Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Workflow management and reproducibility

patRoon

Assemble reproducible non-target screening workflows for environmental mass spectrometry in R.

LC-MSR packageOpen source
Access toolSuggest an update

Overview

patRoon connects feature extraction, suspect screening, formula and compound annotation, transformation-product analysis and reporting through a common interface.

What can this tool do?

Provenance trackingStructure-database searching

Common uses

  • Screen environmental samples for suspect compounds.
  • Compare alternative processing algorithms in a scripted workflow.

Scientific fit

Primary function

Workflow management and reproducibility

Data compatibility

Inputs

Mass spectra, Sample metadata

Outputs

Feature or peak table, Compound list or annotations, Human-readable report

Input formats

mzML

Output formats

CSV or TSV

Scope and considerations

Designed for

  • Screen environmental samples for suspect compounds.

Not designed for

  • Guaranteeing identity or toxicity from a predicted candidate.

Important requirements

  • R plus the external programs required by the selected algorithms.

Considerations

  • Record both patRoon and component versions; external annotation services can require separate accounts or licenses.

Education

Learn this tool

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

patRoon tutorialpatRoon project / Rick Helmus · Tutorial

Browse all education resources →

Access and documentation

Primary access

GPL-3.0 platform; integrated software and databases retain their own terms.

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.

Core publications

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

  1. Helmus R, Ter Laak TL, van Wezel AP, et al. patRoon: open source software platform for environmental mass spectrometry based non-target screening. J Cheminform 13, 1 (2021). doi:10.1186/s13321-020-00477-w

Related tools

MetFragComplementary to · Rank candidate molecular structures by comparing predicted fragments with an experimental MS/MS spectrum.OpenMSComplementary to · An open-source C++ library, command-line toolkit, and Python interface for reproducible mass spectrometry data processing in metabolomics and proteomics.

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 · First committed entry

    Add 50 documented metabolomics resources

    View change · Entry at this revision

Full GitHub history