This paper describes the methodology of providing multiprobability predictions for proteomic mass spectrometry data. The methodology is based on a newly developed machine learning framework called Venn machines. They allow us to output a valid probability interval. We apply this methodology to mass spectrometry data sets in order to predict the diagnosis of heart disease and early diagnoses of ovarian cancer. The experiments show that probability intervals are valid and narrow. In addition, probability intervals were compared with the output of a corresponding probability predictor. © 2012 IFIP International Federation for Information Processing.