Journal Article

Improving peptide identification with single-stage mass spectrum peaks

Zengyou He and Weichuan Yu

in Bioinformatics

Volume 25, issue 22, pages 2969-2974
Published in print November 2009 | ISSN: 1367-4803
Published online August 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp501
Improving peptide identification with single-stage mass spectrum peaks

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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@ust.hk

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  3398 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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