Single-Cell Mass Spectrometry of Subpopulations Selected by Fluorescence Microscopy

Specific subpopulations in a heterogeneous collection of cells, for example, cancer stem cells in a tumor, are often associated with biological or medical conditions. Fluorescence microscopy, based on biomarkers labeled with fluorescent probes, is a widely used technique for the visualization and selection of such cells. Phenotypic differences for these subpopulations at the molecular level can be identified by their untargeted analysis by single-cell mass spectrometry (MS). Here, we combine capillary micro sampling MS with fluorescence microscopy for the analysis of metabolite and lipid levels in single cells to discern the heterogeneity of subpopulations corresponding to mitotic stages, The distributions of ATP, reduced glutathione (GSH), and UDP-N-acetylhexosamine (UDP-HexNAc) levels in mitosis reveal the presence of 2-3 underlying subpopulations. Cellular energy is found to be higher in metaphase compared to prometaphase and slightly declines in anaphase, telophase, and cytokinesis. The [GTP]/[GDP] ratio in cytokinesis is significantly higher than in prometaphase and anaphase. Pairwise correlations between metabolite levels show that some molecules within a group, including certain amino acids and nucleotide sugars, are strongly correlated throughout mitosis, but this is not related to their pathway distances. Correlations are observed between monophosphates (AMP and GMP), diphosphates (ADP and GDP), and triphosphates (ATP and GTP) of different nucleosides. In contrast, there is low correlation between diphosphates and triphosphates of the same nucleoside (ADP and ATP).