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Metabolite annotation and identification

CFM-ID

Predict tandem mass spectra, annotate fragments and rank candidate structures for small molecules.

LC-MSWeb applicationCommand lineFree web service
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Overview

CFM-ID combines learned fragmentation and rule-based components. The version 4 web workflow focuses on ESI-QTOF MS/MS and provides predicted-versus-observed spectral comparisons.

What can this tool do?

In-silico spectrum predictionStructure-database searching

Common uses

  • Compare an observed spectrum with candidate structures.
  • Predict fragmentation for a supplied molecular structure.

Scientific fit

Primary function

Metabolite annotation and identification

Data compatibility

Inputs

Mass spectra, Molecular structures

Outputs

Mass spectra, Compound list or annotations

Input formats

SMILES or InChI, Other, Structure strings or formatted spectral peak lists

Output formats

Other, Predicted peak lists and ranked candidates

Scope and considerations

Designed for

  • Compare an observed spectrum with candidate structures.

Not designed for

  • Proving stereochemistry or identity from a top-ranked candidate alone.

Important requirements

  • A molecular structure for prediction, or a spectrum with appropriate precursor and collision-energy information for annotation.

Considerations

  • Instrument and collision-energy differences affect agreement. The command-line image does not include all web-server spectral databases.

Access and documentation

Primary access

Free web access and downloadable components; consult individual code, model and database 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. Wang F, Allen D, Tian S, et al. CFM-ID 4.0 - a web server for accurate MS-based metabolite identification. Nucleic Acids Res 50, W165-W174 (2022). doi:10.1093/nar/gkac383

Related tools

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

    Add 50 documented metabolomics resources

    View change · Entry at this revision

Full GitHub history