ArticleNature biotechnology2022
Enhancing untargeted metabolomics using metadata-based source annotation.
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Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 46 papers.
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46citing papers in PubMed
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Who cites it
46 citing papers in PubMed.
- Integrating multi-omics technologies to decipher microbiome functions.Nature communications · 2026Review
- Purine-Metabolism Reprogramming Associated with Failed-Repair Proximal Tubule States in the AKI-to-CKD Transition.Metabolites · 2026Article
- The Emerging Role of N-Acetylaspartate in Cancer.International journal of molecular sciences · 2026Review
- Serum metabolomic profile in children with sepsis-associated acute kidney injury.Clinical and experimental pediatrics · 2026Article
- Omics-Guided Construction of Microbial Consortia for Reproducible Traditional Fermented Foods and Beverages.Foods (Basel, Switzerland) · 2026Review
- Pan-Metabolomics Repository Mapping of the Carnitine Landscape.bioRxiv : the preprint server for biology · 2026Article
- Enhanced Untargeted Metabolomics Based on High-Resolution Mass Spectrometry Reveals Global Rewiring Due to Mitochondrial Dysfunction in Yeast.International journal of molecular sciences · 2026Article
- Brazilian Mining Dam Collapse: Molecular Networking-Guided Metabolomics Reveals Species-Specific Plant Detox.ACS omega · 2026Article
- Diversity of specialized metabolites in Phaeoacremonium species revealed by untargeted metabolomics and bioactivity assays.Scientific reports · 2026Article
- SERS Cheminformatics: Opportunities for Data-Driven Discovery and Applications.ACS central science · 2025Review
- Learning molecular fingerprints of foods to decode dietary intake.Research square · 2025Article
- Metabolome informs about the chemical exposome and links to brain health.Environment international · 2025Review
- Article
- Article
- Longitudinal Fragment Profiles Based on Multi-Collision Energy Tandem Mass Spectra Improve the Accuracy of Metabolite Identification in Untargeted Metabolomics.Analytical chemistry · 2025Article
- Effective data visualization strategies in untargeted metabolomics.Natural product reports · 2025Review
- Article
- To Impute or Not To Impute in Untargeted Metabolomics─That is the Compositional Question.Journal of the American Society for Mass Spectrometry · 2025Article
- Discovering organic reactions with a machine-learning-powered deciphering of tera-scale mass spectrometry data.Nature communications · 2025Article
- Human Untargeted Metabolomics in High-Throughput Gut Microbiome Research: Ethanol vs Methanol.Analytical chemistry · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
73 authors.
Julia M Gauglitz *Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Kiana A West *Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Wout Bittremieux *Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-3105-1359
Candace L WilliamsBeckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, USA.ORCID http://orcid.org/0000-0002-1711-1183
Kelly C WeldonCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-1064-8153
Morgan PanitchpakdiCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Francesca Di OttavioCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Christine M AcevesCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Elizabeth BrownSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Nicole C SikoraCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Alan K JarmuschCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Cameron MartinoCenter for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-9334-1258
Anupriya TripathiSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Michael J MeehanCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Kathleen DorresteinCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Justin P ShafferDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-9371-6336
Roxana CorasDivision of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-9547-218X
Fernando VargasCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Lindsay DeRight GoldasichDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Tara SchwartzDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
MacKenzie BryantDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-0749-2995
Gregory HumphreyDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Abigail J JohnsonDivision of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA.
Katharina SpenglerCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Pedro Belda-FerreCenter for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-6532-1161
Edgar DiazDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Daniel McDonaldDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-0876-9060
Qiyun ZhuDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Emmanuel O ElijahCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Mingxun WangCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-7647-6097
Clarisse MarotzDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Kate E SprecherDepartment of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA.
Daniela Vargas-RoblesServicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, Puerto Ayacucho, Amazonas, Venezuela.
Dana WithrowDepartment of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA.
Gail AckermannDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Lourdes HerreraDepartment of Pediatrics, Billings Clinic, Billings, MT, USA.
Barry J BradfordDepartment of Animal Science, Michigan State University, East Lansing, MI, USA.ORCID http://orcid.org/0000-0002-6775-4961
Lucas Maciel Mauriz MarquesDepartment of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil.
Juliano Geraldo AmaralMultidisciplinary Health Institute, Federal University of Bahia, Vitória da Conquista, Bahia, Brazil.ORCID http://orcid.org/0000-0003-1823-1694
Rodrigo Moreira SilvaNPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil.ORCID http://orcid.org/0000-0003-2983-4941
Flavio Protasio VerasDepartment of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil.
Thiago Mattar CunhaDepartment of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil.ORCID http://orcid.org/0000-0003-1084-0065
Rene Donizeti Ribeiro OliveiraDepartment of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil.
Paulo Louzada-JuniorDepartment of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil.
