Proteomic profile analysis and biomarker discovery from mass spectra using independent component analysis combined with uncorrelated linear discriminant analysis

A strategy based on Independent Component Analysis (ICA) and Uncorrelated linear discriminant analysis (ULDA) was proposed for proteomic profile analysis and potential biomarker discovery from proteomic mass spectra of cancer and control samples. The method mainly includes 3 steps: (1) ICA decomposition for the mass spectra; (2) selection of discriminatory independent components (ICs) using nonparametric Mann–Whitney U-test; and (3) selection of special peaks (m/z locations) as potential biomarkers by executing of ULDA on a mass spectra data set which was reconstructed with the m/z locations that collected from the selected discriminatory ICs. A colorectal cancer data set and an ovarian cancer data set were analyzed with the proposed method. As results, 9 and 10 m/z locations were selected as potential biomarkers for the colorectal and ovarian cancer data set respectively. The classification results of ULDA using the selected potential biomarkers yielded better results than fisher discriminant analysis (FDA) and principal component analysis (PCA), and could distinguish the disease samples from healthy controls on the independent test sets with 100% of sensitivities and specificities for the colorectal cancer dataset and 100% of sensitivity and 96.77% of specificity for the ovarian cancer dataset.