What does this strategy enable?
Feature-Based Molecular Networking connects an aligned chromatographic feature table to a network of representative fragmentation spectra. Unlike spectrum-centric networking, it retains feature-level abundance and can keep chromatographically separated isomers distinct. The Strategy is the analytical design; the GNPS2 FBMN workflow is one software implementation, used with compatible upstream feature-processing tools.
Transferable workflow
Workflow
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Run the FBMN workflow in GNPS2
Upload or select the feature table and spectral summary, configure tolerances and networking filters, and launch Feature-Based Molecular Networking.
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Overlay spectral-library annotations
Search compatible nodes against GNPS spectral libraries and inspect molecular families containing annotated and unannotated features.
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Interpret quantitative molecular families
Use feature abundances, metadata, retention time, ion mobility where available, and spectral relationships to compare molecular families across samples or conditions.
Connected resources
Tools used in this strategy
Evidence of reuse
Published implementations and adaptations
These papers applied, adapted, extended, benchmarked or formalized the Strategy after its originating publication. They are examples of precedent, not a ranking of software choices.
Integrative open workflow for confident annotation and molecular networking of metabolomics MSE/DIA data
DIA-IntOpenStream adapts FBMN to MSE/DIA data. Waters2mzML supplies mzML; KNIME assembles custom structure databases; MS-DIAL assigns DIA fragments to precursors and exports FBMN inputs for GNPS and Cytoscape. MZmine 3 is used for a parallel MS1 annotation branch, not DIA fragment deconvolution in this study. Reliable precursor-fragment assignment is required; custom mass matches and network neighbors are not confirmed structures. The demonstrated conversion uses Windows and Waters data; other vendor compatibility is not established here.
Strategy profile
Related objectives
Metabolite annotation, Molecular discovery, Natural-product discovery
Components
Preprocessing and feature extraction, Quality control, Annotation or identification, Spectral search, Molecular networking, Data and workflow sharing
Biological context
Broadly applicable
Ion mobility
Ion mobility not required
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.
Important requirements
- An aligned feature quantification table and representative MS/MS spectra exported from a compatible preprocessing workflow.
- Consistent feature identifiers across the quantification table and spectral export; raw files alone are not ready-to-use FBMN inputs.
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.
Reusable resources
Publication
Nothias L-F, Petras D, Schmid R, et al. Feature-based molecular networking in the GNPS analysis environment. Nature Methods 17, 905–908 (2020).