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Metabolomics is being more and more applied in different aspects of life science including disease subtyping and potential biomarker discovery as well as plant physiology.Mass spectrometry(MS)and NMR are the most widely used analytical techniques.For MS,based on the Web of Science,GC-MS and LC-MS occupied about 65%.Unfortunately,they are only for(semi-)volatile and hydrophobic(RPLC)metabolites analysis.In reverse,capillary electrosphoresis-mass spectrometry(CE-MS)has been very popular in characterization of polar metabolites in complex biological samples due to its advantages of being simple and highly efficient,and being close to green analytical chemistry with the need for only small amount of samples and low consumption of reagents and solvents.Here we report applications of CE-MS in metabolomics study on potential toxicity of BPA,discovery of biomarkers of hepatocellular carcinoma and discrimination of plants from different geographical origins.Validation and evaluation of metabolic biomarkers were conducted in one study to confirm the efficiency of the CE-MSbased biomarker discovery.Our results demonstrated that CE-MS-based metabolomics enables to provide novel insights into the connections between chemical exposure and profound effects on organisms,the complicated biological process of tumor metabolism and the relationship between metabolites and plant growth environment.