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Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service

View ORCID ProfileWout Bittremieux, Christopher Chen, View ORCID ProfilePieter C. Dorrestein, View ORCID ProfileEmma L. Schymanski, View ORCID ProfileTobias Schulze, View ORCID ProfileSteffen Neumann, View ORCID ProfileRene Meier, View ORCID ProfileSimon Rogers, View ORCID ProfileMingxun Wang
doi: https://doi.org/10.1101/2020.05.09.086066
Wout Bittremieux
1Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, 9500 Gilman Dr., La Jolla CA 92093, USA
2Department of Computer Science, University of Antwerp, Middelheimlaan 1, 2020 Antwerpen, Belgium
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Christopher Chen
1Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, 9500 Gilman Dr., La Jolla CA 92093, USA
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Pieter C. Dorrestein
1Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, 9500 Gilman Dr., La Jolla CA 92093, USA
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Emma L. Schymanski
3Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Belvaux, Luxembourg
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Tobias Schulze
4Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, Weinberg 3, 06120 Halle, Germany
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Steffen Neumann
5German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
6Helmholtz Centre for Environmental Research – UFZ, Department of Effect Directed Analysis, Permoserstrasse 15, 04318 Leipzig, Germany
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Rene Meier
4Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, Weinberg 3, 06120 Halle, Germany
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Simon Rogers
7School of Computing Science, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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Mingxun Wang
1Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, 9500 Gilman Dr., La Jolla CA 92093, USA
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  • For correspondence: miw023@ucsd.edu
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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 Initiative’s 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.

Competing Interest Statement

Mingxun Wang is a founder of Ometa Labs LLC, Pieter C. Dorrestein is on the scientific advisory board of Sirenas and Cybele Microbiome

Footnotes

  • https://metabolomics-usi.ucsd.edu/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted September 26, 2020.
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Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service
Wout Bittremieux, Christopher Chen, Pieter C. Dorrestein, Emma L. Schymanski, Tobias Schulze, Steffen Neumann, Rene Meier, Simon Rogers, Mingxun Wang
bioRxiv 2020.05.09.086066; doi: https://doi.org/10.1101/2020.05.09.086066
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Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service
Wout Bittremieux, Christopher Chen, Pieter C. Dorrestein, Emma L. Schymanski, Tobias Schulze, Steffen Neumann, Rene Meier, Simon Rogers, Mingxun Wang
bioRxiv 2020.05.09.086066; doi: https://doi.org/10.1101/2020.05.09.086066

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