Overview
MetGem loads tandem mass spectra and optional metadata, computes spectral similarities and offers molecular-network or projection views. It provides a local route for exploring processed LC-MS/MS spectra. Graph layouts and t-SNE projections are different representations and should not be interpreted as validated chemical structures.
What can this tool do?
Common uses
- Build local molecular networks from processed MS/MS spectra.
- Compare network views with spectral projections.
Scientific fit
Primary function
Molecular networking and chemical similarity
Other functions
Visualization and reporting, Spectral processing and comparison
Data compatibility
Inputs
Mass spectra
Outputs
Human-readable report
Input formats
MGF, MSP, Optional CSV spectrum metadata
Output formats
Interactive network views and exported analysis results
Scope and considerations
Designed for
- Spectral-similarity calculation and interactive exploration.
Not designed for
- Vendor raw-file preprocessing or confident identification from projection position.
Important requirements
- Processed MGF or MSP tandem spectra and suitable precursor metadata.
Considerations
- Record spectral filters, tolerances and similarity thresholds.
- t-SNE emphasizes local relationships; global distances and layout changes can mislead.
Access and documentation
Open-source desktop software with prebuilt and source installation routes. Check operating-system support in the current release instructions; documentation and application versions may differ.
License: GPL-3.0
Evidence and review
Official project documentation and direct tool publications reviewed on 2026-09-12. Included for downstream MS metabolomics. No installation, dataset analysis or independent performance benchmarking performed.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Olivon F, Elie N, Grelier G, et al. MetGem Software for the Generation of Molecular Networks Based on the t-SNE Algorithm. Analytical Chemistry 90, 13900-13908 (2018). doi:10.1021/acs.analchem.8b03099 PMID 30335965
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-12 · First committed entry
Add network visualization specialists and curated relationships
View change · Entry at this revision