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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.



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.


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.


An example of MATLAB scripts used to implement the methods described in this article, along with Supplementary Figures, can be found at


Supplementary data are available at Bioinformatics online.

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