Almost all currently employed analytical "-omics" methods provide data that are averaged over an entire cell population, but even genetically identical cells exposed to the same environmental conditions can show strong variations in molecular content and even in phenotypes. [1] Such heterogeneity is involved in many cellular and also disease-related processes, such as antibiotic resistance, [2] competence for DNA uptake, [3] and in viral life-cycle decisions. [4] The increasing number of such findings suggests that cellular heterogeneity is underestimated, which in turn calls for development of novel single-cell-based analytical methods.
Today, several techniques for chemical analysis of single cells exist, most of which focus on detection of peptides and proteins. In addition to the high sensitivity that is generally required for single cell analysis, the detection of intracellular metabolites (typically small molecules with MW < 1000 Da), poses additional challenges. In contrast to the protein and transcription levels, the metabolic level presents 1) turnover rates on the order of seconds, thus demanding fast cell processing, 2) a large chemical diversity, and 3) small molecular weights, which renders fluorescent tagging difficult without impacting the biological function of metabolites. Only very few studies have so far demonstrated the feasibility of small-molecule analysis in single cells. Capillary electrophoresis coupled with laser-induced fluorescence, a method named metabolic cytometry, [5] has been successfully used to