Robert H MillsCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Paulina K PiotrowskiMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Stephanie L ServetasMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Sandra M Da SilvaMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Christina M JonesMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Nancy J LinMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Katrice A LippaMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Scott A JacksonMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Rima Kaddurah DaoukDepartment of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA.
Douglas GalaskoDepartment of Neurosciences, University of California San Diego, La Jolla, CA, USA.
Parambir S DulaiDivision of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
Tatyana I KalashnikovaDepartment of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
Curt WittenbergDepartment of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-7586-8854
Robert TerkeltaubDivision of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
Megan M DotyDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-2136-3719
Jae H KimDivision of Neonatology, Perinatal Institute, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
Kyung E RheeDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-1423-5970
Julia Beauchamp-WaltersDivision of Pediatric Hospital Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-3312-7115
Kenneth P WrightDepartment of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA.
Maria Gloria Dominguez-BelloDepartment of Biochemistry and Microbiology, School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.ORCID http://orcid.org/0000-0002-8879-6159
Mark ManaryDepartment of Pediatrics, Washington University, St. Louis, MO, USA.
Michelli F OliveiraDepartment of Medicine, University of California San Diego, La Jolla, CA, USA.
Brigid S BolandDivision of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
Norberto Peporine LopesNPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil.ORCID http://orcid.org/0000-0002-8159-3658
Monica GumaDivision of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
Austin D SwaffordCenter for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
Rachel J DuttonDivision of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
Rob KnightCenter for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA. rknight@ucsd.edu.
Pieter C DorresteinCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.ORCID http://orcid.org/0000-0002-3003-1030
Funding
Alzheimer's Disease Neuroimaging Initiative - SupplementU01AG024904 · NIA · NORTHERN CALIFORNIA INSTITUTE RES &EDUC · PI WEINER, MICHAEL W · 2004 to 2015
$121.0MProject 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
$54.1MNIH Prior Approval Process ProfessionalUL1TR002535 · NCATS · UNIVERSITY OF COLORADO DENVER · PI SOKOL, RONALD J. · 2018 to 2022
$51.1MPediatric Scientist Development Program (PSDP) [K12]K12HD000850 · NICHD · YALE UNIVERSITY · PI Sallie R. Permar · 1987 to 2026
$44.1MUCSD/SDSU IRACDAK12GM068524 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI TREJO, JOANN · 2003 to 2025
$24.4MThe Effects of Urate Lowering Therapy on Inflammation, Endothelial function, andP50AR060772 · NIAMS · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI SINGH, JASVINDER A · 2012 to 2021
$12.8MSan Diego Digestive Diseases Research CenterP30DK120515 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Bernd G. Schnabl · 2019 to 2026
$10.8MMetabolomic Signatures for Disease Sub-classification and Target Prioritization in AMP-ADU01AG061359 · NIA · DUKE UNIVERSITY · PI KADDURAH-DAOUK, RIMA F, KASTENMULLER, GABI · 2018 to 2022
$10.0MTraining Grant in GastroenterologyT32DK007202 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GHOSH, PRADIPTA · 1985 to 2022
$7.7MMapping host-microbe-metabolite interactions in 3D to find diet-derived enhancers of immunityDP1AT010885 · NCCIH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI KNIGHT, ROB · 2019 to 2023
$5.5MMetabolic Networks and Pathways in Alzheimer's DiseaseR01AG046171 · NIA · DUKE UNIVERSITY · PI KADDURAH-DAOUK, RIMA F · 2014 to 2017
$4.4MEpidemiology of the gut microbiome, prediabetes and diabetes in LatinosR01MD011389 · NIMHD · ALBERT EINSTEIN COLLEGE OF MEDICINE, INC · PI BURK, ROBERT D, KAPLAN, ROBERT C · 2016 to 2020
$4.3MNCATS NIH HHS UL1 TR002535NCCIH NIH HHS DP1 AT010885NCCIH NIH HHS DP2 AT010401NHLBI NIH HHS T32 HL149646NIAMS NIH HHS P50 AR060772NIAMS NIH HHS R21 AR075990NIAMS NIH HHS T32 AR064194NIA NIH HHS R01 AG046171NIA NIH HHS R01 AG061066NIA NIH HHS RF1 AG058942NIA NIH HHS U01 AG024904NIA NIH HHS U01 AG061359NIA NIH HHS U19 AG063744NICHD NIH HHS K12 HD000850NIDDK NIH HHS P30 DK120515NIDDK NIH HHS T32 DK007202NIGMS NIH HHS K12 GM068524NIMHD NIH HHS R01 MD011389
Abstract
Human untargeted metabolomics studies annotate only ~10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS/MS reference library. Applying this approach to food source data, we show that it increases MS/MS spectral usage 5.1-fold over conventional structural MS/MS library matches and allows empirical assessment of dietary patterns from untargeted data.
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MetadataTandem Mass SpectrometryHumansMetabolomics
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