Spatial metabolomics in medicinal plant research: current advances, technical challenges, and future perspectives

Secondary metabolites derived from medicinal plants represent a critical resource for drug discovery and play an indispensable role in the prevention and treatment of major human diseases. Spatial metabolomics has emerged as a transformative approach that overcomes the inherent limitations of traditional metabolomics, particularly tissue homogenisation, by enabling precise, in situ profiling of the spatial heterogeneity and dynamic accumulation of key bioactive compounds. When integrated with complementary technologies such as spatial multi-omics (SMO), single-cell analysis, and artificial intelligence (AI)-assisted imaging, this paradigm provides a powerful framework for deciphering the spatiotemporal regulatory networks that govern secondary metabolite biosynthesis. This review systematically compares conventional and spatial metabolomics, synthesises recent advances in medicinal plant research, critically evaluates current technical challenges and optimisation strategies, and outlines future directions enabled by multi-omics integration and intelligent computational analytics. Collectively, these insights aim to establish a theoretical foundation for the in-depth investigation of medicinal plants and to support their translational application and industrial advancement.