Cellular metabolomics: From sample preparation to high-throughput data analysis

Cellular metabolomics, which involves targeted and untargeted analyses of metabolites in in vitro systems, plays a pivotal role in system biology. It offers insights into cell phenotypes and provides a means to monitor cellular activities. The power of cellular metabolomics stems from its abilities to quantify and identify metabolites in a cellular system and to distill the acquired information with various data analysis tools. In comparison to in vivo studies that utilize sera, tissues, and body fluids, cellular metabolomics is not only more cost-effective and controllable but also highly informative about biological functions. This review delves into the intricacies of sample preparation workflows, data acquisition platforms, and data mining and analysis techniques for cellular metabolomic studies, with 127 references cited. We explore the merits and limitations of metabolomics strategies, i.e., targeted and untargeted, aiming to provide readers with a clear understanding of the step-by-step procedures and what can be achieved when executing a cellular metabolomics experiment.