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Publisher Summary Biomolecular interaction analysis (BIA) and matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF) are capable of the accurate characterization of biomolecules with extreme speed and sensitivity. Although the two analytical approaches operate on mutually exclusive detection principles (either surface plasmon resonance detection of a refractive index change or the physical determination the molecular mass of a gas-phase ion), they can share a common denominator—the use of affinity interactions in selecting the analyte. Interfacing of the two, thereby creates a unique approach for the investigation of the kinetic parameters of biomolecular interaction (using BIA), and the unambiguous confirmation of the presence of targeted affinity ligands by direct mass analysis. In more recent times, new mass spectrometric approaches for the rapid, sensitive, and accurate characterization of proteins are in development. This chapter discusses some of the findings on the interfacing of biomolecular interaction analysis with mass spectrometry, and the use of enzymatically active—or bioreactive—mass spectrometer probe tips in the characterization of analytes. The use of bioreactive mass spectrometer probe tips to serially digest myoglobin is discussed in the chapter. The object of the serial digestion is to simultaneously view the relative stability of molecule fragments of myoglobin (generated during an initial, limited digestion of the myoglobin under denaturing conditions using pepsin-active tips at low pH), by exposing the fragment set to extensive digestion (using trypsin tips) under renaturing conditions.