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.

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 La Jolla CA USA

Collaborative Mass Spectrometry Innovation Center Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla CA USA

Current address Biological Sciences Division Pacific Northwest National Laboratory Richland WA USA

Department of Bioengineering University of California San Diego La Jolla California USA

Department of Biological Sciences University of Alberta Edmonton AB T6G 2E9 Canada

Department of Computer Science and Engineering University of California Riverside Riverside CA USA

Department of Computer Science and Engineering University of California San Diego La Jolla CA USA

Department of Computer Science University of Antwerp Antwerp Belgium

Department of Computing Science University of Alberta Edmonton AB T6G 2E8 Canada

Department of Medicinal Chemistry University of Washington Seattle WA USA

Department of Medicine Duke University Durham NC USA

Department of Medicine University of California San Diego La Jolla CA USA

Department of Microbiology and Cell Sciences University of Florida Museum Drive Gainesville FL USA

Department of Neurosciences University of California San Diego La Jolla CA USA

Department of Pediatrics University of California San Diego La Jolla CA USA

Department of Pharmacy University of Oslo Oslo Norway

Department of Psychiatry and Behavioral Sciences Duke University Durham NC 27708 USA

Department of Psychiatry University of California San Diego La Jolla CA USA

Duke Institute of Brain Sciences Duke University Durham NC USA

Faculty of Chemistry Federal University of Para Belem PA Brazil

Halicioğlu Data Science Institute University of California San Diego La Jolla CA USA

HIV Neurobehavioral Research Program 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

Institute of Microbiology Eidgenössische Technische Hochschule Zürich Vladimir Prelog Weg 4 8093 Zürich Switzerland

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic

Program in Materials Science and Engineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 0418 USA

Scripps Institution of Oceanography 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

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

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