A robust classification method for cancer detection from mass spectrometry data includes inputting the mass spectrometry data, preprocessing the spectrometry data, conducting robust feature selection, generating predictions for the test data sets using multiple data classifiers, the multiple data classifiers including artificial neural networks, support vector machines, weighted voting on data patterns, classification and regression trees, k-nearest neighbor classification, and logistic regression, and constructing and validating a meta-classifier by combining individual predictions of the multiple data classifiers to generate a robust prediction of a phenotype. The test data sets are used exclusively for validation of the meta-classifier.