Sparse Proteomics Analysis – a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data

  • Motivation: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested how MS spectra dier between patients of different classes, for example spectra from healthy patients vs. spectra from patients having a particular disease. Machine learning algorithms are needed to (a) identify these discriminating features and (b) classify unknown spectra based on this feature set. Since the acquired data is usually noisy, the algorithms should be robust to noise and outliers, and the identied feature set should be as small as possible. Results: We present a new algorithm, Sparse Proteomics Analysis (SPA), based on the theory of Compressed Sensing that allows to identify a minimal discriminating set of features from mass spectrometry data-sets. We show how our method performs on artificial and real-world data-sets.

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Metadaten
Author:T. Conrad, Martin Genzel, Nada Cvetkovic, Niklas Wulkow, Jan Vybiral, Gitta Kutyniok, Ch. Schütte
Document Type:Article
Parent Title (English):BMC Bioinformatics
Volume:18
Issue:160
First Page:1
Last Page:20
Year of first publication:2017
DOI:https://doi.org/10.1186/s12859-017-1565-4