Finding gene-specific peptides by mass spectrometry analysis to pinpoint gene loci responsible for particular protein products is a major challenge in proteomics, especially in highly conserved gene families in higher eukaryotes. We have used a combination of in silico approaches coupled to mass spectrometry analysis to advance the proteomic insight into Arabidopsis cytosolic ribosomal composition and its post-translational modifications. In silico digestion of all 409 ribosomal protein sequences in Arabidopsis defined the proportion of theoretical gene-specific peptides for each gene family and highlighted the need for low m/z cutoffs of MS ion selection for MS/MS to characterize low MW, highly basic ribosomal proteins. We undertook an extensive MS/MS survey of the cytosolic ribosome, using trypsin, and when required, chymotrypsin and pepsin. We then used custom software to extract and filter peptide match information from Mascot result files and implement high confidence criteria for calling gene-specific identifications based on the highest quality unambiguous spectra matching exclusively to certain in silico predicted gene- or gene family-specific peptides. This has provided an in-depth analysis of the protein composition based on 1446 high quality MS/MS spectra matching to 795 peptide sequences from ribosomal proteins. These have identified peptides from 5 gene families of r-proteins not identified previously, providing experimental data on 79 of the 80 different types of ribosomal subunits. We provide strong evidence for gene-specific identification of 87 different ribosomal proteins from these 79 families. We also provided new information on 30 specific sites of co- and post-translational modification of r-proteins in Arabidopsis by initiator methionine removal, N-terminal acetylation, N-terminal methylation, lysine N-methylation and phosphorylation. This site-specific modification data provides a wealth of resources for further assessment of the role of ribosome modification in influencing translation in Arabidopsis.