SMIntegration: A web tool for comprehensive spatial metabolomics and transcriptomics integrated analysis and visualization

Current tools for spatial omics analysis often face challenges in performing integrated transcriptomics and metabolomics analysis, in-depth biological interpretation, and user-friendly operation. To address this, we developed SMIntegration, the first web-based graphical platform designed specifically for integrated spatial metabolomics and transcriptomics analysis. Built with R/Shiny and deployed using Docker containerization, the platform provides a complete integration workflow, starting from pre-processed spatial features through to functional annotation. Its core functions include (1) automated and interactive spatial registration; (2) cross-modal spatial pattern recognition; (3) flexible differential analysis of genes and mass features based on clustering results, user-defined regions, or cell type annotations; and (4) group-specific gene-metabolite network construction and interactive visualization. Using adjacent mouse brain coronal sections (Stereo-seq transcriptomics and AFADESI-MS metabolomics) as an example, SMIntegration successfully identified both the periaqueductal gray and subcommissural organ, which were missed by single-modality clustering. Cell type analysis revealed an association between astrocyte-enriched GABA metabolism and Slc6a11, while a comparison between the cornu ammonis region and the midbrain periaqueductal gray dissected glutamatergic and endogenous cannabinoid signaling pathway modules. With a zero-code interface, SMIntegration enables a wide range of researchers to deeply explore gene-metabolite interaction mechanisms within microenvironments during development, homeostasis, and disease.