Overview
Metabonaut is an executable educational workflow resource for script-based untargeted LC-MS/MS analysis in R and Bioconductor. Its vignettes demonstrate preprocessing, annotation and statistics using a small example dataset and show how to adapt and connect existing packages.
What can this tool do?
Common uses
- Learn a reproducible end-to-end untargeted LC-MS/MS workflow in R.
- Reuse worked examples for preprocessing, quality control, statistics, and annotation.
Scientific fit
Primary function
Workflow management and reproducibility
Other functions
Preprocessing and feature extraction, Quality control and filtering, Statistical analysis, Metabolite annotation and identification
Analysis types
Untargeted metabolomics, Metabolite profiling
MS level
MS1, MS/MS
Acquisition
Full-scan MS, Data-dependent acquisition (DDA), General or unspecified acquisition
Ion mobility
Not specified
Data compatibility
Inputs
Raw instrument data, Mass spectra, Sample metadata
Outputs
Feature or peak table, Statistical results, Compound list or annotations, Human-readable report
Input formats
mzML, CSV or TSV
Output formats
R analysis objects, feature tables and rendered workflow documents
Scope and considerations
Designed for
- Learning and reproducing script-based untargeted LC-MS/MS analysis with R/Bioconductor.
Not designed for
- A single replacement processing engine or automatic transfer of tutorial parameters to every study.
Important requirements
- Basic R and Quarto/RMarkdown familiarity; use the documented local R environment, Docker image or Bioconductor workshop session with its example data and dependencies.
Considerations
- Workshop sessions are ephemeral; export work before stopping them. Adapting workflows requires checking acquisition-specific parameters and reference resources.
Access and documentation
The resource is distributed under CC-BY-SA-4.0. Container and workshop routes provide environments; dependencies retain their own licenses and external services may have separate terms.
License: CC-BY-SA-4.0
Evidence and review
Enveda intake rechecked against official README/documentation, repository access terms and primary publication metadata on 2026-10-27. Editorial source review only; no software execution or independent benchmarking. See docs/enveda-expansion-review-2026-10-27.md.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Metabonaut: an open educational resource for learning reproducible, script-based untargeted LC-MS/MS metabolomics. Metabolomics (2026). doi:10.1007/s11306-026-02538-x
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-10-27 · First committed entry
Add 27 source-reviewed tools from Enveda intake
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