Proteins are decorated with a suite of chemical modifications, which regulate their activity and overall metabolic homeostasis. The most well-studied lysine modification is acetylation, and hyperacetylation of several proteins leads to metabolic dysfunction and potentially contributes to human disease. More recently, new chemical modifications that regulate protein activity have emerged, including succinylation and malonylation, however little is known about the biology regulated by these modifications. The suite of acyl-based chemical modifications of mitochondrial proteins is regulated by a family of NAD+-dependent deacetylase enzymes call the sirtuins (SIRT1-7), which have also been termed “deacylases” for their new enzymatic activities. We recently discovered new protein modifications present on cellular proteins, which provides important insight into the regulatory role of the sirtuins.