Overview
ChemWalker combines molecular-network context with candidate structures evaluated by in-silico fragmentation. Its Python implementation uses MetFrag, while a GNPS2 workflow accepts a networking task and a selected molecular family. Propagated rankings guide annotation follow-up rather than confirming an identity.
What can this tool do?
Common uses
- Prioritize candidate structures for unannotated members of a molecular family.
- Combine candidate fragmentation evidence with neighboring library annotations.
Scientific fit
Primary function
Metabolite annotation and identification
Other functions
Molecular networking and chemical similarity
Data compatibility
Inputs
Mass spectra
Outputs
Compound list or annotations, Human-readable report
Input formats
GNPS networking task ID and component index, Ion mode, adduct and optional pipe-separated candidate database
Output formats
Candidate annotation rankings from the selected network component.
Scope and considerations
Designed for
- Annotation propagation within MS/MS molecular networks.
Not designed for
- Raw feature detection, quantitative statistics or confirmed identification without additional evidence.
Important requirements
- A compatible network task and selected molecular component; the GNPS2 form requests one component per run.
- Appropriate ion/adduct settings and a candidate structure database; local installation requires the documented environment and MetFrag.
Considerations
- Incorrect seed annotations and missing candidate structures can affect propagated rankings.
- The repository reports testing with MetFrag 2.3; compatibility with newer dependencies was not execution-tested.
Access and documentation
Core Python package is BSD-3-Clause; MetFrag and workflow dependencies have their own requirements. Hosted GNPS2 execution requires an account and is restricted to academic/non-commercial use without a separate license.
License: BSD-3-Clause
Evidence and review
Official ChemWalker repository and GNPS2 workflow input definition reviewed; primary DOI/title/year verified through Crossref on 2026-09-23. No software execution or developer verification.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Borelli TC, Arini GS, Feitosa LGP, et al. Improving annotation propagation on molecular networks through random walks: introducing ChemWalker. Bioinformatics 39(3), btad078 (2023). doi:10.1093/bioinformatics/btad078
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 · First committed entry
Add ChemWalker and Everything Bagel and audit GNPS2 downstream coverage
View change · Entry at this revision