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This article is part of the supplement: UT-ORNL-KBRIN Bioinformatics Summit 2010

Open Access Poster presentation

Enabling proteomics-based identification of human cancer variations

Jing Li1, Zeqiang Ma1, Robbert JC Slebos2, David L Tabb13, Daniel C Liebler123 and Bing Zhang1*

Author Affiliations

1 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA

2 Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA

3 Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA

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BMC Bioinformatics 2010, 11(Suppl 4):P29  doi:10.1186/1471-2105-11-S4-P29

The electronic version of this article is the complete one and can be found online at:

Published:23 July 2010

© 2010 Zhang et al; licensee BioMed Central Ltd.


Shotgun proteomics is a powerful technology for protein identification in complex samples with remarkable applications in elucidating cellular and subcellular proteomes [1,2], and discovering disease biomarkers [3,4]. Shotgun proteomics data analysis usually relies on database search. Commonly used protein sequence databases in shotgun proteomics data analysis do not contain mutation information. This becomes a problem in cancer studies in which the detection of disease-related mutated peptides/proteins is crucial for understanding cancer biology [5]. Including protein mutation information into sequence databases can help alleviate this problem.


Based on the human Cancer Proteome Variation Database developed by us recently [6], which comprises 41,541 nonsynonymous SNPs in 30,322 proteins from the dbSNP database and around 9000 cancer-related variations in 2,921 proteins, we created a variation-containing protein sequence database and a data analysis workflow for mutant protein identification in shotgun proteomics (Figure 1). Applying this workflow on colorectal cancer cell lines identified many peptides that contain either non-cancer-specific or very important cancer-related variations, such as a known somatic mutation in K-Ras in HCT116 cell line. Our workflow for mutant peptide identification has been tested for compatibility with various popular database search engines including Sequest, Mascot, X!Tandom as well as MyriMatch.

thumbnailFigure 1. Architecture for identifying mutant peptides from cancer shotgun proteome data


Owing to its protein-centric nature, the approach we proposed can serve as a bridge between genomic variation data and proteomics studies in human cancer.


This work was supported by the National Institutes of Health (NIH)/ National Cancer Institute (NCI) through grant R01 CA126218 and the NIH/National Institute of General Medical Sciences through grant R01 GM88822.


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