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Bioinformatics Advance Access originally published online on November 22, 2007
Bioinformatics 2008 24(1):102-109; doi:10.1093/bioinformatics/btm545
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Fast and accurate identification of semi-tryptic peptides in shotgun proteomics

Pedro Alves 1, Randy J. Arnold 2,4,*, David E. Clemmer 2,4, Yixue Li 5, James P. Reilly 2,4, Quanhu Sheng 1,4,5, Haixu Tang 1,3,4,*, Zhiyin Xun 2, Rong Zeng 5 and Predrag Radivojac 1,*

1School of Informatics, 2Department of Chemistry, 3Department of Biology, Center for Genomics and Bioinformatics, 4National Center for Glycomics & Glycoproteomics, Indiana University, Bloomington, IN, USA and 5Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

*To whom correspondence should be addressed.


  Abstract

Motivation: One of the major problems in shotgun proteomics is the low peptide coverage when analyzing complex protein samples. Identifying more peptides, e.g. non-tryptic peptides, may increase the peptide coverage and improve protein identification and/or quantification that are based on the peptide identification results. Searching for all potential non-tryptic peptides is, however, time consuming for shotgun proteomics data from complex samples, and poses a challenge for a routine data analysis.

Results: We hypothesize that non-tryptic peptides are mainly created from the truncation of regular tryptic peptides before separation. We introduce the notion of truncatability of a tryptic peptide, i.e. the probability of the peptide to be identified in its truncated form, and build a predictor to estimate a peptide's truncatability from its sequence. We show that our predictions achieve useful accuracy, with the area under the ROC curve from 76% to 87%, and can be used to filter the sequence database for identifying truncated peptides. After filtering, only a limited number of tryptic peptides with the highest truncatability are retained for non-tryptic peptide searching. By applying this method to identification of semi-tryptic peptides, we show that a significant number of such peptides can be identified within a searching time comparable to that of tryptic peptide identification.

Contact: predrag{at}indiana.edu; rarnold{at}indiana.edu; hatang{at}indiana.edu

Associate Editor: John Quackenbush

Received on August 7, 2007; revised on October 7, 2007; accepted on October 26, 2007

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