SMAnalyst: A Web Server for Spatial Metabolomic Data Analysis and Annotation

Spatial metabolomics is a rapidly advancing field offering powerful insights into metabolic heterogeneity in biological tissues. However, its widespread adoption is hindered by fragmented tools and the lack of comprehensive, open-source GUI software covering the full analytical workflow (quality control, preprocessing, identification, pattern, and differential analysis). To address this, we developed SManalyst, an open-source, integrated web-based platform. SManalyst consolidates core functionalities, including multi-dimensional data quality assessment (background consistency, noise, intensity, missing values), a comprehensive metabolite annotation scoring system (mass accuracy, isotopic similarity, adduct evidence), and dual-dimension spatial pattern discovery (metabolite co-expression and pixel clustering). It also offers flexible differential analysis (cluster- or user-defined regions). With its intuitive GUI and modular workflow, SManalyst significantly lowers the analysis barrier. Tested with a mouse brain dataset, SManalyst efficiently handles large-scale data (e.g., >14,000 pixels, >3,000 ion peaks), effectively filling a critical gap in integrated analytical solutions for spatial metabolomics. The platform is freely accessible at https://metax.genomics.cn/app/smanalyst.