ArticleNature methods2025
A universal language for finding mass spectrometry data patterns.
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Article in Nature methods, 2025. 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 56 papers.
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56citing papers in PubMed
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Who cites it
56 citing papers in PubMed.
- Perinatal ampicillin exposure alters murine maternal fecal bile acid and acylcarnitine profiles.Gut microbes · 2026Article
- Computational metabolomics at scale: from open data to insight.Current opinion in biotechnology · 2026Review
- X-Align: annotation-independent cross-platform alignment of untargeted metabolomics features.Chemical science · 2026Article
- Bacterial-derived cyclic lipopeptides suppress dauer arrest inbioRxiv : the preprint server for biology · 2026Article
- Intra- and inter-biosynthetic gene cluster allelic variation as drivers of chemical diversification in Streptomyces.Essays in biochemistry · 2026Review
- Bridging complexity and accessibility in metabolomics with MetaboApps.Nature methods · 2026Article
- LC-MS/MS Strategy Using Substructure Searching for the Annotation of Cyanopeptide Classes: Implications for New Compound Discovery and Environmental Monitoring.Environmental science & technology · 2026Article
- Large-scale discovery and annotation of substructure patterns in mass spectrometry profiles.Nature communications · 2026Article
- Agentic AI for Structural Elucidation and Discovery of Drug Metabolites from Mass Spectrometry Data.bioRxiv : the preprint server for biology · 2026Article
- A lipidomics roadmap: from basic research to societal challenges.Nature communications · 2026Review
- Glucuronidation metabolomic fingerprinting to map host-microbe metabolism.Nature communications · 2026Article
- Alkamines reveal a hidden layer of steroid and drug metabolism.bioRxiv : the preprint server for biology · 2026Article
- Single-Injection Multi-Omics Analysis by Direct Infusion Mass Spectrometry.Angewandte Chemie (International ed. in English) · 2026Article
- Native Metabolomics Unveils Suomilide Analogs with Potent Trypsin Inhibitory Activity.Journal of natural products · 2026Article
- Serum metabolic signatures of cognitive resilience in a longitudinal aging cohort.bioRxiv : the preprint server for biology · 2026Article
- Antibiotic Exposure Through Human Milk Influences the Infant Gut Microbiome.bioRxiv : the preprint server for biology · 2026Article
- Pan-Metabolomics Repository Mapping of the Carnitine Landscape.bioRxiv : the preprint server for biology · 2026Article
- Review
- Paenitracins, a novel family of bacitracin-type nonribosomal peptide antibiotics produced by plant-associatedmSystems · 2026Article
- Cooperative siderophore use stabilizes a protective leaf microbiome.bioRxiv : the preprint server for biology · 2026Article
Corrections and comments
- Erratum issued
Authors and funding
74 authors.
Tito Damiani *Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.ORCID http://orcid.org/0000-0002-4616-900X
Alan K Jarmusch *Metabolomics Core Facility, Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.ORCID http://orcid.org/0000-0002-2228-6308
Allegra T Aron *Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA.
Daniel Petras *Functional Metabolomics Lab, CMFI Cluster of Excellence, University of Tuebingen, Tuebingen, Germany.
Vanessa V Phelan *Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Haoqi Nina Zhao *Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Wout BittremieuxCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Deepa D AcharyaBiologicals and Natural Products Discovery, Crop Protection R&D, Corteva Agrisciences, Indianapolis, IN, USA.
Mohammed M A AhmedBioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, USA.ORCID http://orcid.org/0000-0002-3339-1242
Anelize BauermeisterDepartment of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.
Matthew J BertinDepartment of Chemistry, Case Western Reserve University, Cleveland, OH, USA.
Paul D BoudreauBioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, USA.
Ricardo M BorgesWalter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
Benjamin P BowenEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, USA.ORCID http://orcid.org/0000-0003-1368-3958
Christopher J BrownMass Spectrometry Center of Expertise, Regulatory and Stewardship, Corteva Agrisciences, Indianapolis, IN, USA.ORCID http://orcid.org/0000-0001-9543-5071
Fernanda O ChagasWalter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
Kenneth D ClevengerBiologicals and Natural Products, Crop Protection R&D, Corteva Agrisciences, Indianapolis, IN, USA.
Mario S P CorreiaDepartment of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
William J CrandallClinical Biomarkers Laboratory, School of Medicine, Emory University, Atlanta, GA, USA.ORCID http://orcid.org/0000-0002-2537-2033
Max CrüsemannInstitute of Pharmaceutical Biology, University of Bonn, Bonn, Germany.
