Overview
Feature-Based Molecular Networking bridges upstream LC-MS/MS feature-processing tools with GNPS molecular networking. A quantitative feature table and representative MS/MS spectra are exported from software such as MZmine, MS-DIAL, XCMS, or OpenMS and used to build molecular networks in which each node corresponds to an aligned chromatographic feature.
What can this tool do?
Common uses
- Build molecular networks that retain chromatographic feature abundance across samples.
- Layer metadata and quantitative information onto MS/MS molecular families.
Scientific fit
Primary function
Molecular networking and chemical similarity
Data compatibility
Inputs
Feature or peak table, Mass spectra, Sample metadata
Outputs
Feature or peak table, Compound list or annotations, Human-readable report
Input formats
CSV or TSV, MGF, MSP, mzML
Output formats
Network edge and node tables, library matches and downloadable workflow results
Scope and considerations
Designed for
- Untargeted LC-MS/MS studies where chromatographic feature detection and quantitative feature tables are important for molecular-network interpretation.
- Resolving isomeric or chromatographically separated features that would otherwise be combined in purely spectrum-centric networking.
Not designed for
- Definitive structure identification from spectral similarity alone.
- Replacing experimental quality control or validating biological causation.
Important requirements
- An aligned feature quantification table and representative MS/MS spectra exported from a compatible preprocessing workflow.
- Matching feature identifiers between the quantification table and spectral summary; sample metadata is optional.
Considerations
- The quality of the molecular network depends on upstream feature detection, alignment, MS/MS assignment, and preprocessing choices.
- FBMN does not remove the need for independent structural validation; library matches and network propagation represent different levels of annotation evidence.
- Raw mzML files are optional supporting inputs in the documented GNPS2 workflow; they do not replace the required processed feature table and spectral summary.
Education
Learn this tool
External tutorials and workshops collected by Navigator. Entries marked Needs review have not been checked end to end.
Access and documentation
GNPS2 is openly available to the academic community. The current GNPS2 documentation asks industry users to contact the maintainers or UC Riverside Technology Transfer regarding organizational access. Workflow submission requires a GNPS2 account.
From tool to strategy
Strategies using GNPS2 Feature-Based Molecular Networking workflow
Evidence and review
Reviewed against GNPS2 documentation and the linked method publication on 2026-09-09. No analysis job was submitted and no independent benchmarking or developer verification is claimed.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Nothias L-F, Petras D, Schmid R, et al. Feature-based molecular networking in the GNPS analysis environment. Nature Methods 17, 905–908 (2020). doi:10.1038/s41592-020-0933-6
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Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-12 · Entry update
Present FBMN and ion identity networking as analytical strategies
View change · Entry at this revision - 2026-09-09 · First committed entry
Add dedicated GNPS2 molecular networking Tools
View change · Entry at this revision