Large-scale metabolite imaging gallery of mouse organ tissues to study spatial metabolism

Abstract Mass spectrometry imaging (MSI) has revolutionized the study of tissue metabolism by enabling the visualization of small molecule metabolites (SMMs) in high spatial resolution. However, comprehensive SMM imaging databases for different organ tissues are lacking, hindering our understanding of spatial organ metabolism. To address this resource gap, we present a large-scale SMM imaging gallery for mouse brain, kidney, and liver, capturing over 300 SMMs spanning nine chemical superclasses and encompassing over 40 metabolic pathways. Manual curation of these imaging datasets yielded novel insights into organ-specific metabolic processes, unveiling previously unexplored spatial distribution patterns. Specifically, we identify 82 SMMs annotated in coronal sections and 86 in sagittal tissue sections, including novel spatial patterns for neurotransmitters. Furthermore, we map 111 SMMs in kidney and 69 SMMs in liver, providing new insights into their amino acid and glutathione metabolism. Our comprehensive SMM imaging gallery serves as a critical resource for the spatial metabolism research community, filling a significant resource gap. This resource is freely available for download and can be accessed through the BioImage Archive and METASPACE repositories, providing high quality annotated images for training AI-based computational models and advancing our understanding of tissue metabolism at the spatial level.