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arXiv · 0907.3426

SparseCodePicking: feature extraction in mass spectrometry using sparse coding algorithms

Theodore Alexandrov·Klaus Steinhorst·Oliver Keszoecze·Stefan Schiffler
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Abstract

Mass spectrometry (MS) is an important technique for chemical profiling which calculates for a sample a high dimensional histogram-like spectrum. A crucial step of MS data processing is the peak picking which selects peaks containing information about molecules with high concentrations which are of interest in an MS investigation. We present a new procedure of the peak picking based on a sparse coding algorithm. Given a set of spectra of different classes, i.e. with different positions and heights of the peaks, this procedure can extract peaks by means of unsupervised learning. Instead of an $l_1$-regularization penalty term used in the original sparse coding algorithm we propose using an elastic-net penalty term for better regularization. The evaluation is done by means of simulation. We show that for a large region of parameters the proposed peak picking method based on the sparse coding features outperforms a mean spectrum-based method. Moreover, we demonstrate the procedure applying it to two real-life datasets.

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Theodore Alexandrov, Klaus Steinhorst, Oliver Keszoecze, Stefan Schiffler. 2009-10-05. SparseCodePicking: feature extraction in mass spectrometry using sparse coding algorithms. https://arxiv.org/abs/0907.3426

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