Feature extraction and dimensionality reduction for mass spectrometry data

Authors:
Yihui Liu
Affiliations:
School of Computer Science and Information Technology, Shandong Institute of Light Industry, Jinan, Shandong 250353, China
Venue:
Computers in Biology and Medicine
Year:
2009

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Abstract

Mass spectrometry is being used to generate protein profiles from human serum, and proteomic data obtained from mass spectrometry have attracted great interest for the detection of early stage cancer. However, high dimensional mass spectrometry data cause considerable challenges. In this paper we propose a feature extraction algorithm based on wavelet analysis for high dimensional mass spectrometry data. A set of wavelet detail coefficients at different scale is used to detect the transient changes of mass spectrometry data. The experiments are performed on 2 datasets. A highly competitive accuracy, compared with the best performance of other kinds of classification models, is achieved. Experimental results show that the wavelet detail coefficients are efficient way to characterize features of high dimensional mass spectra and reduce the dimensionality of high dimensional mass spectra.