Update publication information. Bacterial resistance has become more and more widespread which seriously threatens human life and health. Therefore, using the natural immune system of host to kill bacteria is particularly fascinating. Here, using mass spectrometry analyses, we depicted the dynamic expression landscape of mitochondria and lysosomes proteins upon five kinds of bacteria (L. monocytogenes, Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa) infection in Macrophages cells. We showed that the protein expression level of Cathepsin D (CTSD) is up-regualated after bacterial infection. The knockout of CTSD indicated that, as a broad-spectrum antibacterial protein in the host, played an indispensable role in killing bacteria. Our study shows that CTSD can serve as a potential molecular drug target for antibacterial treatment.