Journal Article

IPEP: an <i>in silico</i> 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

in Bioinformatics

Volume 24, issue 23, pages 2801-2802
Published in print December 2008 | ISSN: 1367-4803
Published online October 2008 | e-ISSN: 1460-2059 | DOI:
IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry

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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.



Journal Article.  1331 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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