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Bioinformatics Advance Access published online on April 7, 2008
Bioinformatics, 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. Dr. Zengyou He, E-mail: eezyhe{at}ust.hk


  Abstract

Motivation: Mass Spectrometry(MS) based protein identification via peptide mass fingerprinting (PMF) is a key component in highthroughput 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: Dr. Jonathan Wren

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

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