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Bioinformatics Advance Access originally published online on October 7, 2008
Bioinformatics 2008 24(23):2801-2802; doi:10.1093/bioinformatics/btn511
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry

Dihui Lu , Richard Z. Liu , Victoria Izumi , David Fenstermacher , Eric B. Haura , John Koomen * and Steven A. Eschrich *

H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, FL 33612, USA

*To whom correspondence should be addressed.


  Abstract

Peptide-based proteomics supports identification and quantification as well as localization of post-translational modifications (PTMs) within proteins extracted from biological samples. The ‘bottom-up’ approach involves the digestion of proteins into peptide fragments that can be detected and sequenced with liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). A web-based application, iPEP, was developed to compare the effectiveness of different proteolytic digests in detecting specific sequences. Furthermore, peptide populations can be examined to help optimize detection of certain groups of proteins relative to the proteome and the digested peptidome. The application reports proteolytic peptide sequences, theoretical molecular weights and functional annotations using Gene Ontology (GO) terms. The iPEP tool can assist with experimental design by maximizing the detection of proteins, consensus sites and modified residues of interest for individual proteins or as part of large-scale proteomic assays.

Availability: http://ipep.moffitt.org

Contact: steven.eschrich{at}moffitt.org; john.koomen{at}moffitt.org

Associate Editor: John Quackenbush

Received on March 20, 2008; revised on September 17, 2008; accepted on October 1, 2008

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