A resource to empirically establish drug exposure records directly from untargeted metabolomics data

Despite extensive efforts, extracting medication exposure information from clinical records remains challenging. To complement this approach, here we show the Global Natural Product Social Molecular Networking (GNPS) Drug Library, a tandem mass spectrometry (MS/MS) based resource designed for drug screening with untargeted metabolomics. This resource integrates MS/MS references of drugs and their metabolites/analogs with standardized vocabularies on their exposure sources, pharmacologic classes, therapeutic indications, and mechanisms of action. It enables direct analysis of drug exposure and metabolism from untargeted metabolomics data, supporting flexible summarization at multiple ontology levels to align with different research goals. We demonstrate its application by stratifying participants in a human immunodeficiency virus (HIV) cohort based on detected drug exposures. We uncover drug-associated alterations in microbiota-derived N-acyl lipids that are not captured when stratifying by self-reported medication use. Overall, GNPS Drug Library provides a scalable resource for empirical drug screening in clinical, nutritional, environmental, and other research disciplines, facilitating insights into the ecological and health consequences of drug exposures. While not intended for immediate clinical decision-making, it supports data-driven exploration of drug exposures where traditional records are limited or unreliable.

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Publication Details

Journal
Nature Communications
Published
2025-12-09
DOI
https://doi.org/10.1038/s41467-025-65993-5
Citations
3
Primary Topic
Metabolomics and Mass Spectrometry Studies
Type
article
Field-Weighted Citation Impact
2.42
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article

A resource to empirically establish drug exposure records directly from untargeted metabolomics data

Lindsey A. Burnett, David S. Wishart, Scott Letendre, Sagan Girod et al.
3 citations
Nature Communications
Metabolomics and Mass Spectrometry Studies
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article

A resource to empirically establish drug exposure records directly from untargeted metabolomics data

Lindsey A. Burnett, David S. Wishart, Scott Letendre, Sagan Girod, Haoqi Nina Zhao, Pablo Gago-Ferrero, MacKenzie Bryant, Yasin El Abiead, Andrés Mauricio Caraballo‐Rodríguez, Shirley M. Tsunoda, Mohammad Reza Zare Shahneh, Andrés Cumsille, Sydney P. Thomas, Lora A. Khatib, Caitlin Tribelhorn, Rima F Kaddurah-Daouk, Helena M. Tubb, Rob Knight, Jennifer E. Iudicello, Martín Casas Maya, Ronald J. Ellis, Santosh Lamichhane, Manuela Raffatellu, Ipsita Mohanty, Sarolt Magyari, Wout Bittremieux, Lluís Corominas, Mingxun Wang, Libin Xu, Mohammad Sobhan Sheikh Andalibi, Paulo Wender Portal Gomes, Helena Mannochio-Russo, Runbang Tang, Robin Schmid, Shipei Xing, Karsten Zengler, Nicole E. Avalon, Rubén Gil‐Solsona, Corinna Brungs, Kine Eide Kvitne, Pieter C. Dorrestein, Loryn Chin, Alan K. Jarmusch, Vincent Charron‐Lamoureux, Tomáš Pluskal, Simone Zuffa, Crystal X. Wang, Dylan H. Ross, Robert K. Heaton, David J. Moore, Siddharth Mohan, Daniel McDonald, Donald Franklin, Madison Ambre, Prajit Rajkumar, Harshada Sapre, Lauren Hansen, Corinn Walker, Jasmine Zemlin
article en
3 citations

Abstract

Despite extensive efforts, extracting medication exposure information from clinical records remains challenging. To complement this approach, here we show the Global Natural Product Social Molecular Networking (GNPS) Drug Library, a tandem mass spectrometry (MS/MS) based resource designed for drug screening with untargeted metabolomics. This resource integrates MS/MS references of drugs and their metabolites/analogs with standardized vocabularies on their exposure sources, pharmacologic classes, therapeutic indications, and mechanisms of action. It enables direct analysis of drug exposure and metabolism from untargeted metabolomics data, supporting flexible summarization at multiple ontology levels to align with different research goals. We demonstrate its application by stratifying participants in a human immunodeficiency virus (HIV) cohort based on detected drug exposures. We uncover drug-associated alterations in microbiota-derived N-acyl lipids that are not captured when stratifying by self-reported medication use. Overall, GNPS Drug Library provides a scalable resource for empirical drug screening in clinical, nutritional, environmental, and other research disciplines, facilitating insights into the ecological and health consequences of drug exposures. While not intended for immediate clinical decision-making, it supports data-driven exploration of drug exposures where traditional records are limited or unreliable.

Nature CommunicationsVol. 16(1)
University of California, Riverside (US), University of Vienna (AT), Åbo Akademi University (FI), La Jolla Institute for Immunology (US), Consejo Superior de Investigaciones Científicas (ES), University of Wisconsin–Madison (US), Pacific Northwest National Laboratory (US), University of Antwerp (BE), Scripps Institution of Oceanography (US), University of Alberta (CA), University of Turku (FI), Duke University (US), Turku Centre for Computer Science (FI), University of Oslo (NO), University of Washington (US), Board of the Swiss Federal Institutes of Technology (CH), Catalan Institute for Water Research (ES), ETH Zurich (CH), University of California San Diego (US), National Institute of Environmental Health Sciences (US), La Jolla Bioengineering Institute (US), Turku Centre for Biotechnology (FI), Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry (CZ), Neurobehavioral Research (United States) (US), Universidade Federal do Pará (BR), University of Montana (US)
Openalex Percentile: Top 10%
Metabolomics and Mass Spectrometry Studies
2.42
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