Overview
MSMS-Chooser extracts candidate reference tandem mass spectra from measurements of known standards. A submission table connects files to molecular structures and expected precursor information; the GNPS workflow finds candidate scans for subsequent inspection. Its role is reference-spectrum preparation. The identity and purity of the starting material, precursor assignment and spectrum quality still require curator review before library deposition.
Also known as: MS/MS-Chooser
What can this tool do?
Common uses
- Select MS/MS spectra corresponding to known standards from open-format data.
- Prepare candidate reference spectra for validation and library contribution.
- Link the selected spectrum back to its source standard and acquisition metadata before library submission.
Scientific fit
Primary function
Spectral processing and comparison
Other functions
Metabolite annotation and identification
Analysis types
Targeted metabolomics, Metabolite profiling
MS level
MS/MS
Acquisition
Targeted MS/MS, Flow injection, Data-dependent acquisition (DDA)
Ion mobility
Ion mobility not required
Data compatibility
Inputs
Mass spectra, Molecular structures
Outputs
Mass spectra, Human-readable report
Input formats
mzML, mzXML, CSV or TSV, SMILES or InChI
Output formats
CSV or TSV
Scope and considerations
Designed for
- Extracting candidate reference MS/MS scans when structures or formulas of standards are known.
Not designed for
- Untargeted identification of unknown compounds without prior standard information.
Important requirements
- Open-format mzML or mzXML data plus the MSMS-Chooser submission template.
Considerations
- Automated selections should be visually reviewed and validated before use as reference spectra.
- Inspect precursor/adduct assignment and potential co-isolation or contamination before accepting a scan as a reference spectrum.
Access and documentation
Hosted access and any account or usage requirements should be checked at the linked service. Access to a web service does not establish the license of its code or reference data.
From tool to strategy
Strategies using MSMS-Chooser
Evidence and review
Documentation-based editorial pass on 6 September 2026: scope, interpretation limits and practical use reviewed against the linked official documentation and cited literature. Software execution, service availability and developer verification were not assessed. The official workflow documentation is the direct reference. No dedicated methods paper was identified in this pass; cite the GNPS platform and workflow details as applicable.
No dedicated scholarly publication is listed. Follow the official documentation and resource-specific citation guidance.
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-07 · Entry update
Expand and document 31 metabolomics tools and resources
View change · Entry at this revision - 2026-08-24 · Entry update
Apply v5.2 pre-population hardening
View change · Entry at this revision - 2026-08-21 · First committed entry
Add files via upload
View change · Entry at this revision