{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T23:16:21Z","timestamp":1789773381668,"version":"4.0.1"},"reference-count":94,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,12,9]],"date-time":"2025-12-09T00:00:00Z","timestamp":1765238400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,12,9]],"date-time":"2025-12-09T00:00:00Z","timestamp":1765238400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    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                    <jats:italic>N<\/jats:italic>\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.\n                  <\/jats:p>","DOI":"10.1038\/s41467-025-65993-5","type":"journal-article","created":{"date-parts":[[2025,12,9]],"date-time":"2025-12-09T11:00:57Z","timestamp":1765278057000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["A resource to empirically establish drug exposure records directly from untargeted metabolomics data"],"prefix":"10.1038","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3908-630X","authenticated-orcid":false,"given":"Haoqi Nina","family":"Zhao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8118-7660","authenticated-orcid":false,"given":"Kine Eide","family":"Kvitne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Corinna","family":"Brungs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siddharth","family":"Mohan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9440-7036","authenticated-orcid":false,"given":"Vincent","family":"Charron-Lamoureux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3105-1359","authenticated-orcid":false,"given":"Wout","family":"Bittremieux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Runbang","family":"Tang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0922-3887","authenticated-orcid":false,"given":"Robin","family":"Schmid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9292-3595","authenticated-orcid":false,"given":"Santosh","family":"Lamichhane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shipei","family":"Xing","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4392-7706","authenticated-orcid":false,"given":"Yasin","family":"El Abiead","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4895-1214","authenticated-orcid":false,"given":"Mohammadsobhan S.","family":"Andalibi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4961-2353","authenticated-orcid":false,"given":"Helena","family":"Mannochio-Russo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madison","family":"Ambre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3588-892X","authenticated-orcid":false,"given":"Nicole E.","family":"Avalon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0749-2995","authenticated-orcid":false,"given":"MacKenzie","family":"Bryant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lindsey A.","family":"Burnett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9s Mauricio","family":"Caraballo-Rodr\u00edguez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin Casas","family":"Maya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Loryn","family":"Chin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5050-2389","authenticated-orcid":false,"given":"Llu\u00eds","family":"Corominas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4931-752X","authenticated-orcid":false,"given":"Ronald J.","family":"Ellis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donald","family":"Franklin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sagan","family":"Girod","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paulo Wender P.","family":"Gomes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauren","family":"Hansen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert K.","family":"Heaton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer E.","family":"Iudicello","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2228-6308","authenticated-orcid":false,"given":"Alan K.","family":"Jarmusch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lora","family":"Khatib","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott","family":"Letendre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4573-0915","authenticated-orcid":false,"given":"Sarolt","family":"Magyari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"McDonald","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0894-4770","authenticated-orcid":false,"given":"Ipsita","family":"Mohanty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2087-7435","authenticated-orcid":false,"given":"Andr\u00e9s","family":"Cumsille","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David J.","family":"Moore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-5538-5270","authenticated-orcid":false,"given":"Prajit","family":"Rajkumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-2943-2282","authenticated-orcid":false,"given":"Dylan H.","family":"Ross","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harshada","family":"Sapre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5760-3190","authenticated-orcid":false,"given":"Mohammad Reza