Journal Article

A novel comprehensive wave-form MS data processing method

Shuo Chen, Ming Li, Don Hong, Dean Billheimer, Huiming Li, Baogang J. Xu and Yu Shyr

in Bioinformatics

Volume 25, issue 6, pages 808-814
Published in print March 2009 | ISSN: 1367-4803
Published online January 2009 | e-ISSN: 1460-2059 | DOI:
A novel comprehensive wave-form MS data processing method

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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


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  5054 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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