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This article is part of the supplement: Selected articles from the Eighth Asia-Pacific Bioinformatics Conference (APBC 2010)

Open Access Research

Nonnegative principal component analysis for mass spectral serum profiles and biomarker discovery

Henry Han

Author Affiliations

Department of Mathematics and Bioinformatics, Eastern Michigan University, Ypsilanti MI 48109, USA

BMC Bioinformatics 2010, 11(Suppl 1):S1  doi:10.1186/1471-2105-11-S1-S1

Published: 18 January 2010



As a novel cancer diagnostic paradigm, mass spectroscopic serum proteomic pattern diagnostics was reported superior to the conventional serologic cancer biomarkers. However, its clinical use is not fully validated yet. An important factor to prevent this young technology to become a mainstream cancer diagnostic paradigm is that robustly identifying cancer molecular patterns from high-dimensional protein expression data is still a challenge in machine learning and oncology research. As a well-established dimension reduction technique, PCA is widely integrated in pattern recognition analysis to discover cancer molecular patterns. However, its global feature selection mechanism prevents it from capturing local features. This may lead to difficulty in achieving high-performance proteomic pattern discovery, because only features interpreting global data behavior are used to train a learning machine.


In this study, we develop a nonnegative principal component analysis algorithm and present a nonnegative principal component analysis based support vector machine algorithm with sparse coding to conduct a high-performance proteomic pattern classification. Moreover, we also propose a nonnegative principal component analysis based filter-wrapper biomarker capturing algorithm for mass spectral serum profiles.


We demonstrate the superiority of the proposed algorithm by comparison with six peer algorithms on four benchmark datasets. Moreover, we illustrate that nonnegative principal component analysis can be effectively used to capture meaningful biomarkers.


Our analysis suggests that nonnegative principal component analysis effectively conduct local feature selection for mass spectral profiles and contribute to improving sensitivities and specificities in the following classification, and meaningful biomarker discovery.