Overview
FBMN-STATS provides an accompanying app and notebooks for downstream analysis of non-targeted LC-MS/MS feature tables. It connects data cleanup and statistical comparisons to the interpretation of molecular-network results. R and Python notebooks can be run locally; a QIIME2 route and hosted interfaces are documented. The GNPS2 downstream link calls this the Hitchhiker Statistics Guide.
Also known as: FBMN-STATS, FBmnStatsGUIde, Hitchhiker's Guide to Statistical Analysis of Feature-based Molecular Networks, Hitchhiker Statistics Guide
What can this tool do?
Common uses
- Examine group differences and multivariate patterns in processed LC-MS/MS data.
- Prepare statistical results for interpretation alongside molecular networks.
Scientific fit
Primary function
Statistical analysis
Data compatibility
Inputs
Feature or peak table, Sample metadata
Outputs
Statistical results, Human-readable report
Input formats
FBMN quantification and metadata tables; layout depends on interface
Output formats
Statistical result files and notebook or app visualizations
Scope and considerations
Designed for
- Downstream quantitative analysis of feature-based molecular networking results.
Not designed for
- Raw-file feature detection or definitive compound identification.
Important requirements
- Compatible feature tables and sample metadata, including grouping and blank information where applicable.
- Choose an interface and analysis appropriate to the study design.
Considerations
- Legacy GNPS Quickstart exports may lack the reformatted outputs required by the current integration; maintainers recommend GNPS2.
- Normalization, missing values, batch structure and multiple comparisons require study-specific decisions.
- Notebooks and the web app need not expose identical operations; consult the selected interface documentation.
- The browser-only FBMN-STATS Guide at apps.gnps2.org is marked in development and is not interchangeable with the original notebooks and Streamlit app.
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
BSD-3-Clause source with hosted app and R/Python notebook routes. Cloud notebook use may require an account; local execution requires the documented dependencies. Hosted use is recommended by the maintainers for smaller datasets.
License: BSD-3-Clause
Evidence and review
Official repository, license, GNPS2 listing and direct methods publication reviewed on 2026-09-10. No analysis job or independent benchmark performed. Rechecked 2026-09-23: added documented Hitchhiker aliases and local notebook visibility without creating a duplicate.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Pakkir Shah AK, Walter A, Ottosson F, et al. Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data. Nature Protocols 20, 92–162 (2025; published online 2024). doi:10.1038/s41596-024-01046-3
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-23 · Entry update
Add ChemWalker and Everything Bagel and audit GNPS2 downstream coverage
View change · Entry at this revision - 2026-09-10 · First committed entry
Add FBMN Stats and GNPS2 Cytoscape Bridge entries
View change · Entry at this revision