This study aims to elucidate the global proteomic changes in Mycobacterium tuberculosis upon treatment with the novel compound ilamycin E(ILE), which targets the Clp protease system. Label-free quantitative proteomics was employed to assess differential protein expression after ILE exposure. The results reveal that ILE induces significant alterations in the expression of proteins involved in proteolysis, stress response, redox homeostasis, and energy metabolism, providing valuable insights into the adaptive response and potential mechanism of action of ILE in M. tuberculosis. These data support further development of ILE as a candidate anti-mycobacterial agent targeting intracellular proteostasis.