Overview
MetScape maps compound and gene identifiers into metabolic networks and supports exploration of metabolite correlation networks. Its reference context is human metabolism, including mappings from supported mouse and rat inputs. It is included for interpretation of MS-derived results after annotation, not as a method for assigning structures from mass spectra.
What can this tool do?
Common uses
- Place annotated MS metabolites into metabolic context.
- Explore metabolite and gene relationships in Cytoscape.
Scientific fit
Primary function
Pathway and biological interpretation
Other functions
Visualization and reporting, Multi-omics integration
Data compatibility
Inputs
Compound list or annotations, Pathway or reaction data
Outputs
Human-readable report, Pathway or reaction data
Input formats
CSV, TSV or Excel compound/gene tables; supported compound and gene identifiers
Output formats
Interactive network views and exported analysis results
Scope and considerations
Designed for
- Supported identifier mapping and metabolic-network interpretation.
Not designed for
- Raw MS preprocessing or metabolite identification from accurate mass alone.
Important requirements
- Cytoscape with a compatible MetScape app and supported identifiers.
Considerations
- Reference coverage and identifier mapping limit which metabolites appear.
- Legacy installation and remote data-service availability require verification before planning a study.
Access and documentation
Download is offered through the Cytoscape App Store. A current explicit app license was not confirmed in the reviewed pages; do not infer the app license from Cytoscape. The listing reports version 3.1.3 (2017) and compatibility with Cytoscape 3.4; compatibility with newer releases was not tested.
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.
- Karnovsky A, et al. Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data. Bioinformatics 28, 373-380 (2012). doi:10.1093/bioinformatics/btr661
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