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The definition of plant cell identity can be expanded beyond transcriptomes through the development of cell-type-specific metabolic fingerprints—distinct sets of metabolites that act as chemical markers for cell identity. Current approaches in metabolomics often rely on transcriptomic data, but evidence shows that metabolites like pigments and lignin precursors encode cell structure and function. By integrating techniques such as histology, mass spectrometry imaging, and computational synthesis, these metabolic signatures can enhance our understanding of plant single-cell biology, providing valuable insights alongside traditional transcriptomics.