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Bioinformatics Advance Access originally published online on April 7, 2008
Bioinformatics 2008 24(10):1293-1299; doi:10.1093/bioinformatics/btn123
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Peak bagging for peptide mass fingerprinting

Zengyou He *, Can Yang and Weichuan Yu

Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China

*To whom correspondence should be addressed.


  Abstract

Motivation: Mass Spectrometry (MS)-based protein identification via peptide mass fingerprinting (PMF) is a key component in high-throughput proteome research. While PMF was the first commonly used protein identification method, provided higher throughput than the tandem MS-based method, its accuracy is lower than that of the tandem MS method. Thus, it is desirable to develop PMF-based algorithm with higher protein identification accuracy to facilitate proteome research.

Results: We propose a peak bagging method for single MS-based protein identification. It combines results from multiple PMF algorithms, where each PMF algorithm takes a random peak subset as input. Evaluation with a set of real MALDI-TOF MS spectra shows that the new peak bagging method provides consistent improvements over the single PMF algorithm.

Contact: eezyhe{at}ust.hk

Associate Editor: Jonathan Wren

Received on February 4, 2008; revised on March 17, 2008; accepted on April 3, 2008

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