Liquid chromatography-high-resolution mass spectrometry-based cell metabolomics: Experimental design, recommendations, and applications

Cell metabolomics is a comprehensive analytical approach to study small biological molecules involved in many fundamental intracellular functions, linking mechanistic biochemistry to cell phenotype. Metabolism is vital to every aspect of cell function, thus the collection of reliable metabolomic data sets, the culture and sampling conditions used, and the metabolic state of the cells are crucial. Cell-dependent methods, such as cellular quenching and extraction protocols, have been developed, but no universal methodology for sample pretreatment has been developed yet. In this article, various methods to study cell metabolomics are reviewed. High-resolution mass spectrometry can improve analysis, providing excellent mass accuracy and sensitivity. An overview of the sample processing methods commonly used in cell metabolomics based on liquid chromatography-high-resolution mass spectrometry (LC-HRMS) is provided in this study, with details of the critical steps for cell metabolomics. Examples of applications for cellular metabolite profiling are described and perspectives in this field are discussed.