Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service
Wout BittremieuxiD, Christopher Chen, Pieter C. DorresteiniD, Emma SchymanskiiD, Tobias SchulzeiD, Steffen NeumanniD, René MeieriD, Simon RogersiD, Mingxun WangiD
Abstract
The growth of online mass spectrometry metabolomics resources, including data repositories, spectral library databases, and online analysis platforms has created an environment of online/web accessibility. Here, we introduce the Metabolomics Spectrum Resolver (https://metabolomics-usi.ucsd.edu/), a tool that builds upon these exciting developments to allow for consistent data export (in human and machine-readable forms) and publication-ready visualisations of tandem mass spectrometry spectra. This tool supports the Human Proteome Organization - Proteomics Standards Initiatives Universal Spectrum Identifier (USI) specification, which has been extended to deal with the metabolomics use cases. To date, this resource already supports data formats from GNPS, MassBank, MS2LDA, MassIVE, MetaboLights, and Metabolomics Workbench and is integrated into several of these resources.
02 /Specification & Classification
Click any tag to browse matching papers- Citations
- 66
- Assay
- Research Focus
- Approach
Abstract summary
Claude Opus 5.5 · xhigh effort · 18 Oct 2026 · from the abstract · CC BY-NC 4.0
A web service renders tandem mass spectra held in metabolomics repositories as publication-ready figures and consistent exports, addressed through Universal Spectrum Identifiers extended to metabolomics.
Online metabolomics resources - data repositories, spectral libraries and analysis platforms - have grown into a web-accessible environment, each contributing its own data formats. The Metabolomics Spectrum Resolver puts one identifier scheme and one renderer in front of them, supporting the Proteomics Standards Initiative Universal Spectrum Identifier specification, which has been extended to metabolomics use cases.
Key results
ClaimedThe service turns a spectrum reference into both a figure suitable for publication and an export that people and software can read, so the same spectrum can be shown consistently wherever it is stored.
Described as the purpose of the tool, reachable at the stated web address; the abstract reports no usage statistics, rendering benchmarks or comparison with existing spectrum viewers. · Abstract
ClaimedAddressing follows the Universal Spectrum Identifier specification of the Human Proteome Organization Proteomics Standards Initiative, which has been extended to cover metabolomics use cases.
Stated as supported; the abstract does not describe what the extension adds or which identifier fields differ from the proteomics specification. · Abstract
ClaimedData formats from several established metabolomics repositories, libraries and analysis platforms are already handled, and the resolver is embedded in several of those resources.
The supported resources are named in the abstract (among them GNPS, MassBank and Metabolomics Workbench), but which of them embed the service, and the extent of format coverage, are not specified. · Abstract
Methods, data and reproducibility
A web service resolves a spectrum identifier to the underlying tandem mass spectrometry data held in external metabolomics resources, then renders it for publication and exports it in human- and machine-readable form. Identifiers follow the Universal Spectrum Identifier specification, extended from proteomics to metabolomics.
- tandem mass spectra drawn from the supported metabolomics repositories, spectral libraries and analysis platforms
- Methods & tools
- Metabolomics Spectrum Resolver, Universal Spectrum Identifier (USI), GNPS, MassBank, MS2LDA, MassIVE, MetaboLights, Metabolomics Workbench
- Reproducibility gaps
- Only the address of the running service is given; no source repository, licence, version or deployment instructions appear in the abstract.
Limitations (2)
- The abstract describes the service rather than evaluating it: there are no usage figures, no rendering or retrieval performance numbers, and no comparison with other spectrum viewers. · noted in this summary
- Coverage is defined by a list of supported resources at the time of writing, and the abstract does not say which formats or repositories fall outside it, nor how the identifier extension is governed. · noted in this summary
Who should read:Read this if you cite, share or re-plot MS/MS spectra that live in different metabolomics databases and want one identifier scheme and one renderer across them.
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison
Tobias Schmidt, Patroklos Samaras, … Mathias Wilhelm·Journal of Proteome ResearchPeer-reviewed·May 10, 2021
- Universal Spectrum Identifier for mass spectra
Eric W. Deutsch, Yasset Pérez‐Riverol, … Nuno Bandeira·Nature MethodsPeer-reviewed·Jun 28, 2021
- spectrum_utils: A Python package for mass spectrometry data processing and visualization
Wout Bittremieux·Analytical ChemistryPeer-reviewed·Dec 6, 2019
- Tailored mass spectral data exploration using the specXplore interactive dashboard
Kevin Mildau, Henry Ehlers, … Justin J. J. van der Hooft·Analytical ChemistryPeer-reviewed·Apr 2, 2024
- Unified and standardized mass spectrometry data processing in Python using spectrum_utils
Wout Bittremieux, Lev I. Levitsky, … Pieter C. Dorrestein·Journal of Proteome ResearchPeer-reviewed·Jan 23, 2023
- MetAlyzer to Perform Streamlined, Interactive, and Pathway-Mapping Analysis of Targeted Metabolomics Data from the biocrates Platform
Qian-Wu Liao, Luis Herfurth, … Gernot Poschet·bioRxiv·Dec 20, 2025