Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) has in the past decade found routine use in the biological sciences. With this use has evolved several mass spectrometric-based methods directed at the intricate investigation of biomolecular structure and function. One such methodology involves the enzymatic modification of a protein prior to the mass spectrometric readout of the resulting products. The enzyme-modification/mass spectrometric approach has a definite use in a number of applications, including: the verification/identification of protein sequence, elucidation of post-translational modifications, the investigation of protein higher-order structure, and even the characterization of the modifying enzyme. To avoid the potentials of sample loss and autolytic interferences in the mass spectrum, mass spectrometer targets can be covalently derivatized with enzymes for use in the characterization procedures. The enzymatically active, or bioreactive, probes are used by application of the analyte to the activated surface, followed by application of a suitable MALDI matrix and mass analysis from the surface of the probe. Limited transfer and handling steps eliminate sample losses, and surface-tethered enzymes (and autolytic fragments) are prohibited from interfering with analytical signals in the mass spectra. In addition, the probes are rapid and easy to use. Reviewed here are issues of concern during the manufacture and use of the bioreactive probes, and application of the probes to investigate protein structure and function.