The activity of a selected endopeptidase in a body fluid is determined by the mass spectrometric measurement of the reaction products of reporter substrate molecules added to the body fluid. Each reporter substrate molecule includes a peptide with the cleavage motif of the endopeptidase, an anchor group A1 on one side of the cleavage site and a different anchor group A2 on the other side of the cleavage site. One anchor is used to extract the reporter substrate molecules from the body fluid and the other anchor is used to extract digest fragments of the reporter molecules from the body fluid. Mass markers allow several reporter substrates to be used simultaneously in the same body fluid sample to measure the activity of different types of endopeptidase.