Proteomics originated from 2-dimensional electrophoresis more than thirty years ago. Technological advances have made proteomics one of the most flourishing areas of modern biotechnology research. Proteomics mainly characterizes protein functions, protein–protein interactions, and protein modification in cells, tissues or animals. The integration of proteomic data helps to screen bioactive compounds, biomarkers of diseases, or signaling pathways in cells or the whole body. Natural products are valuable resources that contain a variety of bioactive compounds. However, the mechanisms of action of many natural products and bioactive compounds are unclear. The identification of the target proteins of discovered biologically active natural products to understand their mechanisms is a critical hurdle for their development into clinical drugs. This review describes the application of proteomics to determine the mechanisms of natural products, including compounds, peptides and mixtures in the recent years. This article summarizes progress on antimicrobials, antineoplastics, antiparasitics, nervous system drugs, antivirals and cardiovascular disease drugs.Proteomics originated from 2-dimensional electrophoresis more than thirty years ago. Technological advances have made proteomics one of the most flourishing areas of modern biotechnology research. Proteomics mainly characterizes protein functions, protein–protein interactions, and protein modification in cells, tissues or animals. The integration of proteomic data helps to screen bioactive compounds, biomarkers of diseases, or signaling pathways in cells or the whole body. Natural products are valuable resources that contain a variety of bioactive compounds. However, the mechanisms of action of many natural products and bioactive compounds are unclear. The identification of the target proteins of discovered biologically active natural products to understand their mechanisms is a critical hurdle for their development into clinical drugs. This review describes the application of proteomics to determine the mechanisms of natural products, including compounds, peptides and mixtures in the recent years. This article summarizes progress on antimicrobials, antineoplastics, antiparasitics, nervous system drugs, antivirals and cardiovascular disease drugs., {"references":["1.\tChang J, Kwon HJ. Discovery of novel drug targets and their functions using phenotypic screening of natural products. J Ind Microbiol Biotechnol. 2016 Mar;43(2-3):221-31. doi: 10.1007/s10295-015-1681-y.","2.\tDouglas Kinghorn, Young-Won Chin, and Steven M. Swanson .Discovery of Natural Product Anticancer Agents from Biodiverse Organisms. Curr Opin Drug Discov Devel. 2009 Mar; 12(2): 189–196.","3.\tIrkin R, Esmer OK. 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