MetaboAnalyst

MetaboAnalyst is a web-based platform for comprehensive metabolomics data analysis and interpretation. It provides an integrated set of tools designed to support both untargeted and targeted metabolomics workflows, with an emphasis on accessibility for users who may not have extensive programming experience. The platform facilitates data processing, statistical analysis, and biological interpretation within a single online environment.

Key features include data processing and normalization, scaling and transformation, and a range of statistical methods. Users can perform multivariate analyses such as principal component analysis and partial least squares discriminant analysis, as well as univariate tests, ROC analysis, heatmaps, and clustering. MetaboAnalyst also offers pathway analysis and metabolite set enrichment, supporting mapping to databases like KEGG, HMDB, and SMPDB, along with network visualization to aid interpretation of results.

The typical workflow involves importing data in common formats, handling missing values, applying normalization and scaling, selecting appropriate statistical analyses, and generating plots and exportable tables. The platform also supports reproducibility by recording analysis steps and enables batch analyses for multiple datasets. A companion R package, MetaboAnalystR, provides programmatic access to the platform’s algorithms for users who work in R.

Development and impact: MetaboAnalyst was developed by researchers associated with the Xia laboratory and collaborators, and it has undergone multiple major updates to expand its capabilities and improve usability. It has become a widely used, widely cited tool in the metabolomics community, serving as a standard reference platform for data analysis and interpretation.