Zare","family":"Shahneh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruben","family":"Gil-Solsona","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sydney P.","family":"Thomas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caitlin","family":"Tribelhorn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helena M.","family":"Tubb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Corinn","family":"Walker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0525-809X","authenticated-orcid":false,"given":"Crystal X.","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jasmine","family":"Zemlin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7237-3402","authenticated-orcid":false,"given":"Simone","family":"Zuffa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3207-2434","authenticated-orcid":false,"given":"David S.","family":"Wishart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pablo","family":"Gago-Ferrero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1858-5732","authenticated-orcid":false,"given":"Rima","family":"Kaddurah-Daouk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingxun","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6487-4215","authenticated-orcid":false,"given":"Manuela","family":"Raffatellu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8062-3296","authenticated-orcid":false,"given":"Karsten","family":"Zengler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6940-3006","authenticated-orcid":false,"given":"Tom\u00e1\u0161","family":"Pluskal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1021-5200","authenticated-orcid":false,"given":"Libin","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0975-9019","authenticated-orcid":false,"given":"Rob","family":"Knight","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3974-8038","authenticated-orcid":false,"given":"Shirley M.","family":"Tsunoda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3003-1030","authenticated-orcid":false,"given":"Pieter C.","family":"Dorrestein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,12,9]]},"reference":[{"key":"65993_CR1","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1126\/science.aay3164","volume":"367","author":"R Vermeulen","year":"2020","unstructured":"Vermeulen, R., Schymanski, E. L., Barab\u00e1si, A.-L. & Miller, G. W. The exposome and health: Where chemistry meets biology. Science 367, 392\u2013396 (2020).","journal-title":"Science"},{"key":"65993_CR2","unstructured":"National Center for Health Statistics. Health, United States, 2019. Hyattsville, MD (2021)."},{"key":"65993_CR3","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1289\/ehp.1308015","volume":"122","author":"SM Rappaport","year":"2014","unstructured":"Rappaport, S. M., Barupal, D. K., Wishart, D., Vineis, P. & Scalbert, A. The blood exposome and its role in discovering causes of disease. Environ. Health Perspect. 122, 769\u2013774 (2014).","journal-title":"Environ. Health Perspect."},{"key":"65993_CR4","doi-asserted-by":"publisher","first-page":"786","DOI":"10.1016\/j.chom.2024.05.009","volume":"32","author":"J de la Cuesta-Zuluaga","year":"2024","unstructured":"de la Cuesta-Zuluaga, J., Boldt, L. & Maier, L. Response, resistance, and recovery of gut bacteria to human-targeted drug exposure. Cell Host Microbe 32, 786\u2013793 (2024).","journal-title":"Cell Host Microbe"},{"key":"65993_CR5","doi-asserted-by":"publisher","first-page":"eadg8357","DOI":"10.1126\/scitranslmed.adg8357","volume":"16","author":"AA Verdegaal","year":"2024","unstructured":"Verdegaal, A. A. & Goodman, A. L. Integrating the gut microbiome and pharmacology. Sci. Transl. Med. 16, eadg8357 (2024).","journal-title":"Sci. Transl. Med."},{"key":"65993_CR6","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-14177-z","volume":"11","author":"AV Vila","year":"2020","unstructured":"Vila, A. V. et al. Impact of commonly used drugs on the composition and metabolic function of the gut microbiota. Nat. Commun. 11, 362 (2020).","journal-title":"Nat. Commun."},{"key":"65993_CR7","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1038\/nature25979","volume":"555","author":"L Maier","year":"2018","unstructured":"Maier, L. et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 555, 623\u2013628 (2018).","journal-title":"Nature"},{"key":"65993_CR8","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/j.jclinepi.2015.05.026","volume":"69","author":"S-J Sinnott","year":"2016","unstructured":"Sinnott, S.-J., Polinski, J. M., Byrne, S. & Gagne, J. J. Measuring drug exposure: concordance between defined daily dose and days\u2019 supply depended on drug class. J. Clin. Epidemiol. 69, 107\u2013113 (2016).","journal-title":"J. Clin. Epidemiol."},{"key":"65993_CR9","doi-asserted-by":"publisher","first-page":"211","DOI":"10.2147\/JMDH.S104807","volume":"9","author":"A Althubaiti","year":"2016","unstructured":"Althubaiti, A. Information bias in health research: definition, pitfalls, and adjustment methods. J. Multidiscip. Healthc. 9, 211\u2013217 (2016).","journal-title":"J. Multidiscip. Healthc."},{"key":"65993_CR10","doi-asserted-by":"publisher","first-page":"449","DOI":"10.2471\/BLT.19.242370","volume":"98","author":"Y Gong","year":"2020","unstructured":"Gong, Y. et al. Over-the-counter antibiotic sales in community and online pharmacies, China. Bull. World Health Organ. 