A novel comprehensive wave-form MS data processing method.

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.