This article describes the use of two mass spectrometric techniques, matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectrometry, toward a variety of challenging problems in drug discovery and identification. Quantitative ESI was used to screen for inhibitor activity of two different enzymatic glycosylation reactions resulting in the identification of the most effective inhibitors and the determination of their IC50 (inhibitor concentration at 50% inhibition). Also described is a combinatorial extraction method used with automated MALDI mass spectrometry to improve upon the clinical analysis of the immunosuppressant drug cyclosporin A (CsA). Optimization was performed by generating an array of solvent systems which were screened (by MALDI-MS) for the most efficient extraction of CsA from whole blood. Ultimately a 70/30 hexane:CHCl3 mixture was identified as the most efficient binary solvent system for such extractions. In addition it was demonstrated that peptides and carbohydrates, covalently linked to a polymeric support (through a photolabile linker), can be directly analyzed by MALDI in a single step which requires no pretreatment of the sample to induce cleavage from the support. The UV laser light in the MALDI experiment was used to simultaneously promote the analyte＇s photolytic cleavage from the solid support and its gas phase ionization for subsequent mass spectral analysis. Overall, the strength of mass spectrometry lies in its versatility, making it a powerful analytical technique with which to characterize the diversity of compounds found in combinatorial libraries.