Eoin FahyDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-3196-522X
Oliver FiehnWest Coast Metabolomics Center, University of California Davis, Davis, CA, USA.ORCID http://orcid.org/0000-0002-6261-8928
Neha GargSchool of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.ORCID http://orcid.org/0000-0002-2760-7123
William H GerwickCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Jeffrey R GilbertMass Spectrometry Center of Expertise, Regulatory and Stewardship, Corteva Agrisciences, Indianapolis, IN, USA.
Daniel GlobischDepartment of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.ORCID http://orcid.org/0000-0002-4526-5788
Paulo Wender P GomesFaculty of Chemistry, Institute of Exact and Natural Science, Federal University of Para, Belem, Brazil.
Steffen HeuckerothInstitute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany.ORCID http://orcid.org/0000-0002-4928-2526
C Andrew JamesCenter for Urban Waters, University of Washington, Tacoma, WA, USA.
Scott A JarmuschDepartment of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.ORCID http://orcid.org/0000-0002-1021-1608
Sarvar A KakhkhorovLaboratory of Physical and Chemical Methods of Research, Center for Advanced Technologies, Tashkent, Uzbekistan.ORCID http://orcid.org/0000-0002-4698-8793
Kyo Bin KangCollege of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea.ORCID http://orcid.org/0000-0003-3290-1017
Nikolas KesslerSW R&D Bioinformatics, Life Science Mass Spectrometry, Bruker Daltonics GmbH & Co. KG, Bremen, Germany.
Roland D KerstenDepartment of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA.
Hyunwoo KimCollege of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, Republic of Korea.ORCID http://orcid.org/0000-0003-2473-8360
Riley D KirkCollege of Pharmacy, University of Rhode Island, Kingston, RI, USA.
Oliver KohlbacherApplied Bioinformatics, Department of Computer Science, University of Tuebingen, University of Tuebingen; Institute for Bioinformatics and Medical Informatics, University of Tuebingen; Institute for Translational Bioinformatics, University Hospital Tuebingen, Tübingen, Germany.ORCID http://orcid.org/0000-0003-1739-4598
Eftychia E KontouThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
Ken LiuClinical Biomarkers Laboratory, School of Medicine, Emory University, Atlanta, GA, USA.
Itzel Lizama-ChamuDepartment of Chemistry and Biochemistry, UC Santa Cruz, Santa Cruz, CA, USA.
Gordon T LuuDepartment of Chemistry and Biochemistry, UC Santa Cruz, Santa Cruz, CA, USA.
Tal Luzzatto KnaanDepartment of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.
Helena Mannochio-RussoCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Michael T MartyDepartment of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA.ORCID http://orcid.org/0000-0001-8115-1772
Yuki MatsuzawaDepartment of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Japan.
Andrew C McAvoySchool of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
Laura-Isobel McCallDepartment of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USA.
Osama G MohamedPharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt.ORCID http://orcid.org/0000-0003-3216-6948
Omri NahorDepartment of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.
Heiko NeuwegerSW R&D Bioinformatics, Life Science Mass Spectrometry, Bruker Daltonics GmbH & Co. KG, Bremen, Germany.
Timo H J NiedermeyerInstitute of Pharmacy, Freie Universität Berlin, Berlin, Germany.ORCID http://orcid.org/0000-0003-1779-7899
Kozo NishidaDepartment of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Japan.
Trent R NorthenEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, USA.ORCID http://orcid.org/0000-0001-8404-3259
Kirsten E OverdahlMetabolomics Core Facility, Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
Johannes RainerInstitute for Biomedicine, Eurac Research, Bolzano, Italy.ORCID http://orcid.org/0000-0002-6977-7147
Raphael ReherDepartment of Pharmacy, University of Marburg, Marburg, Germany.ORCID http://orcid.org/0000-0002-5858-1173
Elys RodriguezWest Coast Metabolomics Center, University of California Davis, Davis, CA, USA.
Timo T SachsenbergApplied Bioinformatics, Department of Computer Science, University of Tuebingen, University of Tuebingen, Tübingen, Germany.ORCID http://orcid.org/0000-0002-2833-6070
Laura M SanchezDepartment of Chemistry and Biochemistry, UC Santa Cruz, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0001-9223-7977
Robin SchmidInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.ORCID http://orcid.org/0000-0003-0922-3887
Cole StevensDepartment of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, USA.
Shankar SubramaniamDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Zhenyu TianChemistry and Chemical Biology, Northeastern University, Boston, MA, USA.ORCID http://orcid.org/0000-0002-7491-7028
Ashootosh TripathiDepartment of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA.ORCID http://orcid.org/0000-0003-2297-8088
Hiroshi TsugawaDepartment of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Japan.ORCID http://orcid.org/0000-0002-2015-3958
Justin J J van der HooftBioinformatics Group, Wageningen University & Research, Wageningen, the Netherlands.ORCID http://orcid.org/0000-0002-9340-5511
Andrea ViciniInstitute for Biomedicine, Eurac Research, Bolzano, Italy.
