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

Authors:
Anna Gambin;Ewa Szczurek;Janusz Dutkowski;Magda Bakun;Michał Dadlez
Affiliations:
Institute of Informatics, Warsaw University, Banacha 2, 02-097 Warsaw, Poland;Institute of Informatics, Warsaw University, Banacha 2, 02-097 Warsaw, Poland and Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany;Institute of Informatics, Warsaw University, Banacha 2, 02-097 Warsaw, Poland;Institute of Biochemistry and Biophysics PAS, Pawińskiego 5A, 02-106 Warsaw, Poland;Institute of Biochemistry and Biophysics PAS, Pawińskiego 5A, 02-106 Warsaw, Poland and Biology Department, Warsaw University, Miecznikowa 1, 02-096 Warsaw, Poland
Venue:
Computers in Biology and Medicine
Year:
2009

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Abstract

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.