ArticleNature communications2025
A resource to empirically establish drug exposure records directly from untargeted metabolomics data.
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In one paragraph
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8citing papers in PubMed
–field-weighted citation impact
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- Environmental Contaminants in Surface Snow Samples Made from Reclaimed Water at a Ski Resort: A Mass Spectrometry Analysis.ACS environmental Au · 2026Article
- Antibiotic Exposure Through Human Milk Influences the Infant Gut Microbiome.bioRxiv : the preprint server for biology · 2026Article
- Retrieval-Augmented Language Models Enable Scalable Chemical Source Classification in Metabolomics Workflows.Analytical chemistry · 2026Article
- Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data.bioRxiv : the preprint server for biology · 2026Article
- Fecal microbial and metabolic signatures in children with very early onset inflammatory bowel disease.NPJ biofilms and microbiomes · 2025Article
- Review
- Reaction-Guided Metabolomics Accelerates High-Throughput Annotation of Xenobiotic Metabolites for Human Exposome.Environmental science & technology · 2025Article
- Metabolome informs about the chemical exposome and links to brain health.Environment international · 2025Review
Corrections and comments
- Update of
Authors and funding
59 authors.
Haoqi Nina Zhao *Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-3908-630X
Kine Eide Kvitne *Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-8118-7660
Corinna Brungs *Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czechia.
Siddharth MohanSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Vincent Charron-LamoureuxCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-9440-7036
Wout BittremieuxCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-3105-1359
Runbang TangSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Robin SchmidCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-0922-3887
Santosh LamichhaneSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-9292-3595
Shipei XingCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Yasin El AbieadCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-4392-7706
Mohammadsobhan S AndalibiDepartment of Neurosciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-4895-1214
Helena Mannochio-RussoCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-4961-2353
Madison AmbreDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Nicole E AvalonScripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-3588-892X
MacKenzie BryantDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-0749-2995
Lindsey A BurnettDepartment of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.
Andrés Mauricio Caraballo-RodríguezCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Martin Casas MayaDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Loryn ChinDepartment of Bioengineering, University of California San Diego, La Jolla, California, USA.
Lluís CorominasCatalan Institute for Water Research (ICRA-CERCA), Girona, Spain.ORCID http://orcid.org/0000-0002-5050-2389
Ronald J EllisDepartment of Neurosciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-4931-752X
Donald FranklinDepartment of Psychiatry, University of California San Diego, La Jolla, CA, USA.
Sagan GirodDepartment of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
Paulo Wender P GomesCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Lauren HansenDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Robert K HeatonDepartment of Psychiatry, University of California San Diego, La Jolla, CA, USA.
Jennifer E IudicelloDepartment of Psychiatry, University of California San Diego, La Jolla, CA, USA.
Alan K JarmuschCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-2228-6308
Lora KhatibDepartment of Neurosciences, University of California San Diego, La Jolla, CA, USA.
Scott LetendreHIV Neurobehavioral Research Program, University of California San Diego, La Jolla, CA, USA.
Sarolt MagyariSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-4573-0915
Daniel McDonaldDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Ipsita MohantyCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-0894-4770
Andrés CumsilleSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-2087-7435
David J MooreDepartment of Psychiatry, University of California San Diego, La Jolla, CA, USA.
Prajit RajkumarSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0009-0002-5538-5270
Dylan H RossDepartment of Medicinal Chemistry, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0009-0005-2943-2282
Harshada SapreSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Mohammad Reza Zare ShahnehDepartment of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA.ORCID http://orcid.org/0000-0002-5760-3190
Ruben Gil-SolsonaDepartment of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Spanish Council of Scientific Research (CSIC), Barcelona, Spain.
Sydney P ThomasCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Caitlin TribelhornDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Helena M TubbDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Corinn WalkerDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Crystal X WangDepartment of Psychiatry, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-0525-809X
Jasmine ZemlinCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Simone ZuffaCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-7237-3402
David S WishartDepartment of Biological Sciences, University of Alberta, Edmonton, AB, Canada.ORCID http://orcid.org/0000-0002-3207-2434
Pablo Gago-FerreroDepartment of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Spanish Council of Scientific Research (CSIC), Barcelona, Spain.
Rima Kaddurah-DaoukDepartment of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA.ORCID http://orcid.org/0000-0003-1858-5732
Mingxun WangDepartment of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA.
Manuela RaffatelluDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-6487-4215
Karsten ZenglerDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-8062-3296
Tomáš PluskalInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czechia.ORCID http://orcid.org/0000-0002-6940-3006
Libin XuDepartment of Medicinal Chemistry, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0003-1021-5200
Rob KnightDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-0975-9019
Shirley M TsunodaSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-3974-8038
Pieter C DorresteinCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.ORCID http://orcid.org/0000-0002-3003-1030
Funding
Project 4 - Mechanistic studies on the role of the gut microbiome in models for Alzheimer's diseaseU19AG063744 · NIA · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI Rima F Kaddurah-Daouk · 2019 to 2026
$54.1MSTRUCTURAL NEUROIMAGING COREP30MH062512 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Jessica Lynette Montoya · 2001 to 2026
$50.4MUC San Diego FIRST ProgramU54CA272220 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Deborah L Wingard · 2022 to 2026
$21.2MThe impact of ampicillin and breast milk oligosaccharides on the infant microbiome and immune functionsP50HD106463 · NICHD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Lars Bode, CHRISTINA CHAMBERS · 2021 to 2026
$19.6MMass Spectrometry-based Untargeted MetabolomicsZICES103363 · NIEHS · NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES · PI JARMUSCH, ALAN · 2021 to 2025
$6.5MCollaborative Microbial Metabolite CenterU24DK133658 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PIETER C DORRESTEIN · 2022 to 2026
$2.9MReverse Metabolomics for the Discovery of Disease Associated Microbial MoleculesR01DK136117 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PIETER C DORRESTEIN · 2023 to 2026
$2.9MNutritional immunity during Salmonella infectionR37AI126277 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Manuela Raffatellu · 2023 to 2026
$1.8MA Genomic Approach to Discovering Novel Cathepsin Inhibitors from CyanobacteriaF32AT011475 · NCCIH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI AVALON, NICOLE ELIZABETH · 2022 to 2024
$218kMapping Xenobiotic Metabolism by the Human Gut MicrobiomeK99ES037746 · NIEHS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ZHAO, HAOQI NINA · 2025 to 2025
$95kIntramural NIH HHS ZIC ES103363NCCIH NIH HHS F32 AT011475NCI NIH HHS U54 CA272220NIAID NIH HHS R37 AI126277NIA NIH HHS U19 AG063744NICHD NIH HHS P50 HD106463NIDDK NIH HHS R01 DK136117NIDDK NIH HHS U24 DK133658NIEHS NIH HHS K99 ES037746NIMH NIH HHS P30 MH062512
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.
Indexed as
MetabolomicsHIV InfectionsHumansTandem Mass Spectrometry
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