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Bioinformatics Advance Access published online on January 28, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp060
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A Novel Comprehensive Wave-form MS Data Processing Method

Shuo Chen a,b,c,*, Ming Li a,b,*, Don Hong d, Dean Billheimer e, Huiming Li b, Baogang J. Xu f and Yu Shyr a,b,{dagger}

aDivision of Cancer Biostatistics, Department of Biostatistics, Vanderbilt University, Nashville,Tennessee 37232, USA
bCancer Biostatistics Center, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232, USA
cDepartment of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia 30322, USA
dDepartment of Mathematical Sciences, Middle Tennessee State University, Murfreesboro,Tennessee 37132, USA
eDepartment of Oncological Sciences, University of Utah, Salt Lake City, Utah 84112, USA
fDepartment of Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, USA

{dagger}To whom correspondence should be addressed. Prof. Yu Shyr, E-mail: yu.shyr{at}vanderbilt.edu


  Abstract

Motivation: Mass spectrometry (MS) can generate high-throughput protein profiles for biomedical research to discover biologically-related protein patterns/biomarkers. The noisy functional MS data collected by current technologies, however, require consistent, sensitive, and robust data-processing techniques for successful biomedical application. Therefore, it is important to detect features precisely for each spectrum, quantify them well, and assign a unique label to features from the same protein/peptide across spectra.

Results: In this paper, we propose a new comprehensive MS data preprocessing package, Wave-spec, which includes several novel algorithms. It can overcome several conventional difficulties. Wavespec can be applied to multiple types of MS data generated with different MS technologies. Results from this new package were evaluated and compared to several existing approaches based on a MALDI-TOF MS data set.

Availability: An example of MATLAB scripts used to implement the methods described in this paper, along with Supplementary Figures, can be found at http://www.vicc.org/biostatistics/supp.php.

Contact: yu.shyr{at}vanderbilt.edu

*These authors contributed equally.

Associate Editor: Dr. Jonathan Wren

Received on October 2, 2008; revised on January 22, 2009; accepted on January 23, 2009

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