ArticlebioRxiv : the preprint server for biology2024
Empirically establishing drug exposure records directly from untargeted metabolomics data.
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Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Authors and funding
55 authors.
Haoqi Nina ZhaoCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-3908-630X
Kine Eide KvitneSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-8118-7660
Corinna BrungsInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.ORCID 0000-0002-2571-5235
Siddharth MohanSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0009-0008-4524-1875
Vincent Charron-LamoureuxCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-9440-7036
Wout BittremieuxCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 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, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-0922-3887
Santosh LamichhaneSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-9292-3595
Yasin El AbieadCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-4392-7706
Mohammadsobhan S AndalibiDepartment of Neurosciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-4895-1214
Helena Mannochio-RussoCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-4961-2353
Madison AmbreDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID 0009-0006-5018-898X
Nicole E AvalonScripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-3588-892X
MacKenzie BryantDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-0749-2995
Andrés Mauricio Caraballo-RodríguezCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-5499-2728
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.
Ronald J EllisDepartment of Neurosciences, University of California San Diego, La Jolla, CA, USA.ORCID 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 T6G 2E9, Canada.ORCID 0000-0002-8667-0907
Paulo Wender P GomesCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-5478-2448
Lauren HansenDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Robert 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.ORCID 0000-0003-2854-7684
Alan K JarmuschCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-2228-6308
Lora KhatibDepartment of Neurosciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-6998-8278
Scott LetendreHIV Neurobehavioral Research Program, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-3490-4975
Sarolt MagyariSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-4573-0915
Daniel McDonaldDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-0876-9060
Ipsita MohantyCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-5311-6443
Andrés CumsilleSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 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 0009-0002-5538-5270
Dylan H RossDepartment of Medicinal Chemistry, University of Washington, Seattle, WA, USA.ORCID 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 0000-0002-5760-3190
Sydney P ThomasCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-8261-1195
Caitlin TribelhornDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID 0009-0002-8788-471X
Helena M TubbDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-7637-5090
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 0000-0002-0525-809X
Shipei XingCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-6227-6959
Jasmine ZemlinCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-0713-9956
Simone ZuffaCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-7237-3402
David S WishartDepartment of Bioengineering, University of California San Diego, La Jolla, California, USA.ORCID 0000-0002-3207-2434
Rima Kaddurah-DaoukDepartment of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, 27708, USA.
Mingxun WangDepartment of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA.ORCID 0000-0001-7647-6097
Manuela RaffatelluDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0001-6487-4215
Karsten ZenglerScripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
Tomáš PluskalInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.ORCID 0000-0002-6940-3006
Libin XuDepartment of Medicinal Chemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0003-1021-5200
Rob KnightDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-0975-9019
Shirley M TsunodaSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-3974-8038
Pieter C DorresteinCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Funding
National Centralized Repository for Alzheimer's Disease and Related Dementias (NCRAD)U24AG021886 · NIA · INDIANA UNIV-PURDUE UNIV AT INDIANAPOLIS · PI TATIANA M. FOROUD · 2002 to 2026
$119.8MProject 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
$50.4MThe 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
$19.6MCollaborative 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
$218kNCCIH NIH HHS F32 AT011475NIAID NIH HHS R37 AI126277NIA NIH HHS U19 AG063744NIA NIH HHS U24 AG021886NICHD NIH HHS P50 HD106463NIDDK NIH HHS R01 DK136117NIDDK NIH HHS U24 DK133658NIMH NIH HHS P30 MH062512
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
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