Axel WalterApplied Bioinformatics, Department of Computer Science, University of Tuebingen, University of Tuebingen, Tübingen, Germany.
Tilmann WeberThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.ORCID http://orcid.org/0000-0002-8260-5120
Quanbo XiongCrop Protection R&D, Corteva Agrisciences, Indianapolis, IN, USA.
Tao XuData Science and Bioinformatics, Corteva Agrisciences, Dublin, OH, USA.
Tomáš PluskalInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.ORCID http://orcid.org/0000-0002-6940-3006
Pieter C DorresteinCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-3003-1030
Mingxun WangDepartment of Computer Science, University of California Riverside, Riverside, CA, USA. mingxun.wang@cs.ucr.edu.ORCID http://orcid.org/0000-0001-7647-6097
Funding
National Metabolomics Data Repository - nextgen Metabolomics WorkbenchU2CDK119886 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SUBRAMANIAM, SHANKAR · 2018 to 2021
$12.7MUnified Computation Tools for Natural Products ResearchR01GM107550 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI COTTRELL, GARRISON W, GERWICK, WILLIAM HENRY · 2013 to 2025
$8.2MMetabolomics Workbench - National Metabolomics Data RepositoryU24DK141185 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Shankar Subramaniam · 2024 to 2026
$4.2MCollaborative Microbial Metabolite CenterU24DK133658 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PIETER C DORRESTEIN · 2022 to 2026
$2.9MUC San Diego RAPID Faculty Development Program in Infectious DiseasesR25AI147376 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ADRIANA H TREMOULET, Joann Trejo · 2020 to 2026
$2.5MMALDI-TOF MS/IDBac to discover antibiotics from the Great Lakes sponge microbiomeR01GM125943 · NIGMS · UNIVERSITY OF ILLINOIS AT CHICAGO · PI MURPHY, BRIAN THACHER, SANCHEZ, LAURA MARGARET · 2018 to 2021
$2.1MCharacterizing Natural Product Mediated Microbial InteractionsR35GM128690 · NIGMS · UNIVERSITY OF COLORADO DENVER · PI PHELAN, VANESSA V · 2018 to 2022
$1.9MDiscovery, Biosynthesis and Engineering of Side-Chain-Macrocyclic Plant PeptidesR35GM146934 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Roland David Kersten · 2022 to 2026
$1.8MA reproducible database for untargeted metabolomics data processing across laboratoriesR01GM155383 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI CHARLES ROBERT EVANS, Oliver Fiehn · 2024 to 2026
$1.5MMicrobiota Metallophores: Probing Interactions and Nutrient Dynamics of the Human GutR35GM155026 · NIGMS · UNIVERSITY OF DENVER (COLORADO SEMINARY) · PI Allegra Aron · 2024 to 2026
$1.1MSmall molecule biomarkers of cardiac Chagas disease progressionR21AI156669 · NIAID · UNIVERSITY OF OKLAHOMA · PI BOWMAN, NATALIE MCCARTER, GILMAN, ROBERT H · 2021 to 2022
$458kMyxobacterial predatory antimicrobial production in response to quorum sensing signal interceptionR15AI137996 · NIAID · UNIVERSITY OF MISSISSIPPI · PI STEVENS, DAVID COLE · 2019 to 2019
$422kNIAID NIH HHS R15 AI137996NIAID NIH HHS R21 AI156669NIAID NIH HHS R25 AI147376NIDDK NIH HHS U24 DK133658NIDDK NIH HHS U24 DK141185NIDDK NIH HHS U2C DK119886NIGMS NIH HHS R01 GM107550NIGMS NIH HHS R01 GM125943NIGMS NIH HHS R01 GM155383NIGMS NIH HHS R35 GM128690NIGMS NIH HHS R35 GM146934NIGMS NIH HHS R35 GM155026NIH HHS R03 OD034493
Abstract
Despite being information rich, the vast majority of untargeted mass spectrometry data are underutilized; most analytes are not used for downstream interpretation or reanalysis after publication. The inability to dive into these rich raw mass spectrometry datasets is due to the limited flexibility and scalability of existing software tools. Here we introduce a new language, the Mass Spectrometry Query Language (MassQL), and an accompanying software ecosystem that addresses these issues by enabling the community to directly query mass spectrometry data with an expressive set of user-defined mass spectrometry patterns. Illustrated by real-world examples, MassQL provides a data-driven definition of chemical diversity by enabling the reanalysis of all public untargeted metabolomics data, empowering scientists across many disciplines to make new discoveries. MassQL has been widely implemented in multiple open-source and commercial mass spectrometry analysis tools, which enhances the ability, interoperability and reproducibility of mining of mass spectrometry data for the research community.
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