:  4821-9     Citation Subset:  IM    
Affiliation:
Department of Chemistry, University of Kansas, Lawrence, Kansas 66047, United States.
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Amino Acid Sequence
Glycopeptides / analysis*,  chemistry
Glycosylation
Humans
Internet
Molecular Sequence Data
Molecular Weight
Polysaccharides / analysis*
Sialic Acids / analysis*
Software*
Tandem Mass Spectrometry
Grant Support
ID/Acronym/Agency:
R01 GM103547/GM/NIGMS NIH HHS; R01 RR026061/RR/NCRR NIH HHS; R01RR026061/RR/NCRR NIH HHS
Chemical
Reg. No./Substance:
0/Glycopeptides; 0/Polysaccharides; 0/Sialic Acids
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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