The work describes the accelerated enzymatic digestion of several proteins in various solvent systems under microwave irradiation. The tryptic fragments of the proteins were analyzed by matrix-assisted laser desorption/ionization mass spectrometry. Under the influence of rapid microwave heating, these enzymatic reactions can proceed in a solvent such as chloroform, which, under traditional digestion conditions, renders the enzyme inactive. The digestion efficiencies and sequence coverages were increased when the trypsin digestions occurred in acetonitrile-, methanol-and chloroform-containing solutions that were heated under microwave irradiation for 10 min using a commercial microwave applicator. The percentage of the protein digested under microwave irradiation increased with the relative acetonitrile content, but decreased as the methanol content was increased. These observations suggest that acetonitrile does not deactivate the enzyme during the irradiation period; in contrast, methanol does deactivate it. In all cases, the digestion efficiencies under microwave irradiation exceed those under conventional conditions. A dvances in mass spectrometric ionization methods, such as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI), make it possible to analyze complex biomolecules quite readily [1][2][3][4][5]. Tandem mass spectrometry (MS/MS) allows fragment ions to be generated from mass-selected precursor peptide ions, which, in turn, reveal sequence information for the peptide. The protein databases that are available in the public domain allow rapid identification of proteins by partial sequence analysis using tandem mass spectrometry; this process eliminates the need for complete protein sequence analysis [6 -12]. The enzymatic cleavage of proteins into smaller peptide fragments is an important step to undertake before MS analysis for the characterization of protein structures.To obtain detailed structural information, proteins are first subjected to proteolytic cleavage and then subjected to MS analysis of the resulting peptide mixture. This method of protein analysis is known as peptide mass fingerprinting. For a mass spectrometer capable of performing MS/MS analysis, the peptides are further sequenced by tandem MS before the identities of the proteins are analyzed. Efficient protein digestion requires production of peptides with a high coverage of protein sequence as well as fast digestion times. Generally, enzymatic digestions of proteins are carried out for several hours, or overnight, to generate sufficient amounts of peptides for analysis. To improve the efficiency of protein digestion, additives such as surfactants, organic solvents, and urea are often used to increase the proteins' solubilities and, thus, facilitate more-complete digestion [13,14]. Recently, Gilar et al. reported that a novel acid-labile anionic surfactant solubilizes proteins and improves digestion rates without inhibiting the activity of trypsin or other common endopeptidases [13]. An alternative ...