Overview
MassQL (Mass Spectrometry Query Language) is a domain-specific language for expressing chemically meaningful patterns directly in mass-spectrometry data. Queries can combine precursor and fragment masses, neutral-loss-like constraints, intensity rules, Boolean logic, retention-time constraints, and ion-mobility constraints. The ecosystem includes a reference Python engine, web interfaces, repository-scale workflows, a Nextflow implementation, APIs, a community query compendium, and native implementations in multiple metabolomics software platforms.
Also known as: Mass Query Language
What can this tool do?
Common uses
- Encode reusable searches for MS1 isotopic/adduct patterns, MS/MS fragments, neutral losses, mass defects, and combinations of these constraints.
- Combine spectral constraints with retention-time and ion-mobility conditions and Boolean logic.
- Run the same conceptual query in local files, software implementations, or repository-scale workflows without writing a bespoke analysis script.
- Reuse a chemical-pattern query across compatible engines while checking their supported syntax.
Scientific fit
Primary function
Spectral processing and comparison
Other functions
Reference data and database search, Data management and sharing, Workflow management and reproducibility
Analysis types
Targeted metabolomics, Untargeted metabolomics, Metabolite profiling
MS level
MS1, MS/MS
Acquisition
Full-scan MS, Data-dependent acquisition (DDA), Data-independent acquisition (DIA), Targeted MS/MS, General or unspecified acquisition
Ion mobility
Ion mobility supported
Data compatibility
Inputs
Mass spectra, Raw instrument data
Outputs
Mass spectra, Feature or peak table, Human-readable report
Input formats
mzML, mzXML, MGF
Output formats
CSV or TSV
Scope and considerations
Designed for
- Flexible, human-readable interrogation of mass-spectrometry data using chemically or biologically motivated signal patterns.
Not designed for
- Proving an exact structure merely because a spectrum satisfies a diagnostic-fragment query.
Important requirements
- A MassQL-compatible engine or application and mass-spectrometry data in a supported format.
Considerations
- MassQL retrieves spectra/scans that satisfy user-defined constraints; the specificity and biological interpretation depend on the query design.
- Different software packages implement the shared MassQL grammar with their own optimized query engines, so supported syntax should be checked against the implementation in use.
- Store the exact query and engine version; inspect matched and unmatched examples to assess whether the intended chemistry is captured.
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
The software license applies to the code; separately acquired libraries, vendor readers and hosted services may have their own terms.
License: MIT
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.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Damiani T, Jarmusch AK, Aron AT, et al. A universal language for finding mass spectrometry data patterns. Nat Methods 22, 1247-1254 (2025). doi:10.1038/s41592-025-02660-z
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-08 · Entry update
Audit core publications across existing tools
View change · Entry at this revision - 2026-09-07 · Entry update
Expand and document 31 metabolomics tools and resources
View change · Entry at this revision - 2026-08-24 · Entry update
Complete GNPS SIRIUS and MZmine tool ecosystems
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 · Entry update
Add files via upload
View change · Entry at this revision - 2026-08-20 · First committed entry
Add files via upload
View change · Entry at this revision