98, 449\u2013457 (2020).","journal-title":"Bull. World Health Organ."},{"key":"65993_CR11","doi-asserted-by":"publisher","DOI":"10.2196\/41834","volume":"8","author":"TK Mackey","year":"2022","unstructured":"Mackey, T. K. et al. Multifactor quality and safety analysis of antimicrobial drugs sold by online pharmacies that do not require a prescription: Multiphase observational, content analysis, and product evaluation study. JMIR Public Health Surveill. 8, e41834 (2022).","journal-title":"JMIR Public Health Surveill."},{"key":"65993_CR12","doi-asserted-by":"crossref","unstructured":"Essigmann, H. T. et al. Epidemiology of antibiotic use and drivers of cross-border procurement in a Mexican American border community. Front. Public Health 10, (2022).","DOI":"10.3389\/fpubh.2022.832266"},{"key":"65993_CR13","doi-asserted-by":"publisher","DOI":"10.2196\/12076","volume":"21","author":"B Walmsley","year":"2019","unstructured":"Walmsley, B. et al. The PrEP You Want: A web-based survey of online cross-border shopping for HIV prophylaxis medications. J. Med. Internet Res. 21, e12076 (2019).","journal-title":"J. Med. Internet Res."},{"key":"65993_CR14","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1111\/j.1476-5381.2010.00936.x","volume":"161","author":"G Vauquelin","year":"2010","unstructured":"Vauquelin, G. & Charlton, S. J. Long-lasting target binding and rebinding as mechanisms to prolong in vivo drug action. Br. J. Pharmacol.161, 488\u2013508 (2010).","journal-title":"Br. J. Pharmacol."},{"key":"65993_CR15","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1038\/nrd.2015.18","volume":"15","author":"RA Copeland","year":"2016","unstructured":"Copeland, R. A. The drug\u2013target residence time model: a 10-year retrospective. Nat. Rev. Drug Discov. 15, 87\u201395 (2016).","journal-title":"Nat. Rev. Drug Discov."},{"key":"65993_CR16","doi-asserted-by":"publisher","first-page":"D668","DOI":"10.1093\/nar\/gkj067","volume":"34","author":"DS Wishart","year":"2006","unstructured":"Wishart, D. S. et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 34, D668\u2013D672 (2006).","journal-title":"Nucleic Acids Res."},{"key":"65993_CR17","doi-asserted-by":"publisher","first-page":"D1074","DOI":"10.1093\/nar\/gkx1037","volume":"46","author":"DS Wishart","year":"2018","unstructured":"Wishart, D. S. et al. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res 46, D1074\u2013D1082 (2018).","journal-title":"Nucleic Acids Res"},{"key":"65993_CR18","doi-asserted-by":"publisher","first-page":"D932","DOI":"10.1093\/nar\/gkw993","volume":"45","author":"O Ursu","year":"2017","unstructured":"Ursu, O. et al. DrugCentral: online drug compendium. Nucleic Acids Res 45, D932\u2013D939 (2017).","journal-title":"Nucleic Acids Res"},{"key":"65993_CR19","unstructured":"DailyMed. https:\/\/dailymed.nlm.nih.gov\/dailymed\/index.cfm."},{"key":"65993_CR20","doi-asserted-by":"publisher","first-page":"D353","DOI":"10.1093\/nar\/gkw1092","volume":"45","author":"M Kanehisa","year":"2017","unstructured":"Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y. & Morishima, K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353\u2013D361 (2017).","journal-title":"Nucleic Acids Res."},{"key":"65993_CR21","doi-asserted-by":"crossref","unstructured":"Wan, M. et al. TnT-LLM: Text mining at scale with large language models. Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 5836\u20135847 (2024).","DOI":"10.1145\/3637528.3671647"},{"key":"65993_CR22","doi-asserted-by":"publisher","first-page":"1930","DOI":"10.1038\/s41591-023-02448-8","volume":"29","author":"AJ Thirunavukarasu","year":"2023","unstructured":"Thirunavukarasu, A. J. et al. Large language models in medicine. Nat. Med. 29, 1930\u20131940 (2023).","journal-title":"Nat. Med."},{"key":"65993_CR23","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s43856-023-00370-1","volume":"3","author":"J Clusmann","year":"2023","unstructured":"Clusmann, J. et al. The future landscape of large language models in medicine. Commun. Med. 3, 1\u20138 (2023).","journal-title":"Commun. Med."},{"key":"65993_CR24","doi-asserted-by":"publisher","first-page":"340","DOI":"10.1002\/mas.20128","volume":"26","author":"C Prakash","year":"2007","unstructured":"Prakash, C., Shaffer, C. L. & Nedderman, A. Analytical strategies for identifying drug metabolites. Mass Spectrom. Rev. 26, 340\u2013369 (2007).","journal-title":"Mass Spectrom. Rev."},{"key":"65993_CR25","doi-asserted-by":"publisher","first-page":"9828","DOI":"10.1021\/acs.est.4c00968","volume":"58","author":"C Meyer","year":"2024","unstructured":"Meyer, C., Stravs, M. A. & Hollender, J. How wastewater reflects human metabolism\u2500suspect screening of pharmaceutical metabolites in wastewater influent. Environ. Sci. Technol. 58, 9828\u20139839 (2024).","journal-title":"Environ. Sci. Technol."},{"key":"65993_CR26","doi-asserted-by":"publisher","first-page":"828","DOI":"10.1038\/nbt.3597","volume":"34","author":"M Wang","year":"2016","unstructured":"Wang, M. et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat. Biotechnol. 