Capillary electrophoresis-mass spectrometry (CE-MS) has emerged as a powerful new tool for comprehensive analysis of charged compounds. In this review, we provide a general description of the application of CE-MS in metabolome analysis, including the separation modes of CE, various interfaces and the mass spectrometers used. We also discuss strategies for sample pretreatment, data processing and peak identification, which are important processes in metabolome analysis. In addition, we highlight a number of new techniques to improve metabolite extraction, peak resolution and sensitivity. Finally, we provide some general conclusions and future perspectives.
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