A universal language for finding mass spectrometry data patterns
Tito DamianiInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech RepublicAlan K. JarmuschMetabolomics 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, USAAllegra T. AronDepartment of Chemistry and Biochemistry, University of Denver, Denver, CO, USADaniel PetrasDepartment of Biochemistry, University of California Riverside, Riverside, CA, USAVanessa V. PhelanDepartment of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USAHaoqi Nina ZhaoCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USAWout BittremieuxCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USADeepa AcharyaBiologicals and Natural Products Discovery, Crop Protection R&D, Corteva Agrisciences, Indianapolis, IN, USAMohammed M. A. AhmedBioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, USAAnelize BauermeisterDepartment of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, BrazilMatthew J. BertinDepartment of Chemistry, Case Western Reserve University, Cleveland, OH, USAPaul D. BoudreauBioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, USARicardo M. BorgesWalter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro, BrazilBenjamin P. BowenEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, USAChristopher J. BrownMass Spectrometry Center of Expertise, Regulatory and Stewardship, Corteva Agrisciences, Indianapolis, IN, USAFernanda O. ChagasWalter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro, BrazilKenneth D. ClevengerBiologicals and Natural Products, Crop Protection R&D, Corteva Agrisciences, Indianapolis, IN, USAMário S. P. CorreiaDepartment of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, SwedenWilliam J. CrandallClinical Biomarkers Laboratory, School of Medicine, Emory University, Atlanta, GA, USAMax CrüsemannInstitute of Pharmaceutical Biology, Goethe University Frankfurt, Frankfurt, GermanyEoin FahyDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USAOliver FiehnWest Coast Metabolomics Center, University of California Davis, Davis, CA, USANeha GargSchool of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USAWilliam H. GerwickCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USAJeffrey R. GilbertMass Spectrometry Center of Expertise, Regulatory and Stewardship, Corteva Agrisciences, Indianapolis, IN, USADaniel GlobischDepartment of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, SwedenPaulo Wender Portal GomesFaculty of Chemistry, Institute of Exact and Natural Science, Federal University of Para, Belem, BrazilSteffen HeuckerothInstitute of Inorganic and Analytical Chemistry, University of Münster, Münster, GermanyC. Andrew JamesCenter for Urban Waters, University of Washington, Tacoma, WA, USAScott A. JarmuschDepartment of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, DenmarkSarvar A. KakhkhorovLaboratory of Physical and Chemical Methods of Research, Center for Advanced Technologies, Tashkent, UzbekistanKyo Bin KangCollege of Pharmacy, Sookmyung Women's University, Seoul, Republic of KoreaNikolas KesslerSW R&D Bioinformatics, Life Science Mass Spectrometry, Bruker Daltonics GmbH & Co. KG, Bremen, GermanyRoland D. KerstenDepartment of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USAHyun Woo KimCollege of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, Republic of KoreaRiley D. KirkCollege of Pharmacy, University of Rhode Island, Kingston, RI, USAOliver 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, GermanyEftychia Eva KontouThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, DenmarkKen LiuClinical Biomarkers Laboratory, School of Medicine, Emory University, Atlanta, GA, USAItzel Lizama-ChamuDepartment of Chemistry and Biochemistry, UC Santa Cruz, Santa Cruz, CA, USAGordon T. LuuDepartment of Chemistry and Biochemistry, UC Santa Cruz, Santa Cruz, CA, USATal Luzzatto‐KnaanDepartment of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, IsraelHelena Mannochio-RussoCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USAMichael T. MartyDepartment of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USAYuki MatsuzawaDepartment of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, JapanAndrew C. McAvoySchool of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USALaura‐Isobel McCallDepartment of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USAOsama G. MohamedNatural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USAOmri NahorDepartment of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, IsraelHeiko NeuwegerSW R&D Bioinformatics, Life Science Mass Spectrometry, Bruker Daltonics GmbH & Co. KG, Bremen, GermanyTimo H. J. NiedermeyerInstitute of Pharmacy, Freie Universität Berlin, Berlin, GermanyKozo NishidaDepartment of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, JapanTrent R. NorthenEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, USAKirsten 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, USAJohannes RainerInstitute for Biomedicine, Eurac Research, Bolzano, ItalyRaphael ReherDepartment of Pharmacy, University of Marburg, Marburg, GermanyElys P. RodríguezWest Coast Metabolomics Center, University of California Davis, Davis, CA, USATimo SachsenbergApplied Bioinformatics, Department of Computer Science, University of Tuebingen, University of Tuebingen, Tübingen, GermanyLaura M. SanchezDepartment of Chemistry and Biochemistry, UC Santa Cruz, Santa Cruz, CA, USARobin SchmidCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USACole StevensDepartment of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, USAShankar SubramaniamDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USAZhenyu TianChemistry and Chemical Biology, Northeastern University, Boston, MA, USAAshootosh TripathiDepartment of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USAHiroshi TsugawaDepartment of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, JapanJustin J. J. van der HooftBioinformatics Group, Wageningen University & Research, Wageningen, the NetherlandsAndrea ViciniInstitute for Biomedicine, Eurac Research, Bolzano, ItalyAxel WalterApplied Bioinformatics, Department of Computer Science, University of Tuebingen, University of Tuebingen, Tübingen, GermanyTilmann WeberThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, DenmarkQuanbo XiongCrop Protection R&D, Corteva Agrisciences, Indianapolis, IN, USATao XuData Science and Bioinformatics, Corteva Agrisciences, Dublin, OH, USATomáš PluskalInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech RepublicPieter C. DorresteinCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USAMingxun WangDepartment of Computer Science, University of California Riverside, Riverside, CA, USA. [email protected]
ABI
Annotatsiya
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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