Single-Cell Metabolomics

Abstract

A high-throughput and non-destructive tool with complete coverage of metabolites is required to study single-cell metabolomics, with Raman analysis of single cells being shown to be a recent candidate for these analyses. Single-cell Raman spectra (SCRS) are derived from the sum of all molecular vibrational characteristics within a single cell and thus reflect the intrinsic biochemical profile of the individual cell and can serve as a metabolic fingerprint. Either the entire Raman spectra or specific Raman band of the SCRS can be used as a whole-cell metabolic fingerprint or indicators of specific molecules or chemical structures. Furthermore, in combination with stable isotope probing (e.g. 13C-, 15N-substrates or 2H from heavy water (D2O)), SCRS can be used to link individual cells and their substrate metabolism pathways due to SCRS bands shifting after cellular incorporation of heavier stable isotope elements. This protocol provides the detailed description of cell preparation, single-cell Raman spectral acquisition, data analysis and a table of Raman wavenumber assignments to specific biological molecules which can be used to interpret SCRS.