Acetylation of lysine residues in proteins is a reversible and highly regulated posttranslational modification. However, it has not been systematically studied in prokaryotes. By affinity immunoseparation using an anti-acetyllysine antibody together with nano-HPLC/MS/MS, we identified 125 lysine-acetylated sites in 85 proteins among proteins derived from Escherichia coli. The lysine-acetylated proteins identified are involved in diverse cellular functions including protein synthesis, carbohydrate metabolism, the TCA cycle, nucleotide and amino acid metabolism, chaperones, and transcription. Interestingly, we found a higher level of acetylation during the stationary phase than in the exponential phase; proteins acetylated during the stationary phase were immediately deacetylated when the cells were transferred to fresh LB culture medium. These results demonstrate that lysine acetylation is abundant in E. coli and might be involved in modifying or regulating the activities of various enzymes involved in critical metabolic processes and the synthesis of building blocks in response to environmental changes.