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Journal Article

Classification of peptide mass fingerprint data by novel no-regret boosting method.


Szczurek,  Ewa
Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Gambin, A., Szczurek, E., Dutkowski, J., Bakun, M., & Dadlez, M. (2009). Classification of peptide mass fingerprint data by novel no-regret boosting method. Computers in Biology and Medicine, 39(5), 460-473. doi:10.1016/j.compbiomed.2009.03.006.

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We have developed an integrated tool for statistical analysis of large-scale LC-MS profiles of complex protein mixtures comprising a set of procedures for data processing, selection of biomarkers used in early diagnostic and classification of patients based on their peptide mass fingerprints. Here, a novel boosting technique is proposed, which is embedded in our framework for MS data analysis. Our boosting scheme is based on Hannan-consistent game playing strategies. We analyze boosting from a game-theoretic perspective and define a new class of boosting algorithms called H-boosting methods. In the experimental part of this work we apply the new classifier together with classical and state-of-the-art algorithms to classify ovarian cancer and cystic fibrosis patients based on peptide mass spectra. The methods developed here provide automatic, general, and efficient means for processing of large scale LC-MS datasets. Good classification results suggest that our approach is able to uncover valuable information to support medical diagnosis.