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In this study,a reliable approach for identifying mammalian target of rapamycin inhibitors in natural extracts by using capillary electrophoresis(CE)combined with high performance liquid chromatography tandem mass spectrometry(HPLC–MS/MS)has been developed.5-Carboxyfluorescein-labeld peptide substrate of mTOR,a commercially available mTOR inhibitor AZD8055,and a small chemical library composing of 18 natural extracts were utilized for method development and validation.Firstly,enzymatic inhibition activity of natural extracts were assayed by using capillary electrophoresis.Once the bioactivity of a natural extract was confirmed,the active compounds were identified by an assay-guided isolation and structure elucidation accomplished using LC–MS/MS.By using this approach,salvianolic acid A and salvianolic acid C in extract of Salvia miltiorrhiza were identified as the new mTOR inhibitors from the natural extracts library.The result demonstrates that CE combined with HPLC–MS/MS can become a high throughput,high effective and high-quality platform for discovery of the bioactive compounds in natural products.