Mass spectrometry imaging in plants: Methods and applications

Mass spectrometry imaging (MSI) has emerged as a powerful platform for spatial metabolomics, enabling direct mapping of metabolites within plant tissues. However, successful application of MSI in plants remains strongly dependent on effective sample preparation, as the unique structural features of plant tissues pose significant analytical challenges. In this review, we highlight recent advances in sample preparation strategies designed to address these limitations across diverse plant tissues. We then discuss how the methodological and technological innovations improve spatial resolution, sensitivity, specificity, and analytical throughput. Building on this technical progress, we survey the expanding biological applications of MSI in plant science, from decoding plant-environment interactions and resolving gene function to tracing the dynamics of metabolism through stable isotope labeling. By linking chemical distributions with biological processes, MSI is playing an increasingly important role in uncovering how metabolic pathways are organized and regulated within plant tissues, ultimately enabling a spatially resolved understanding of plant metabolism.