Empirically establishing drug exposure records from untargeted MS/MS data

Introduction: Drugs represent one of the most important human chemical exposures. To study the relationships between drug exposure and health outcomes, clinical research relies on medical records or self-reported medication usage. However, such information is costly to acquire and often inaccurate, and does not reflect drug exposure from non-medication routes. Untargeted metabolomics offers the opportunity to provide objective drug read-out, but it suffers from the limited number of reference spectra of drugs and even lower coverage for drug metabolites. Moreover, interpretation of the annotations requires extensive literature searches to understand the therapeutic indications of the drugs. To overcome these challenges, we developed GNPS Drug Library, a tandem mass spectrometry (MS/MS) based resource that 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 MS/MS data, supporting flexible summarization at multiple ontology levels to align with diverse research goals. We demonstrate its utility by stratifying participants in a human immunodeficiency virus (HIV) cohort based on detected drug exposures and uncovering drug-associated alterations in microbiota-derived N-acyl lipids.