34, 828\u2013837 (2016).","journal-title":"Nat. Biotechnol."},{"key":"65993_CR27","doi-asserted-by":"crossref","unstructured":"Brungs, C. et al. MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries. Nat. Methods 22, 2028\u20132031 (2025).","DOI":"10.1038\/s41592-025-02813-0"},{"key":"65993_CR28","doi-asserted-by":"publisher","first-page":"D1373","DOI":"10.1093\/nar\/gkac956","volume":"51","author":"S Kim","year":"2023","unstructured":"Kim, S. et al. PubChem 2023 update. Nucleic Acids Res 51, D1373\u2013D1380 (2023).","journal-title":"Nucleic Acids Res"},{"key":"65993_CR29","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1038\/nm.4306","volume":"23","author":"SM Corsello","year":"2017","unstructured":"Corsello, S. M. et al. The Drug Repurposing Hub: a next-generation drug library and information resource. Nat. Med. 23, 405\u2013408 (2017).","journal-title":"Nat. Med."},{"key":"65993_CR30","doi-asserted-by":"publisher","first-page":"D1180","DOI":"10.1093\/nar\/gkad1004","volume":"52","author":"B Zdrazil","year":"2024","unstructured":"Zdrazil, B. et al. The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods. Nucleic Acids Res 52, D1180\u2013D1192 (2024).","journal-title":"Nucleic Acids Res"},{"key":"65993_CR31","doi-asserted-by":"crossref","unstructured":"Nahler, G. Anatomical therapeutic chemical classification system (ATC). In Dictionary of Pharmaceutical Medicine 8\u20138 (Springer, Vienna, 2009).","DOI":"10.1007\/978-3-211-89836-9_64"},{"key":"65993_CR32","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1021\/jasms.2c00111","volume":"33","author":"DH Ross","year":"2022","unstructured":"Ross, D. H., Seguin, R. P., Krinsky, A. M. & Xu, L. High-throughput measurement and machine learning-based prediction of collision cross sections for drugs and drug metabolites. J. Am. Soc. Mass Spectrom. 33, 1061\u20131072 (2022).","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"65993_CR33","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1016\/j.tips.2016.10.011","volume":"38","author":"RA Quinn","year":"2017","unstructured":"Quinn, R. A. et al. Molecular networking as a drug discovery, drug metabolism, and precision medicine strategy. Trends Pharmacol. Sci. 38, 143\u2013154 (2017).","journal-title":"Trends Pharmacol. Sci."},{"key":"65993_CR34","doi-asserted-by":"publisher","first-page":"1377","DOI":"10.1038\/s41592-021-01303-3","volume":"18","author":"L Chen","year":"2021","unstructured":"Chen, L. et al. Metabolite discovery through global annotation of untargeted metabolomics data. Nat. Methods 18, 1377\u20131385 (2021).","journal-title":"Nat. Methods"},{"key":"65993_CR35","doi-asserted-by":"publisher","first-page":"8335","DOI":"10.1021\/acs.est.2c07774","volume":"57","author":"N Yu","year":"2023","unstructured":"Yu, N. et al. Nontarget discovery of antimicrobial transformation products in wastewater based on molecular networks. Environ. Sci. Technol. 57, 8335\u20138346 (2023).","journal-title":"Environ. Sci. Technol."},{"key":"65993_CR36","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-44035-y","volume":"14","author":"W Bittremieux","year":"2023","unstructured":"Bittremieux, W. et al. Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics. Nat. Commun. 14, 8488 (2023).","journal-title":"Nat. Commun."},{"key":"65993_CR37","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1038\/s41587-019-0375-9","volume":"38","author":"M Wang","year":"2020","unstructured":"Wang, M. et al. Mass spectrometry searches using MASST. Nat. Biotechnol. 38, 23\u201326 (2020).","journal-title":"Nat. Biotechnol."},{"key":"65993_CR38","doi-asserted-by":"crossref","unstructured":"Mongia, M. et al. Fast mass spectrometry search and clustering of untargeted metabolomics data. Nat. Biotechnol. 42, 1672\u20131677 (2024).","DOI":"10.1038\/s41587-023-01985-4"},{"key":"65993_CR39","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-60067-y","volume":"16","author":"Y El Abiead","year":"2025","unstructured":"El Abiead, Y. et al. Enabling pan-repository reanalysis for big data science of public metabolomics data. Nat. Commun. 16, 4838 (2025).","journal-title":"Nat. Commun."},{"key":"65993_CR40","doi-asserted-by":"publisher","first-page":"1534","DOI":"10.1002\/pmic.200300744","volume":"4","author":"DM Creasy","year":"2004","unstructured":"Creasy, D. M. & Cottrell, J. S. Unimod: Protein modifications for mass spectrometry. Proteomics 4, 1534\u20131536 (2004).","journal-title":"Proteomics"},{"key":"65993_CR41","doi-asserted-by":"publisher","first-page":"6463","DOI":"10.1021\/acs.jcim.3c00837","volume":"63","author":"AS Kolodnitsky","year":"2023","unstructured":"Kolodnitsky, A. S., Ionov, N. S., Rudik, A. V., Filimonov, D. A. & Poroikov, V. V. HGMMX: Host Gut Microbiota Metabolism Xenobiotics Database. J. Chem. Inf. Model. 63, 6463\u20136468 (2023).","journal-title":"J. Chem. Inf. Model."