Single cell metabolomics

Abstract

Recent discoveries suggest that cells of a clonal population often display multiple metabolic phenotypes at the same time. Motivated by the success of mass spectrometry (MS) in the investigation of population-level metabolomics, the analytical community has initiated efforts towards MS-based single cell metabolomics to investigate metabolic phenomena that are buried under the population average. Here, we review the current approaches and illustrate their advantages and disadvantages. Because of significant advances in the field, different technologies are now at the verge of generating data that are useful for exploring and investigating metabolic heterogeneity. IntroductionQuantitative metabolomics, the technology for large-scale quantification of intracellular metabolite concentrations, is a powerful tool in systems biology research that has recently led to a series of interesting findings (e.g. [1][2][3][4]). Because of the metabolome's chemical diversity, mass spectrometry (MS) is the analytical method of choice [5]. In addition to analytical challenges, quantitative metabolomics as required for addressing (systems) biology questions poses significant challenges in sample processing. One important challenge is the need to preserve the original metabolome during sample processing, which is often difficult because of the presence of enzymes in the sample and the fast metabolic turnover rates.For sensitivity reasons, current metabolomics methods require samples that contain a large number of cells. However, cell populations are not necessarily homogeneous. Besides genetic differences, several other sources for population heterogeneity exist, of which several are also known to cause metabolic differences. Today, methods capable of resolving differences in metabolite levels on the single cell level are provided, within limits, by molecular sensors such as FRET sensors [6,7] or aptamer-based technology [8 ,9]. Both types of molecular sensors, however, are difficult to develop, are limited to specific analytes, and quantitative analyses (e.g. in terms of mol/L) are hardly possible with them. Laserinduced fluorescence, as introduced by Dovichi for single cell proteomics, is limited to fluorescent compounds or labelled species [10,11]. In addition, all these existing methods share the limitation that they can never be extended to the ''-omics'' level, that is to measuring a large number of metabolites at the same time. They will thus not be applicable to discovery type research and research that requires a large number of metabolites to be measured in the same cell.Because of the success of mass spectrometry in population-level metabolome analyses, the analytical community has recently made great strides towards single cell level metabolite analyses (for a review, see [12]). So far, however, hardly any new biological insight has been generated from these endeavours. In this Current Opinion paper, we will thus not only review the current status of MS-based single cell metabolomics but also discuss which of the differ...

High-resolution metabolic mapping of cell types in plant roots

“…For the final experiment, we used four biological replicates of WEREWOLF and SCARECROW and three of PET111, CORTEX, and WOODEN LEG. Nylon mesh was placed on top of the solidified media [1.0% agar (10 g), 0.5 g of Mes (M-2933; Sigma), 1% sucrose (10 g), 4.33 g of MS salts (catalog no. 11117-066; Invitrogen), pH to 5.7-5.8 with KOH].…”

“…3C) also demonstrated the The mass signal intensity is measured in values of ion current, and the y axes represent the relative peak abundances (%). The y axes of the cell population chromatograms are linked, and 100% abundance of each chromatogram corresponds to the TIC of 5·10 4 , to enable comparison of the different chromatograms. Selected GSLs are marked: (1) 4-methylthiobutyl GSL (4MTB; metabolite 25 in Table S1); (2) 8-methylsulfinyloctyl GSL (8MSOO; metabolite 27 in Table S1); (3) 4-methoxyindole I3M GSL (4MO-I3M: metabolite 31 in Table S1); (4) 7-methylthioheptyl GSL (7MTH; metabolite 33 in Table S1); and (5) 8-methylthio-octyl GSL (8MTO; metabolite 34 in Table S1).…”

“…Understanding metabolism and the function of small molecules in specific cell types requires the isolation of individual cell populations for metabolic analysis. For sensitivity reasons, current metabolomics methods require samples that contain a relatively large number of cells (4).…”

Mass spectrometry-based metabolomics of single yeast cells

“…single-cell measurements | MALDI mass spectrometry | baker's yeast E ven genetically identical cells present in the same microenvironment can express different phenotypes, for a number of reasons: cell-to-cell heterogeneity can stem from differences in the cell age and differences in the cell cycle stage, and stochastic effects together with feedback mechanisms can lead to distinctively different phenotypes, too (1)(2)(3)(4)(5)(6). As population-level measurement techniques inherently average out such cell-to-cell differences, biochemical mechanisms underlying a studied system cannot be deduced from such measurements.…”

“…Motivated by advances of mass spectrometry (MS) in metabolomics, the analytical chemistry community has stepped up its efforts toward realizing MS-based single-cell metabolomics (1,2). A number of analytical approaches were developed with detection limits low enough for single-cell metabolite analyses [e.g., nanostructured surfaces (7,8), postionization techniques (9,10), modified laser optics (11), the use of microsampling tools (12,13), microarrays for MS measurements (14,15), etc.].…”