Overview
Workflow4Metabolomics combines preprocessing, QC, normalization, statistics and annotation tools for MS-based metabolomics through a browser-based workflow system. This entry covers its MS workflows.
What can this tool do?
Common uses
- Run a documented workflow without writing every analysis step.
- Share analysis histories and parameters with collaborators.
Scientific fit
Primary function
Workflow management and reproducibility
Data compatibility
Inputs
Mass spectra, Feature or peak table, Sample metadata
Outputs
Feature or peak table, Compound list or annotations, Statistical results, Human-readable report
Input formats
Other, Files accepted by the chosen Galaxy tools
Output formats
Other, Galaxy datasets, histories and workflows
Scope and considerations
Designed for
- Run a documented workflow without writing every analysis step.
Not designed for
- Making an analysis valid merely because the workflow is reproducible.
Important requirements
- An account on a suitable Galaxy instance and data compatible with the chosen tools.
Considerations
- W4M also supports NMR metabolomics, including workflows starting from FID data. This Navigator entry describes its MS-based applications.
- Record tool versions and histories; public-server quotas, installed tools and job availability vary by instance.
Education
Learn this tool
External tutorials and workshops collected by Navigator. Entries marked Needs review have not been checked end to end.
Access and documentation
Free account on the public instance; individual tools and datasets retain their licenses.
Evidence and review
Documentation-based editorial review on 7 September 2026. Scope and limitations summarize the linked official sources; software execution and developer verification were not assessed. Scope correction contributed by Yann Guitton (ORCID 0000-0002-4479-0636), W4M Coreteam, in https://github.com/scottjarmusch/metabolomics-navigator/issues/23.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Delporte C, Tremblay-Franco M, Guitton Y, et al. Workflow4Metabolomics (W4M): A User-Friendly Metabolomics Platform for Analysis of Mass Spectrometry and Nuclear Magnetic Resonance Data. Curr Protoc 5, e70095 (2025). doi:10.1002/cpz1.70095
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-15 · Entry update
Recover MS2DECIDE submission and credit W4M scope correction
View change · Entry at this revision - 2026-09-08 · Entry update
Focus shared resource entries on MS workflows
View change · Entry at this revision - 2026-09-08 · Entry update
Audit core publications across existing tools
View change · Entry at this revision - 2026-09-07 · First committed entry
Add 50 documented metabolomics resources
View change · Entry at this revision