Presented in this work is a novel "bottom up" proteomics approach to protein identification and characterization that utilizes microwave-accelerated acid hydrolysis combined with mass spectrometric methods and bioinformatics. Results of this study demonstrate that this strategy is a robust alternative to residue specific enzymatic cleavage methods for generating peptides. Cleavage of proteins was shown to be site-specific at aspartate, as evaluated by matrix-assisted laser desorption ionization time of flight mass spectrometry and liquid chromatography tandem mass spectrometry. A bioinformatic analysis indicates that proteins will be cleaved at Asp to provide peptides that are longer than tryptic peptides, and which contain more basic residues, on average. The feasibility of this digestion method was first demonstrated on a pure protein standard, ovalbumin, and further developed for applications in rapid microorganism identification, and whole organelle processing. Digestion of ovalbumin and analysis by mass spectrometry provided ~80% sequence coverage. Bacillus spores, the RNA virus, bacteriophage MS2, and the DNA virus, human adenovirus type 5, were identifiable, based on the analysis digestion products generated by rapid digestion of protein biomarkers released by acid. Whole ribosomes isolated from Saccharomyces cervasiae were processed directly to peptides, which enabled identification of 58 of 79 ribosomal proteins by LC tandem mass spectrometry. Finally, this digestion method was shown to be compatible with a proteolytic 18O labeling strategy, which enables rapid relative quantitation of proteins.