},{"key":"65993_CR42","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1016\/j.aca.2008.04.043","volume":"627","author":"BO Keller","year":"2008","unstructured":"Keller, B. O., Sui, J., Young, A. B. & Whittal, R. M. Interferences and contaminants encountered in modern mass spectrometry. Anal. Chim. Acta 627, 71\u201381 (2008).","journal-title":"Anal. Chim. Acta"},{"key":"65993_CR43","doi-asserted-by":"publisher","first-page":"1647","DOI":"10.1038\/s42255-024-01076-x","volume":"6","author":"M Giera","year":"2024","unstructured":"Giera, M., Aisporna, A., Uritboonthai, W. & Siuzdak, G. The hidden impact of in-source fragmentation in metabolic and chemical mass spectrometry data interpretation. Nat. Metab. 6, 1647\u20131648 (2024).","journal-title":"Nat. Metab."},{"key":"65993_CR44","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1038\/s42255-025-01239-4","volume":"7","author":"Y El Abiead","year":"2025","unstructured":"El Abiead, Y. et al. Discovery of metabolites prevails amid in-source fragmentation. Nat. Metab. 7, 435\u2013437 (2025).","journal-title":"Nat. Metab."},{"key":"65993_CR45","doi-asserted-by":"crossref","unstructured":"Shahneh, M. R. Z. et al. ModiFinder: Tandem mass spectral alignment enables structural modification site localization. J. Am. Soc. Mass Spectrom. 35, 2564\u20132578 (2024).","DOI":"10.1021\/jasms.4c00061"},{"key":"65993_CR46","doi-asserted-by":"publisher","first-page":"D1220","DOI":"10.1093\/nar\/gkac919","volume":"51","author":"DS Wishart","year":"2023","unstructured":"Wishart, D. S. et al. ChemFOnt: the chemical functional ontology resource. Nucleic Acids Res. 51, D1220\u2013D1229 (2023).","journal-title":"Nucleic Acids Res."},{"key":"65993_CR47","doi-asserted-by":"publisher","first-page":"e0271794","DOI":"10.1371\/journal.pone.0271794","volume":"17","author":"M Panitchpakdi","year":"2022","unstructured":"Panitchpakdi, M. et al. Non-invasive skin sampling detects systemically administered drugs in humans. PloS One 17, e0271794 (2022).","journal-title":"PloS One"},{"key":"65993_CR48","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1002\/j.1552-4604.1998.tb04466.x","volume":"38","author":"JM Scavone","year":"1998","unstructured":"Scavone, J. M., Greenblatt, D. J., Harmatz, J. S., Engelhardt, N. & Shader, R. I. Pharmacokinetics and pharmacodynamics of diphenhydramine 25 mg in young and elderly volunteers. J. Clin. Pharmacol. 38, 603\u2013609 (1998).","journal-title":"J. Clin. Pharmacol."},{"key":"65993_CR49","doi-asserted-by":"publisher","first-page":"972","DOI":"10.1111\/cts.12785","volume":"13","author":"AK Jarmusch","year":"2020","unstructured":"Jarmusch, A. K. et al. Enhanced characterization of drug metabolism and the influence of the intestinal microbiome: A pharmacokinetic, microbiome, and untargeted metabolomics study. Clin. Transl. Sci. 13, 972\u2013984 (2020).","journal-title":"Clin. Transl. Sci."},{"key":"65993_CR50","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1038\/s41592-020-0916-7","volume":"17","author":"AK Jarmusch","year":"2020","unstructured":"Jarmusch, A. K. et al. ReDU: a framework to find and reanalyze public mass spectrometry data. Nat. Methods 17, 901\u2013904 (2020).","journal-title":"Nat. Methods"},{"key":"65993_CR51","doi-asserted-by":"publisher","first-page":"e00031","DOI":"10.1128\/mSystems.00031-18","volume":"3","author":"D McDonald","year":"2018","unstructured":"McDonald, D. et al. American Gut: an open platform for citizen science microbiome research. mSystems 3, e00031\u201318 (2018).","journal-title":"mSystems"},{"key":"65993_CR52","doi-asserted-by":"publisher","first-page":"2562","DOI":"10.1111\/bcp.13709","volume":"84","author":"S Audi","year":"2018","unstructured":"Audi, S. et al. The \u2018top 100\u2019 drugs and classes in England: an updated \u2018starter formulary\u2019 for trainee prescribers. Br. J. Clin. Pharmacol. 84, 2562\u20132571 (2018).","journal-title":"Br. J. Clin. Pharmacol."},{"key":"65993_CR53","first-page":"43","volume":"6","author":"AV Fuentes","year":"2018","unstructured":"Fuentes, A. V., Pineda, M. D. & Venkata, K. C. N. Comprehension of top 200 prescribed drugs in the US as a resource for pharmacy teaching, training and practice. Pharm. J. Pharm. Educ. Pract. 6, 43 (2018).","journal-title":"Pharm. J. Pharm. Educ. Pract."},{"key":"65993_CR54","doi-asserted-by":"publisher","first-page":"1046","DOI":"10.1002\/pds.5093","volume":"29","author":"CE Wylie","year":"2020","unstructured":"Wylie, C. E., Daniels, B., Brett, J., Pearson, S.-A. & Buckley, N. A. A national study on prescribed medicine use in Australia on a typical day. Pharmacoepidemiol. Drug Saf. 29, 1046\u20131053 (2020).","journal-title":"Pharmacoepidemiol. Drug Saf."},{"key":"65993_CR55","unstructured":"National Center for Health Statistics, Prescription Drug Use Among Adults Aged 40-79 in the United States and Canada. https:\/\/www.cdc.gov\/nchs\/products\/databriefs\/db347.htm (2019)."},{"key":"65993_CR56","doi-asserted-by":"publisher","first-page":"684","DOI":"10.1111\/j.1365-2125.2005.02404.x","volume":"59","author":"PJ Helms","year":"2005","unstructured":"Helms, P. J., Ekins Daukes, S., Taylor, M. W., Simpson, C. R. & McLay, J. S. Utility of routinely acquired primary care data for paediatric disease epidemiology and pharmacoepidemiology. Br. J. Clin. Pharmacol. 59, 684\u2013690 (2005).","journal-title":"Br. J. Clin. Pharmacol."