Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Metabolite annotation and identification

MetFrag

Rank candidate molecular structures by comparing predicted fragments with an experimental MS/MS spectrum.

LC-MSDirect-infusion MSWeb applicationCommand lineR package
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Overview

MetFrag retrieves structures using precursor information and scores their in silico fragments against measured peaks. Optional evidence scores can supplement fragmentation. Use it after extracting spectra when you need a transparent, configurable candidate-ranking workflow.

What can this tool do?

Structure-database searchingIn-silico spectrum prediction

Common uses

  • Prioritize structures for an unknown MS/MS spectrum.
  • Repeat annotation with an explicitly recorded candidate database and scoring configuration.

Scientific fit

Primary function

Metabolite annotation and identification

Data compatibility

Inputs

Mass spectra, Molecular structures

Outputs

Compound list or annotations, Molecular structures

Input formats

Text peak list (m/z and intensity), MetFrag parameter file

Output formats

SDF, CSV or TSV

Scope and considerations

Designed for

  • Database-constrained structure annotation from prepared spectra.

Not designed for

  • Detecting or aligning chromatographic features from raw files.

Important requirements

  • Supply precursor mass or formula, ion/adduct settings, a peak list and mass tolerances; Java is needed for local command-line use.

Considerations

  • A correct structure must be represented in the candidate set. A high rank is supporting evidence, not confirmation with an authentic standard.

Education

Learn this tool

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

MetFrag Hands-onMetFrag project / IPB Halle · TutorialLC/MS data analysis with XCMS and MetFrag on PhenoMeNalEMBL's European Bioinformatics Institute EMBL-EBI · Video · Needs review

Browse all education resources →

Access and documentation

Primary accessDocumentation

Available through the web interface, Java command line and R interface. External databases may have separate access conditions.

License: LGPL-2.1-or-later

Evidence and review

Editorial review on 7 September 2026 against official documentation and the sources listed here. Scope and practical guidance are editorial synthesis; software execution and service availability were not validated.

Core publications

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

  1. Ruttkies C, Schymanski EL, Wolf S, et al. MetFrag relaunched: incorporating strategies beyond in silico fragmentation. J Cheminform 8, 3 (2016). doi:10.1186/s13321-016-0115-9

Related tools

CSI:FingerIDAlternative to · A SIRIUS-integrated machine-learning method and webservice for predicting molecular fingerprints from MS/MS data and ranking candidate structures from molecular-structure databases.MoNAComplementary to · Search aggregated mass spectra and download reference libraries for local annotation workflows.MS-FINDERAlternative to · Explore formula and structure candidates using fragmentation rules and EI-MS or MS/MS library searches.CFM-IDComplementary to · Predict tandem mass spectra, annotate fragments and rank candidate structures for small molecules.patRoonComplementary to · Assemble reproducible non-target screening workflows for environmental mass spectrometry in R.ChemWalkerIntegrates with · Rank candidate molecular structures by propagating spectral-library annotation evidence through molecular networks using random walks.LC-MS2StructIntegrates with · Jointly rank molecular candidates using LC retention order and precomputed MS/MS scores.

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

    Expand and document 31 metabolomics tools and resources

    View change · Entry at this revision

Full GitHub history