Biological mass spectrometry has expanded rapidly during the last decade. Proteomics, the description and quantification of the protein contents of cells, tissues, or whole organisms, has been one of the most visible facets of this growth. The research presented here focuses on the proteome of a single subcelluar complex, the bacterial 70S ribosome, to develop procedures for rapid, confident protein identification. Ribosomal proteins isolated from Caulobacter crescentus CB15N were separated using a unique two dimensional chromatography system with strong cation exchange as the first dimension and reversed phase chromatography as the second dimension. This separation provided an effective method to analyze the mass and post-translational modifications of any given protein, and tentative identifications based on whole protein data could be readily confirmed with peptide LC-MS/MS experiments. The experience gained from the analysis of one bacterial ribosomal proteome was applied to probe protein-rRNA interactions in Deinococcus radiodurans R1 ribosomes by chemical modification with S-methylthioacetimidate (SMTA). Quantifying the extent and location of the chemical modifications revealed details of the proteins' native interactions in the ribosome. Chemical modification procedures also increase the information obtained from proteomic analyses, and have aided in the identification of post-translational modifications in D. radiodurans R1 ribosomal proteins. The solution conditions for protein modification with SMTA were expanded across a physiologically relevant pH range to study the effects of solution pH on protein-rRNA interactions in the ribosomes of Thermus thermophilus HB8. These results were extended by studying the pH dependence of SMTA reactivity in Brome Mosaic Virus (BMV) virions. This capsid of this plant virus shows a well-defined structural transition as a function of pH, increasing its diameter from 28 Å to 32 Å. This swelling transition has been studied by monitoring changes in lysine reactivity with SMTA as a function of pH. Distinct changes in the reactivity of the twelve lysine residues in BMV virions have been observed.