Plant Single-Cell Metabolomics and Metabolite Imaging: Current Advances and Future Directions

Plants are multicellular systems composed of highly specialized cell types, whose distinct transcriptomes, proteomes, and metabolomes collectively shape growth, development, defense, and environmental adaptation. While single-cell transcriptomics has transformed our understanding of plant cellular heterogeneity, metabolites provide a direct and integrative readout of cellular biochemical activity and physiological state and can offer valuable insights into phenotype. They provide essential information that gene expression alone does not capture. Recent advances in mass spectrometry-based single-cell metabolomics (scMet) have enabled direct measurement of metabolic variation across individual cells and subcellular domains. In parallel, mass spectrometry imaging (MSI) has emerged as a powerful approach for mapping the spatial organization of metabolites within intact plant organs, offering new opportunities to connect chemical diversity with anatomy, cell identity, and biological functions. This review summarizes current technologies for plant single-cell sampling, scMet, and MSI for spatial metabolomics. It further highlights emerging efforts to illuminate the plant’s cellular and spatial dark metabolome through spectral libraries, computational metabolomics, and AI-assisted annotation. A long-term objective is to build quantitative, spatially resolved, and biologically interpretable plant signaling and metabolic networks at single-cell resolution.