While histone proteins are the founding members of lysine acetylation substrates, it is now clear that hundreds of other proteins can be acetylated in multiple compartments of the cell. Our knowledge of the scope of this modification throughout the kingdom of life is beginning to emerge, as proteome-wide lysine acetylation has been documented in prokaryotes, Arabidopsis thaliana, Drosophila melanogaster, and human cells. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify parasite peptides enriched by immunopurification with acetyl-lysine antibody, we produced the first proteome-wide analysis of acetylation for a protozoan organism, the opportunistic apicomplexan parasite Toxoplasma gondii. The results show that lysine acetylation is abundant in the actively proliferating tachyzoite form of the parasite, which causes acute toxoplasmosis. Our approach successfully identified known acetylation marks on Toxoplasma histones and ␣-tubulin and detected over 400 novel acetylation sites on a wide variety of additional proteins, including those with roles in transcription, translation, metabolism, and stress responses. Importantly, an extensive set of parasite-specific proteins, including those found in organelles unique to Apicomplexa, is acetylated in the parasite. Our data provide a wealth of new information that improves our understanding of the evolution of this vital regulatory modification while potentially revealing novel therapeutic avenues. We conclude from this study that lysine acetylation was prevalent in the early stages of eukaryotic cell evolution and occurs on proteins involved in a remarkably diverse array of cellular functions, including those that are specific to parasites. P rotozoan parasites are responsible for significant morbidity and mortality around the world, and new drug targets are sorely needed. Using the intracellular apicomplexan parasite Toxoplasma gondii as a model, we and others have established that histone acetylation is a critical posttranslational modification involved in parasite viability and development (11,36). Lysine acetylation is also a validated drug target in protozoan parasites based on the antiparasite effects of lysine deacetylase (KDAC) inhibitors, such as apicidin and FR235222 (4, 9).Recent studies have demonstrated that lysine acetylation occurs on a multitude of other proteins beyond histones (22, 31). Not only are there nonhistone proteins acetylated in the nucleus, but proteins in the cytoplasm and mitochondria contain acetylated residues as well. The development of specific acetyl-lysine antibodies to enrich acetylated tryptic peptides prior to identification by mass spectrometry has allowed lysine acetylation to be mapped at the whole-proteome level. So-called "acetylomes" have been described for prokaryotes (15,42,50), plants (12, 45), Drosophila melanogaster (43), and human cells (6, 21, 51). Proteins involved in nearly every facet of cell biology, particularly proteins with roles in metabolism, translation, folding, DNA packaging, and ...