MetaboAnalyst 4.0 is an updated version of the comprehensive web-based tool for metabolomic data analysis, interpretation, and integration with other omics data. This update includes four key features: (1) real-time R command tracking and display with a companion MetaboAnalystR package; (2) a MS Peaks to Pathways module for predicting pathway activity from untargeted mass spectral data using the mummichog algorithm; (3) a Biomarker Meta-analysis module for robust biomarker identification through the combination of multiple metabolomic datasets; and (4) a Network Explorer module for integrative analysis of metabolomics, metagenomics, and/or transcriptomics data. The user interface has been reengineered for a modern look and feel, and the underlying knowledgebases have been updated based on the latest data from the Human Metabolome Database (HMDB). A Docker image of MetaboAnalyst is available for local installation. MetaboAnalyst 4.0 is freely available at http://metaboanalyst.ca.MetaboAnalyst 4.0 is an updated version of the comprehensive web-based tool for metabolomic data analysis, interpretation, and integration with other omics data. This update includes four key features: (1) real-time R command tracking and display with a companion MetaboAnalystR package; (2) a MS Peaks to Pathways module for predicting pathway activity from untargeted mass spectral data using the mummichog algorithm; (3) a Biomarker Meta-analysis module for robust biomarker identification through the combination of multiple metabolomic datasets; and (4) a Network Explorer module for integrative analysis of metabolomics, metagenomics, and/or transcriptomics data. The user interface has been reengineered for a modern look and feel, and the underlying knowledgebases have been updated based on the latest data from the Human Metabolome Database (HMDB). A Docker image of MetaboAnalyst is available for local installation. MetaboAnalyst 4.0 is freely available at http://metaboanalyst.ca.