A novel comprehensive wave-form MS data processing method.
BACKGROUND
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.


BACKGROUND
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.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Chen
Shuo
S
Division of Cancer Biostatistics, Department of Biostatistics, Vanderbilt University, Nashville, TN 37232, USA.
Li
Ming
M
Hong
Don
D
Billheimer
Dean
D
Li
Huiming
H
Xu
Baogang J
BJ
Shyr
Yu
Y
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D011506:Proteins / Q000737:chemistry*
D011506:Proteins