Empirically establishing drug exposure records directly from untargeted metabolomics data.
| Title: | Empirically establishing drug exposure records directly from untargeted metabolomics data. |
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| Authors: | Zhao HN; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Kvitne KE; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Department of Pharmacy, University of Oslo, Oslo, Norway.; Brungs C; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.; Mohan S; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Charron-Lamoureux V; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Bittremieux W; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Department of Computer Science, University of Antwerp, Antwerp, Belgium.; Tang R; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Schmid R; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.; Lamichhane S; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistönkatu 6A, 20520 Turku, Finland.; El Abiead Y; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Andalibi MS; Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.; Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.; HIV Neurobehavioral Research Program, University of California San Diego, La Jolla, CA, USA.; Mannochio-Russo H; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Ambre M; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Avalon NE; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.; Bryant M; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Caraballo-Rodríguez AM; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Maya MC; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Chin L; Department of Bioengineering, University of California San Diego, La Jolla, California, USA.; Ellis RJ; Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.; Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.; Franklin D; Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.; Girod S; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.; Gomes PWP; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Faculty of Chemistry, Federal University of Para, Belem, PA, Brazil.; Hansen L; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Heaton R; Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.; Iudicello JE; Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.; Jarmusch AK; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.; Khatib L; Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.; Letendre S; HIV Neurobehavioral Research Program, University of California San Diego, La Jolla, CA, USA.; Department of Medicine, University of California San Diego, La Jolla, CA, USA.; Magyari S; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.; McDonald D; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Mohanty I; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Cumsille A; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Department of Microbiology and Cell Sciences, University of Florida, Museum Drive, Gainesville, FL, USA.; Moore DJ; Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.; HIV Neurobehavioral Research Program, University of California San Diego, La Jolla, CA, USA.; Rajkumar P; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Ross DH; Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA.; Current address: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.; Sapre H; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Shahneh MRZ; Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA.; Thomas SP; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Tribelhorn C; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Tubb HM; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Walker C; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Wang CX; Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.; HIV Neurobehavioral Research Program, University of California San Diego, La Jolla, CA, USA.; Xing S; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Zemlin J; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.; Zuffa S; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Wishart DS; Department of Bioengineering, University of California San Diego, La Jolla, California, USA.; Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.; Kaddurah-Daouk R; Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, 27708, USA.; Duke Institute of Brain Sciences, Duke University, Durham, NC, USA.; Department of Medicine, Duke University, Durham, NC, USA.; Wang M; Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA.; Raffatellu M; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.; Chiba University, UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA.; Zengler K; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.; Program in Materials Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0418, USA.; Pluskal T; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.; Xu L; Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA.; Knight R; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.; Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.; Halicioğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA.; Tsunoda SM; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Dorrestein PC; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. |
| Source: | BioRxiv : the preprint server for biology [bioRxiv] 2024 Oct 26. Date of Electronic Publication: 2024 Oct 26. |
| Publication Type: | Journal Article; Preprint |
| Language: | English |
| Journal Info: | Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE |
| Abstract: | Despite extensive efforts, extracting information on medication exposure from clinical records remains challenging. To complement this approach, we developed the tandem mass spectrometry (MS/MS) based GNPS Drug Library. This resource integrates MS/MS data for drugs and their metabolites/analogs with controlled vocabularies on exposure sources, pharmacologic classes, therapeutic indications, and mechanisms of action. It enables direct analysis of drug exposure and metabolism from untargeted metabolomics data independent of clinical records. Our library facilitates stratification of individuals in clinical studies based on the empirically detected medications, exemplified by drug-dependent microbiota-derived N-acyl lipid changes in a cohort with human immunodeficiency virus. The GNPS Drug Library holds potential for broader applications in drug discovery and precision medicine. |
| Comments: | Update in: Nat Commun. 2025 Dec 9;16(1):10600. doi: 10.1038/s41467-025-65993-5.. (PMID: 41366203) |
| Grant Information: | P50 HD106463 United States HD NICHD NIH HHS; U24 AG021886 United States AG NIA NIH HHS; U19 AG063744 United States AG NIA NIH HHS; R01 DK136117 United States DK NIDDK NIH HHS; P30 MH062512 United States MH NIMH NIH HHS; R37 AI126277 United States AI NIAID NIH HHS; F32 AT011475 United States AT NCCIH NIH HHS; U24 DK133658 United States DK NIDDK NIH HHS |
| Entry Date(s): | Date Created: 20241017 Date Completed: 20251216 Latest Revision: 20251216 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC11482764 |
| DOI: | 10.1101/2024.10.07.617109 |
| PMID: | 39416075 |
| Database: | MEDLINE |
Journal Article; Preprint