},{"key":"65993_CR57","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1097\/00003643-200219261-00003","volume":"26","author":"D Isacson","year":"2002","unstructured":"Isacson, D. & Bingefors, K. Epidemiology of analgesic use: a gender perspective. Eur. J. Anaesthesiol. Suppl. 26, 5\u201315 (2002).","journal-title":"Eur. J. Anaesthesiol. Suppl."},{"key":"65993_CR58","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1089\/jwh.2007.0731","volume":"17","author":"M Anthony","year":"2008","unstructured":"Anthony, M. et al. Gender and age differences in medications dispensed from a national chain drugstore. J. Women\u2019s Health 17, 735\u2013743 (2008).","journal-title":"J. Women\u2019s Health"},{"key":"65993_CR59","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1007\/s11306-007-0082-2","volume":"3","author":"LW Sumner","year":"2007","unstructured":"Sumner, L. W. et al. Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI). Metabolomics 3, 211\u2013221 (2007).","journal-title":"Metabolomics"},{"key":"65993_CR60","doi-asserted-by":"publisher","first-page":"e504","DOI":"10.1016\/S2352-3018(20)30107-7","volume":"7","author":"A Winston","year":"2020","unstructured":"Winston, A. & Spudich, S. Cognitive disorders in people living with HIV. Lancet HIV 7, e504\u2013e513 (2020).","journal-title":"Lancet HIV"},{"key":"65993_CR61","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1111\/pcn.12097","volume":"68","author":"S Arseniou","year":"2014","unstructured":"Arseniou, S., Arvaniti, A. & Samakouri, M. HIV infection and depression. Psychiatry Clin. Neurosci. 68, 96\u2013109 (2014).","journal-title":"Psychiatry Clin. Neurosci."},{"key":"65993_CR62","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1016\/S1473-3099(04)00971-5","volume":"4","author":"K Donati","year":"2004","unstructured":"Donati, K., de, G., Rabagliati, R., Iacoviello, L. & Cauda, R. HIV infection, HAART, and endothelial adhesion molecules: current perspectives. Lancet Infect. Dis. 4, 213\u2013222 (2004).","journal-title":"Lancet Infect. Dis."},{"key":"65993_CR63","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1093\/brain\/awac465","volume":"146","author":"RK Heaton","year":"2023","unstructured":"Heaton, R. K. et al. Twelve-year neurocognitive decline in HIV is associated with comorbidities, not age: a CHARTER study. Brain J. Neurol. 146, 1121\u20131131 (2023).","journal-title":"Brain J. Neurol."},{"key":"65993_CR64","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23953-9","volume":"12","author":"R Schmid","year":"2021","unstructured":"Schmid, R. et al. Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment. Nat. Commun. 12, 3832 (2021).","journal-title":"Nat. Commun."},{"key":"65993_CR65","doi-asserted-by":"publisher","first-page":"3617","DOI":"10.1016\/j.cell.2022.08.003","volume":"185","author":"AG Cheng","year":"2022","unstructured":"Cheng, A. G. et al. Design, construction, and in vivo augmentation of a complex gut microbiome. Cell 185, 3617\u20133636.e19 (2022).","journal-title":"Cell"},{"key":"65993_CR66","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1038\/nrd1010","volume":"2","author":"L Olbe","year":"2003","unstructured":"Olbe, L., Carlsson, E. & Lindberg, P. A proton-pump inhibitor expedition: the case histories of omeprazole and esomeprazole. Nat. Rev. Drug Discov. 2, 132\u2013139 (2003).","journal-title":"Nat. Rev. Drug Discov."},{"key":"65993_CR67","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1002\/jms.3260","volume":"48","author":"C Boix","year":"2013","unstructured":"Boix, C., Ib\u00e1\u00f1ez, M., Sancho, J. V., Niessen, W. M. A. & Hern\u00e1ndez, F. Investigating the presence of omeprazole in waters by liquid chromatography coupled to low and high resolution mass spectrometry: degradation experiments. J. Mass Spectrom. 48, 1091\u20131100 (2013).","journal-title":"J. Mass Spectrom."},{"key":"65993_CR68","doi-asserted-by":"publisher","first-page":"965","DOI":"10.3109\/03639049509026660","volume":"21","author":"M Mathew","year":"1995","unstructured":"Mathew, M., Gupta, V. D. & Bailey, R. E. Stability of omeprazole solutions at various ph values as determined by high-performance liquid chromatography. Drug Dev. Ind. Pharm. 21, 965\u2013971 (1995).","journal-title":"Drug Dev. Ind. Pharm."},{"key":"65993_CR69","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1038\/s41586-023-06906-8","volume":"626","author":"EC Gentry","year":"2024","unstructured":"Gentry, E. C. et al. Reverse metabolomics for the discovery of chemical structures from humans. Nature 626, 419\u2013426 (2024).","journal-title":"Nature"},{"key":"65993_CR70","doi-asserted-by":"publisher","first-page":"792","DOI":"10.1038\/s41564-021-00887-y","volume":"6","author":"F-Y Chang","year":"2021","unstructured":"Chang, F.-Y. et al. Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids. Nat. Microbiol. 6, 792\u2013805 (2021).","journal-title":"Nat. Microbiol."},{"key":"65993_CR71","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1007\/s11481-015-9595-z","volume":"10","author":"A Mann","year":"2015","unstructured":"Mann, A. et al. Palmitoyl serine: An endogenous neuroprotective endocannabinoid-like entity after traumatic brain injury. J. Neuroimmune Pharmacol. 