Overview
MS2Query searches reference MS/MS spectra for both exact-match candidates and structurally related analogues. It combines Spec2Vec, MS2DeepScore and precursor information to rank library candidates, with a Python implementation and a hosted GNPS2 workflow.
What can this tool do?
Common uses
- Find plausible structural relatives when an exact library match is unavailable.
- Prioritize spectra for closer structural investigation.
Scientific fit
Primary function
Spectral processing and comparison
Data compatibility
Inputs
Mass spectra
Outputs
Compound list or annotations, Statistical results
Input formats
MGF, MSP, mzML, mzXML, JSON, Universal Spectrum Identifiers (USIs), where supported by the selected interface
Output formats
CSV or TSV
Scope and considerations
Designed for
- Library searching of small-molecule MS/MS spectra, including analogue retrieval.
Not designed for
- De novo structure generation or conclusive identification of an unknown molecule.
- Chromatographic feature detection, alignment or quantification.
Important requirements
- MS/MS spectra with precursor information and the correct ionization mode.
- Compatible reference-library and model files; hosted jobs require uploaded spectra and a GNPS2 account.
Considerations
- An analogue is a related reference molecule, not necessarily the measured compound.
- Filter results by model score and inspect precursor differences; class labels describe the proposed library molecule.
- Results depend on reference-library coverage and model compatibility. Record the library, model and software versions.
Access and documentation
The Python software is distributed under Apache-2.0. For the hosted workflow: 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.
License: Apache-2.0
Evidence and review
Editorial review of official documentation, repository and the direct tool publication on 2026-09-10. No analysis job, independent benchmark or developer verification was performed.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- de Jonge NF, Louwen JJR, Chekmeneva E, et al. MS2Query: reliable and scalable MS2 mass spectra-based analogue search. Nature Communications 14, 1752 (2023). doi:10.1038/s41467-023-37446-4 PMID 36990978
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-10 · First committed entry
Add three GNPS2 Tools and expose complete related-tool lists
View change · Entry at this revision