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Metabolite annotation and identification

MetaboAnnotatoR

An R package for annotating LC-MS all-ion-fragmentation metabolomics features using fragment-ion databases and centroided chromatographic data.

LC-MSUntargeted metabolomicsR packageOpen source
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Overview

MetaboAnnotatoR annotates LC-MS all-ion-fragmentation features using chromatographic information and metabolite fragment databases. The R workflow links processed AIF data to candidate metabolites and includes guidance for constructing fragment-database entries.

What can this tool do?

Spectral-library matchingMS/MS processing

Common uses

  • Annotate AIF LC-MS features by matching fragment-ion evidence to reference databases.

Scientific fit

Primary function

Metabolite annotation and identification

Other functions

Spectral processing and comparison

Analysis types

Untargeted metabolomics

MS level

MS1, MS/MS

Acquisition

All-ion fragmentation

Ion mobility

Ion mobility not required

Data compatibility

Inputs

Raw instrument data, Mass spectra, Spectral library

Outputs

Compound list or annotations

Input formats

Centroided LC-MS AIF data and R feature/group/fragment-database objects

Output formats

R candidate annotations and feature-to-fragment evidence

Scope and considerations

Designed for

  • An R package for annotating LC-MS all-ion-fragmentation metabolomics features using fragment-ion databases and centroided chromatographic data.

Not designed for

  • Treating all coeluting fragments as compound-specific evidence or direct transfer of the AIF workflow to every DDA/DIA design.

Important requirements

  • R/Bioconductor dependencies, centroided AIF chromatograms, compatible processed feature/group information and an appropriate ion-fragment database; follow the xcms/RAMClustR vignette for the documented example.

Considerations

  • Fragment coverage, chromatographic coelution and upstream grouping affect annotations. Candidate matches need assessment of competing explanations and additional evidence.

Access and documentation

Primary accessDocumentation

GPL-3.0 source distribution. External datasets, dependent packages and any hosted routes retain their own terms; software operation was not tested.

License: GPL-3.0

Evidence and review

Enveda intake rechecked against official repository documentation, package/license metadata and primary publication identity on 2026-10-27. Editorial source review only; no software execution or independent benchmark. See docs/enveda-expansion-review-2026-10-27-batch2.md.

Core publications

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

  1. Automated Annotation of Untargeted All-Ion Fragmentation LC–MS Metabolomics Data with MetaboAnnotatoR. Analytical Chemistry (2022). doi:10.1021/acs.analchem.1c03032

Related tools

BAMSimilar function · BAM generates and ranks structural candidates for suspect metabolites by applying biotransformation rules to known anchor structures.BUDDY / msbuddySimilar function · Generate and rank molecular formula annotations for small-molecule mass-spectrometry queries.CANOPUSSimilar function · A SIRIUS-integrated machine-learning method and webservice for predicting compound classes directly from high-resolution MS/MS data without requiring an exact database structure match.CFM-IDSimilar function · Predict tandem mass spectra, annotate fragments and rank candidate structures for small molecules.

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 24 reviewed Enveda tools in a separate second batch

    View change · Entry at this revision

Full GitHub history