Since the advent of matrix-assisted laser desorption͞ionization and electrospray ionization, mass spectrometry has played an increasingly important role in protein functional characterization, identification, and structural analysis. Expanding this role, desorption͞ionization on silicon (DIOS) is a new approach that allows for the analysis of proteins and related small molecules. Despite the absence of matrix, DIOS-MS yields little or no fragmentation and is relatively tolerant of moderate amounts of contaminants commonly found in biological samples. Here, functional assays were performed on an esterase, a glycosidase, a lipase, as well as exoand endoproteases by using enzyme-specific substrates. Enzyme activity also was monitored in the presence of inhibitors, successfully demonstrating the ability of DIOS to be used as an inhibitor screen. Because DIOS is a matrix-free desorption technique, it also can be used as a platform for multiple analyses to be performed on the same protein. This unique advantage was demonstrated with acetylcholine esterase for qualitative and quantitative characterization and also by its subsequent identification directly from the DIOS platform.M ass spectrometry is quickly becoming an essential tool for characterizing protein function, substrate specificity, and protein identity (1-5) as it complements or, in some cases, supersedes the utility of traditional biological methods (6, 7). For some of the most important proteomics applications, the high sensitivity and accuracy provided by modern mass spectrometry allow for unequivocal characterization and quantitative analysis of proteins and their chemical products (5,8,9). Ionization methods such as electrospray ionization used in liquid chromatography͞MS and matrix-assisted laser desorption͞ionization (MALDI) are the core innovations that allow for mass spectrometry to be used in protein characterization as well as in the determination of protein structure͞function relationships (10, 11). MALDI mass spectrometry has been particularly effective as a proteomics tool because of its relatively high tolerance of mixtures and biological contaminants (12, 13); however, its matrix requirement represents a limitation in interference in the low-mass region, preparation time, and the potential to perform sample manipulation after mass analysis. In addition, a prevailing obstacle toward protein characterization by using both MALDI and liquid chromatography͞MS is the loss of analyte material during protein separations, chromatographic separations, or functional studies that require the transfer of the sample for subsequent identification. One way to overcome these obstacles would be to both identify and functionally characterize proteins on a single surface.Desorption͞ionization on porous silicon (DIOS), a new method for the generation of intact gas phase ions (14), uses UV laser light to desorb intact analytes from the surface without matrix assistance. The procedure for producing DIOS surfaces involves a simple galvanostatic etching procedure (15...
