The number of research topics and medical projects linked to single-cell genomics, transcriptome, proteomics, and metabolomics has expanded dramatically in recent years, as interest in the potential of single-cell omics in the diagnosis and treatment of diseases has started to grow. A collection of small molecule metabolites present in a certain cell, organ, or organism is referred to as a metabolome. Because cellular metabolism is so dynamic, single-cell metabolomics can be utilized to identify the chemical defense mechanisms cells employ in response to environmental or chemical stressors. Metabolomics is by far the most challenging single-cell omics to measure, yet it provides a more direct and dynamic description of cell function than other single-cell omics.