Organizing a competition on clinical mass spectrometry based proteomic diagnosis

This paper gives a description of the structure of the classification competition on mass spectrometry proteomic data which is presented in this issue. All steps according to which the competition was run, leading up to the joint meeting, are explained. The paper gives further details on the data analyzed by all participants. This includes information on the preprocessing steps carried out, with references to appropriate sources describing algorithms used, dimensionalities, definition of calibration and validation sets, sample and group sizes and a description of which data and information was made available to participants. The paper starts with a review of mass spectrometry proteomics from a statistical and bioinformatic viewpoint. We conclude with a discussion on the nature of the competition and some of the decisions made in implementing it.