10, 356\u2013363 (2015).","journal-title":"J. Neuroimmune Pharmacol."},{"key":"65993_CR72","doi-asserted-by":"publisher","first-page":"24770","DOI":"10.1073\/pnas.1916288116","volume":"116","author":"TJ Grevengoed","year":"2019","unstructured":"Grevengoed, T. J. et al. N-acyl taurines are endogenous lipid messengers that improve glucose homeostasis. Proc. Natl Acad. Sci. 116, 24770\u201324778 (2019).","journal-title":"Proc. Natl Acad. Sci."},{"key":"65993_CR73","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1016\/j.bbrc.2012.11.026","volume":"430","author":"DP Waluk","year":"2013","unstructured":"Waluk, D. P., Vielfort, K., Derakhshan, S., Aro, H. & Hunt, M. C. N-Acyl taurines trigger insulin secretion by increasing calcium flux in pancreatic \u03b2-cells. Biochem. Biophys. Res. Commun. 430, 54\u201359 (2013).","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"65993_CR74","doi-asserted-by":"publisher","first-page":"1334","DOI":"10.1016\/j.cmet.2017.04.012","volume":"25","author":"M Aichler","year":"2017","unstructured":"Aichler, M. et al. N-acyl taurines and acylcarnitines cause an imbalance in insulin synthesis and secretion provoking \u03b2 cell dysfunction in type 2 diabetes. Cell Metab. 25, 1334\u20131347.e4 (2017).","journal-title":"Cell Metab."},{"key":"65993_CR75","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.cell.2025.05.015","volume":"188","author":"H Mannochio-Russo","year":"2025","unstructured":"Mannochio-Russo, H. et al. The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids. Cell 188, 1\u201316 (2025).","journal-title":"Cell"},{"key":"65993_CR76","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1111\/hiv.12797","volume":"21","author":"A Inciarte","year":"2020","unstructured":"Inciarte, A. et al. Post-exposure prophylaxis for HIV infection in sexual assault victims. HIV Med. 21, 43\u201352 (2020).","journal-title":"HIV Med."},{"key":"65993_CR77","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1097\/QAI.0000000000002345","volume":"84","author":"E Kamitani","year":"2020","unstructured":"Kamitani, E. et al. Growth in proportion and disparities of HIV PrEP use among key populations identified in the United States national goals: systematic review and meta-analysis of published surveys. J. Acquir. Immune Defic. Syndr. 84, 379 (2020).","journal-title":"J. Acquir. Immune Defic. Syndr."},{"key":"65993_CR78","doi-asserted-by":"publisher","first-page":"1807","DOI":"10.1056\/NEJMoa1215541","volume":"369","author":"SL Walmsley","year":"2013","unstructured":"Walmsley, S. L. et al. Dolutegravir plus abacavir-lamivudine for the treatment of HIV-1 infection. N. Engl. J. Med. 369, 1807\u20131818 (2013).","journal-title":"N. Engl. J. Med."},{"key":"65993_CR79","doi-asserted-by":"publisher","first-page":"1169","DOI":"10.1016\/S0140-6736(07)60497-8","volume":"369","author":"B Clotet","year":"2007","unstructured":"Clotet, B. et al. Efficacy and safety of darunavir-ritonavir at week 48 in treatment-experienced patients with HIV-1 infection in POWER 1 and 2: a pooled subgroup analysis of data from two randomised trials. Lancet Lond. Engl. 369, 1169\u20131178 (2007).","journal-title":"Lancet Lond. Engl."},{"key":"65993_CR80","doi-asserted-by":"publisher","first-page":"3110","DOI":"10.1093\/cid\/ciz1213","volume":"71","author":"GD Huhn","year":"2020","unstructured":"Huhn, G. D. et al. Darunavir\/cobicistat\/emtricitabine\/tenofovir alafenamide in a rapid-initiation model of care for human immunodeficiency virus type 1 infection: Primary analysis of the DIAMOND study. Clin. Infect. Dis. 71, 3110\u20133117 (2020).","journal-title":"Clin. Infect. Dis."},{"key":"65993_CR81","doi-asserted-by":"publisher","first-page":"e355","DOI":"10.1016\/S2352-3018(19)30077-3","volume":"6","author":"DA Wohl","year":"2019","unstructured":"Wohl, D. A. et al. Bictegravir combined with emtricitabine and tenofovir alafenamide versus dolutegravir, abacavir, and lamivudine for initial treatment of HIV-1 infection: week 96 results from a randomised, double-blind, multicentre, phase 3, non-inferiority trial. Lancet HIV 6, e355\u2013e363 (2019).","journal-title":"Lancet HIV"},{"key":"65993_CR82","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1038\/s41538-022-00137-3","volume":"6","author":"KA West","year":"2022","unstructured":"West, K. A., Schmid, R., Gauglitz, J. M., Wang, M. & Dorrestein, P. C. foodMASST a mass spectrometry search tool for foods and beverages. Npj Sci. Food 6, 22 (2022).","journal-title":"Npj Sci. Food"},{"key":"65993_CR83","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-020-00456-1","volume":"12","author":"AP Bento","year":"2020","unstructured":"Bento, A. P. et al. An open source chemical structure curation pipeline using RDKit. J. Cheminformatics 12, 51 (2020).","journal-title":"J. Cheminformatics"},{"key":"65993_CR84","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1038\/s41564-023-01575-9","volume":"9","author":"S Zuffa","year":"2024","unstructured":"Zuffa, S. et al. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nat. Microbiol. 9, 336\u2013345 (2024).","journal-title":"Nat. Microbiol."