Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Workflow management and reproducibility

UmetaFlow

A Snakemake workflow for high-throughput untargeted metabolomics that combines file conversion, OpenMS preprocessing, SIRIUS-family annotation, GNPS export, spectral matching, and graph-based outputs.

LC-MSUntargeted metabolomicsCommand lineWorkflow language or engineOpen source
Access toolSuggest an update

Overview

UmetaFlow organizes untargeted metabolomics processing with Snakemake and OpenMS/pyOpenMS. It combines feature detection, alignment and optional re-quantification with configurable spectral matching, formula/class prediction and GNPS-compatible exports.

What can this tool do?

Provenance trackingContainer supportPeak or feature detectionRetention-time alignmentGap fillingSpectral-library matchingMolecular-formula predictionCompound-class prediction

Common uses

  • Execute a reproducible untargeted LC-MS pipeline around OpenMS.
  • Prepare outputs for SIRIUS-family annotation and GNPS feature-based molecular networking.

Scientific fit

Primary function

Workflow management and reproducibility

Other functions

Data conversion and import, Preprocessing and feature extraction, Metabolite annotation and identification, Spectral processing and comparison, Molecular networking and chemical similarity

Analysis types

Untargeted metabolomics

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, Mass spectra, Compound list or annotations

Input formats

Vendor raw format, mzML

Output formats

CSV or TSV, MGF

Scope and considerations

Designed for

  • High-throughput untargeted metabolomics workflows combining preprocessing and downstream annotation/export.

Not designed for

  • A guarantee of structural identification or identical processing for every vendor's proprietary raw format.

Important requirements

  • A documented Linux/macOS conda and Snakemake environment, acquisition-appropriate configuration and sample tables; enable only annotation modules whose external software, models and libraries are available.

Considerations

  • Thermo raw conversion is integrated; other vendor files generally require independent mzML conversion. Module-dependent candidate annotations need inspection beyond workflow completion.

Access and documentation

Primary accessDocumentation

Apache-2.0 workflow code. External programs, databases and hosted annotation services retain separate licenses and access requirements.

License: Apache-2.0

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.

  1. UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis. Journal of Cheminformatics (2023). doi:10.1186/s13321-023-00724-w

Related tools

MAWSimilar function · A reproducible metabolome-annotation workflow combining spectral-database dereplication and compound-database annotation from tandem mass-spectrometry data.MetaboAppsSimilar function · A modular collection of browser-based downstream analysis applications that extend GNPS2 results with targeted interpretation, statistics, metadata, and domain-specific readouts.MetabonautSimilar function · An open educational and reproducible workflow resource for script-based untargeted LC-MS/MS metabolomics using R and Bioconductor packages across preprocessing, QC, statistics, and annotation.msiFlowSimilar function · msiFlow provides Snakemake workflows for MSI preprocessing, segmentation, registration to immunofluorescence microscopy and region-based statistical or machine-learning analysis.

Entry history

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

  1. 2026-10-27 · First committed entry

    Add 27 source-reviewed tools from Enveda intake

    View change · Entry at this revision

Full GitHub history