Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Statistical analysis

MetaboAnalyst

A web platform and associated R package for metabolomics data processing, statistical analysis, visualization, functional interpretation, and multi-omics integration.

Multiple analytical platformsPlatform-independentTargeted metabolomicsUntargeted metabolomicsMetabolite profiling
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Overview

MetaboAnalyst combines web modules for statistical analysis, functional interpretation and integration of metabolomics results. Researchers can start with abundance tables and sample metadata, annotated metabolite lists, or supported LC-MS spectra. MetaboAnalyst 6.0 includes MS/MS annotation, analysis with covariates, dose-response analysis and genetic association-based causal analysis. MetaboAnalystR supports scripted workflows. Inputs and outputs depend on the module, so users should identify the analysis performed rather than report only the platform name.

What can this tool do?

Univariate statisticsMultivariate statisticsFeature selectionPathway enrichmentInteractive dashboard

Common uses

  • Perform exploratory and inferential statistics on metabolomics data tables.
  • Generate visualizations and pathway-level interpretations.
  • Integrate metabolomics with transcriptomics or other omics results.
  • Save result tables and the analysis settings so statistical and pathway results can be reconstructed.

Scientific fit

Primary function

Statistical analysis

Other functions

Normalization and batch correction, Visualization and reporting, Pathway and biological interpretation, Multi-omics integration, Preprocessing and feature extraction

Analysis types

Targeted metabolomics, Untargeted metabolomics, Metabolite profiling, Lipidomics, Multi-omics

MS level

MS1, MS/MS

Acquisition

Data-dependent acquisition (DDA), Data-independent acquisition (DIA)

Ion mobility

Ion mobility not required

Data compatibility

Inputs

Feature or peak table, Compound list or annotations, Sample metadata, Statistical results, Mass spectra

Outputs

Statistical results, Pathway or reaction data, Human-readable report

Input formats

CSV or TSV, mzML, mzXML, MSP

Output formats

CSV or TSV, PNG, PDF, SVG

Scope and considerations

Designed for

  • Exploratory and inferential analysis of metabolomics abundance tables with a defined study design.
  • Pathway and metabolite-set analysis using annotated compounds or supported untargeted peak lists.

Not designed for

  • Treating a predictive model or pathway association as experimentally established biological causation.

Important requirements

  • Prepare sample labels and covariates consistently with the selected statistical module.
  • For pathway analysis, inspect identifier mapping and choose the relevant organism and background; raw-data modules have separate input requirements.

Considerations

  • Report missing-value handling, normalization, transformation, scaling and multiple-testing choices.
  • Evaluate supervised models with appropriate validation; a separated score plot alone is insufficient evidence of predictive performance.
  • The public web service and optional commercial services have different limits and deployment options.
  • Check the number of compounds that map to the selected pathway resource and report the background used for enrichment.

Education

Learn this tool

External tutorials and workshops collected by Navigator. Entries marked Needs review have not been checked end to end.

MetaboAnalyst 5.0 LC-MS and tandem-MS workshop Part 1Metabolomics Society · Video Workshop · Needs reviewMetaboAnalyst tutorialsMetaboAnalyst / Xia Lab · Training hubMetabolomic Data Analysis Using MetaboAnalystBioinformatics DotCa · Video Workshop · Needs review

Browse all education resources →

Access and documentation

Primary accessDocumentationSource repositoryTutorial

A public web service is available. The project also offers commercial Pro deployments and training; MetaboAnalystR has its own installation and licensing information.

Evidence and review

Documentation-based editorial pass on 6 September 2026: scope, interpretation limits and practical use reviewed against the linked official documentation and cited literature. Software execution, service availability and developer verification were not assessed.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. Pang Z, Chong J, Zhou G, et al. MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights. Nucleic Acids Res 49, W388-W396 (2021). doi:10.1093/nar/gkab382
  2. Pang Z, Lu Y, Zhou G, et al. MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation. Nucleic Acids Res 52, W398-W406 (2024). doi:10.1093/nar/gkae253

Related tools

MetaboAnalystRComplementary to · Run metabolomics processing, statistics and functional interpretation through R.MetaboShinyComplementary to · Explore mass-spectrometry metabolomics tables through an R/Shiny interface.mummichogComplementary to · Generate pathway and network hypotheses from untargeted metabolomics feature tables.RaMP-DBComplementary to · Integrated metabolite, gene/protein, reaction, ontology and pathway resource for metabolomics and multi-omics pathway analysis.roplsComplementary to · Fit and assess multivariate PCA, PLS and OPLS models for omics data in R.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-09-08 · Entry update

    Audit core publications across existing tools

    View change · Entry at this revision
  2. 2026-09-07 · Entry update

    Expand and document 31 metabolomics tools and resources

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  3. 2026-08-21 · Entry update

    Add files via upload

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  4. 2026-08-20 · First committed entry

    Add files via upload

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Full GitHub history