Single-cell metabolomics is an emerging field that addresses fundamental biological questions and allows one to observe metabolic phenomena in heterogeneous populations of single cells. In this review, we assess the suitability of different detection techniques and present considerations on sample preparation for single-cell metabolomics. Although targeted analysis of single cells can readily be conducted using fluorescent probes and optical instruments (microscopes, fluorescence detectors), a comprehensive metabolomic approach requires a powerful label-free method, such as mass spectrometry (MS). Mass-spectrometric techniques applied to study small molecules in single cells include electrospray MS, matrix-assisted laser desorption/ionization MS, and secondary ion MS. Sample preparation is an important aspect to be taken into account during further development of methods for single-cell metabolomics.

Functional high-density micro-arrays for mass spectrometry enable rapid picolitre-volume aliquoting and ultrasensitive analysis of microscale samples, for example, single cells.

Getting a look‐in: An optimized MALDI‐MS procedure has been developed to detect endogenous primary metabolites directly in the cell extract. A detection limit corresponding to metabolites from less than a single cell has been attained, opening the door to single‐cell metabolomics by mass spectrometry.

Heterogeneity is a characteristic feature of all populations of living organisms. Here we make an attempt to validate a single-cell mass spectrometric method for detection of changes in metabolite levels occurring in populations of unicellular organisms. Selected metabolites involved in central metabolism (ADP, ATP, GTP, and UDP-Glucose) could readily be detected in single cells of Closterium acerosum by means of negative-mode matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS). The analytical capabilities of this approach were characterized using standard compounds. The method was then used to study populations of individual cells with different levels of the chosen metabolites. With principal component analysis and support vector machine algorithms, it was possible to achieve a clear separation of individual C. acerosum cells in different metabolic states. This study demonstrates the suitability of mass spectrometric analysis of metabolites in single cells to measure cell-population heterogeneity.

We demonstrate a facile label-free approach for performing multidimensional chemical analysis on individual single-cell organisms by combining optical, fluorescence, and Raman microspectroscopy with matrix-free laser desorption/ionization mass spectrometry (MS). Single unicellular algae are seeded on a bare stainless steel plate and analyzed microspectroscopically. This provides information on the content and distribution of photoactive species, such as β-carotene, as well as chlorophyll and other components of the photosynthetic apparatus. Exactly the same cells are then analyzed by mass spectrometry in the negative ion mode. Phospholipid species are readily ionized by laser desorption/ionization of intact cells, without the need for an auxiliary matrix. This not only facilitates sample preparation but also preserves high spatial resolution and high sensitivity. Using this method, we were able to study the content and arrangement of proplastids and photosystem components, as well as the amounts of various phospholipid species in individual algal cells. The methodology can be used in the fundamental biological studies on these unicellular organisms, which require information on the internal structure as well as the chemical composition of individual cells.