Over the past 30 years, biotechnology has evolved as a multibillion dollar industry. A large sector of this industry is associated with translating human genetic information to discover, develop and commercialize bio-therapeutics. A broad range of disciplines across the Life Sciences is necessary for the selection of bio-molecules as biotechnological drug targets. Global and targeted proteomic approaches, as well as in-depth characterization of select proteins, are part of the process necessary for drug discovery and validation. Recently, microwave-assisted proteomic methodologies have emerged as useful tools for increasing the bio-catalysis and, therefore, throughput of analytical processes associated with protein characterization. Several microwave-assisted protocols that have become integrated into the drug discovery research process in the biotechnology industry are discussed.