MetaboAnalyst 5.0 is a web-based platform that enhances the analysis of metabolomics data by bridging the gap between raw data and functional insights. This version introduces three key modules: (1) an LC-MS Spectra Processing module that automates parameter optimization and simplifies the analysis of LC-MS1 spectra; (2) a Functional Analysis module that allows users to select peak groups and evaluate their functional enrichment based on metabolic pathways and metabolite sets; and (3) a Functional Meta-Analysis module that integrates multiple global metabolomics datasets to provide comprehensive insights. Additional features include weighted joint-pathway analysis, data-driven network analysis, batch effect correction, and improved compound name matching. The web interface, graphics, and codebase have been optimized for better performance and user experience. MetaboAnalyst 5.0 is freely available at https://www.metaboanalyst.ca and supports various data formats, including mzTab 2.0-M and data from the Metabolomics Workbench. The platform also includes new tutorials, FAQs, and two mirror sites for raw data processing. MetaboAnalyst 5.0 improves the integration of metabolomics data with other 'omics' data, supports lipidomics, and enhances the accuracy of functional analysis through updated knowledge bases and pathway libraries. It also provides tools for batch effect correction, merging technical replicates, and automated data analysis. The platform is designed to be user-friendly, with a modular structure that allows for streamlined data analysis and integration with other tools. MetaboAnalyst 5.0 is a comprehensive tool for metabolomics data analysis and interpretation, offering improved support for global metabolomics and functional insights.MetaboAnalyst 5.0 is a web-based platform that enhances the analysis of metabolomics data by bridging the gap between raw data and functional insights. This version introduces three key modules: (1) an LC-MS Spectra Processing module that automates parameter optimization and simplifies the analysis of LC-MS1 spectra; (2) a Functional Analysis module that allows users to select peak groups and evaluate their functional enrichment based on metabolic pathways and metabolite sets; and (3) a Functional Meta-Analysis module that integrates multiple global metabolomics datasets to provide comprehensive insights. Additional features include weighted joint-pathway analysis, data-driven network analysis, batch effect correction, and improved compound name matching. The web interface, graphics, and codebase have been optimized for better performance and user experience. MetaboAnalyst 5.0 is freely available at https://www.metaboanalyst.ca and supports various data formats, including mzTab 2.0-M and data from the Metabolomics Workbench. The platform also includes new tutorials, FAQs, and two mirror sites for raw data processing. MetaboAnalyst 5.0 improves the integration of metabolomics data with other 'omics' data, supports lipidomics, and enhances the accuracy of functional analysis through updated knowledge bases and pathway libraries. It also provides tools for batch effect correction, merging technical replicates, and automated data analysis. The platform is designed to be user-friendly, with a modular structure that allows for streamlined data analysis and integration with other tools. MetaboAnalyst 5.0 is a comprehensive tool for metabolomics data analysis and interpretation, offering improved support for global metabolomics and functional insights.