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Bioinformatics Advance Access originally published online on August 18, 2009
Bioinformatics 2009 25(22):2969-2974; doi:10.1093/bioinformatics/btp501
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Improving peptide identification with single-stage mass spectrum peaks

Zengyou He * and Weichuan Yu

Laboratory for Bioinformatics and Computational Biology, Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China

*To whom correspondence should be addressed.


  Abstract

Motivation: Database searching is the major peptide identification method in shotgun proteomics. It searches tandem mass spectrometry (MS/MS) spectra against a protein database to identify target peptides. The success of such a database searching method relies on a scoring algorithm that can evaluate the quality of peptide-spectrum matches (PSMs) accurately. However, current scoring algorithms frequently generate inaccurate assignments due to variations and noises in the MS/MS spectra. To address this issue, we like to improve peptide identification by using additional information from other data sources.

Results: Single-stage MS data is complementary to MS/MS data in the sense that it provides broader mass coverage but less sequence information. In this article, we show that single-stage MS data can be used to re-rank PSMs. The proposed method explores a linear combination of scores between MS and MS/MS data to perform re-ranking. Experimental results on real data show that such a re-ranking strategy improves the identification performance significantly.

Availability: http://bioinformatics.ust.hk/ReRankPSMwMS1.rar

Contact: eezyhe{at}ust.hk

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Thomas Lengauer

Received on March 18, 2009; revised on August 12, 2009; accepted on August 13, 2009

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