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Bioinformatics. 2009 Mar 15;25(6):808-14. doi: 10.1093/bioinformatics/btp060. Epub 2009 Jan 28.

A novel comprehensive wave-form MS data processing method.

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  • 1Division of Cancer Biostatistics, Department of Biostatistics, Vanderbilt University, Nashville, TN 37232, USA.

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 article, we propose a new comprehensive MS data preprocessing package, Wave-spec, which includes several novel algorithms. It can overcome several conventional difficulties. Wave-spec 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 dataset.

AVAILABILITY:

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

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

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