Metabolome analysis based on capillary electrophoresis-mass spectrometry

• Capillary electrophoresis-mass spectrometry (CE-MS) analysis of charged metabolites.
• A sheathless interface can increase the sensitivity of CE-MS.
• Different mass spectrometers present advantages and disadvantages for CE-MS.
• Appropriate sample preparation is necessary for CE-MS-based metabolomics.
• It is important for CE-MS to develop software to predict unknown metabolites.

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.