Microwave-accelerated proteolysis using acetic acid has been shown to occur specifically on either or both sides of aspartate residues. This chemical cleavage is applied to the yeast ribosome proteome to evaluate its suitability for incorporation into high-throughput automated workflows. Peptide product mixtures were analyzed using either an HPLC-ESI-LTQ-Orbitrap or an HPLC-MALDI-TOF2. The peptides were readily identified, using MASCOT with a modified enzyme rule, and provided information about 73% of the proteome. Implications are considered of the extended length and the presence of multiple basic residues in these peptides.