One form of functional proteomics entails profiling of genuine activities, as opposed to surrogates of activity or active ‘states’, in a complex biological matrix. For example, tracking enzyme-catalyzed changes, in real time, ranging from simple modifications to complex anabolic or catabolic reactions. Here, we present a test to compare defined exoprotease activities within individual proteomes of two or more groups of biological samples. It tracks degradation of artificial substrates, under strictly controlled conditions, using semi-automated MALDI-TOF mass spectrometric analysis of the resulting patterns. Each fragment is quantitated by comparison with double-labeled, non-degradable internal standards (all-D-amino acid peptides), spiked into the samples at the same time as the substrates to reflect adsorptive and processing-related losses. The full array of metabolites is then quantitated (CVs of 6.3 to 14.3% over 5 replicates) and subjected to multivariate statistical analysis. Using this approach, we tested serum samples of 48 metastatic thyroid cancer patients and 48 healthy controls, with selected peptide substrates taken from earlier standard peptidomic screens (i.e., the ‘discovery’ phase), and obtained class predictions with 94% sensitivity and 90% specificity, without prior feature selection (24 features). The test all but eliminates reproducibility problems related to sample collection, storage and handling, as well as to possible variability in endogenous peptide precursor levels owing to hemostatic alterations in cancer patients.