},{"key":"65993_CR85","doi-asserted-by":"publisher","unstructured":"Bittremieux, W. et al. Universal MS\/MS visualization and retrieval with the metabolomics spectrum resolver web service. Preprint at https:\/\/doi.org\/10.1101\/2020.05.09.086066 (2020).","DOI":"10.1101\/2020.05.09.086066"},{"key":"65993_CR86","doi-asserted-by":"crossref","unstructured":"Bittremieux, W., Laukens, K., Noble, W. S. & Dorrestein, P. C. Large-scale tandem mass spectrum clustering using fast nearest neighbor searching. Rapid Commun. Mass Spectrom. e9153 (2021).","DOI":"10.1101\/2021.02.05.429957"},{"key":"65993_CR87","doi-asserted-by":"crossref","unstructured":"Schmid, R. et al. Integrative analysis of multimodal mass spectrometry data in MZmine 3. Nat. Biotechnol. 41, 1\u20133 (2023).","DOI":"10.1038\/s41587-023-01690-2"},{"key":"65993_CR88","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1038\/s41592-020-0933-6","volume":"17","author":"L-F Nothias","year":"2020","unstructured":"Nothias, L.-F. et al. Feature-based molecular networking in the GNPS analysis environment. Nat. Methods 17, 905\u2013908 (2020).","journal-title":"Nat. Methods"},{"key":"65993_CR89","doi-asserted-by":"publisher","first-page":"e00199","DOI":"10.1128\/mSphere.00199-16","volume":"1","author":"D McDonald","year":"2016","unstructured":"McDonald, D. et al. Extreme Dysbiosis of the Microbiome in Critical Illness. mSphere 1, e00199\u201316 (2016).","journal-title":"mSphere"},{"key":"65993_CR90","first-page":"e00985","volume":"0","author":"C Brennan","year":"2024","unstructured":"Brennan, C. et al. Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies. mSystems 0, e00985\u201324 (2024).","journal-title":"mSystems"},{"key":"65993_CR91","doi-asserted-by":"publisher","first-page":"918","DOI":"10.1038\/nbt.2377","volume":"30","author":"MC Chambers","year":"2012","unstructured":"Chambers, M. C. et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 30, 918\u2013920 (2012).","journal-title":"Nat. Biotechnol."},{"key":"65993_CR92","doi-asserted-by":"publisher","unstructured":"Zhao, H. N., Kvitne, K., Brungs, C., & Dorrestein, P. GNPS Drug Library spectral files and metadata [Data set]. Zenodo. https:\/\/doi.org\/10.5281\/zenodo.17232042 (2025).","DOI":"10.5281\/zenodo.17232042"},{"key":"65993_CR93","doi-asserted-by":"publisher","unstructured":"Zhao, H. N. ninahaoqizhao\/Manuscript_GNPS_Drug_Library: v1.0. Zenodo. https:\/\/doi.org\/10.5281\/zenodo.17232336 (2025).","DOI":"10.5281\/zenodo.17232336"},{"key":"65993_CR94","doi-asserted-by":"publisher","unstructured":"Kvitne, K. E. kinekvitne\/manuscript_drug_library: v1.0.0. Zenodo. https:\/\/doi.org\/10.5281\/zenodo.17230320 (2025).","DOI":"10.5281\/zenodo.17230320"}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-65993-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-65993-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-65993-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,9]],"date-time":"2025-12-09T11:01:07Z","timestamp":1765278067000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-65993-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,9]]},"references-count":94,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["65993"],"URL":"https:\/\/doi.org\/10.1038\/s41467-025-65993-5","relation":{},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,9]]},"assertion":[{"value":"23 July 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 October 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 December 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"R.S. is a co-founder of mzio GmbH. D.M.: D.M. is a consultant for BiomeSense, Inc., has equity, and receives income. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. R.K.-D.: R.K.-D. is an inventor on a series of patents on use of metabolomics for the diagnosis and treatment of CNS diseases and holds equity in Metabolon Inc., Chymia LLC, and PsyProtix. M.W. is a co-founder of Ometa Labs LLC. T.P. is a co-founder of mzio GmbH. R.K. is a scientific advisory board member, and consultant for BiomeSense, Inc., has equity, and receives income. He is a scientific advisory board member and has equity in GenCirq. He has equity in and acts as a consultant for Cybele. He is a co-founder of Biota, Inc., and has equity. He is a cofounder of Micronoma and has equity and is a scientific advisory board member. He is a board member of Microbiota Vault, Inc. He is a board member of\n                      N\n                      \u2009=\u20091 IBS advisory board and receives income. He is a Senior Visiting Fellow of HKUST Jockey Club Institute for Advanced Study. The terms of these arrangements have been reviewed and approved by the University of California, San Diego, in accordance with its conflict of interest policies. S.M.T.: S.M.T. receives research funding from Veloxis Pharmaceuticals. P.C.D.: P.C.D. is a scientific advisor and holds equity in Cybele, and bileOmix, and is a Scientific Co-founder, advisor, holds equity\u00a0and\/or received income from Ometa, Arome, and Enveda, with prior approval by UC-San Diego. The remaining authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"10600"}}