The characterization of proteins is a major challenge because of a multitude of in vivo post-translational processing reactions. A key analytical procedure is the generation of smaller fragments by chemical or enzymatic procedures, followed by reversed phase HPLC. The advent of on-line systems has allowed use of electrospray mass spectrometry for the detailed characterization of peptide maps. The analysis of high molecular weight, heterogeneous proteins by matrix assisted, laser desorption time of flight mass spectroscopy (MALDI-TOF) can give high sensitivity results with crude samples even in the presence of high salt concentrations.

The complementary application of these two new MS approaehes will be illustrated by the analysis of several complex samples, including single chain plasminogen activator, a potential thrombolytic agent.