Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment
Robin SchmidInstitute of Inorganic and Analytical Chemistry, University of Münster, Münster, GermanyDaniel PetrasCMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, Tübingen, GermanyLouis‐Félix NothiasSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USAMingxun WangSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USAAllegra T. AronSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USAAnnika JagelsInstitute of Food Chemistry, University of Münster, Münster, GermanyHiroshi TsugawaDepartment of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, JapanJohannes RainerInstitute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, ItalyMar Garcia‐AloyInstitute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, ItalyKai DührkopChair for Bioinformatics, Friedrich-Schiller-University, Jena, GermanyAnsgar KorfInstitute of Inorganic and Analytical Chemistry, University of Münster, Münster, GermanyTomáš PluskalInstitute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech RepublicZdeněk KameníkInstitute of Microbiology, Czech Academy of Sciences, Prague, Czech RepublicAlan K. JarmuschSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USAAndrés Mauricio Caraballo‐RodríguezSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USAKelly C. WeldonSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USAMélissa Nothias-EspositoSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USAAlexander A. AksenovCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, San Diego, CA, USAAnelize BauermeisterInstitute of Biomedical Sciences, Universidade de São Paulo, São Paulo, SP, BrazilAndrea G. Albarracín OrioIRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, ArgentinaCarlismari O. GrundmannSchool of Pharmaceutical Sciences of Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, BrazilFernando VargasSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USAIrina KoesterScripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USAJulia M. GauglitzSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USAEmily C. GentrySkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USAYannick HövelmannInstitute of Food Chemistry, University of Münster, Münster, GermanySvetlana A. KalininaInstitute of Food Chemistry, University of Münster, Münster, GermanyMatthew A. PendergraftScripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USAMorgan PanitchpakdiSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USARichard M. TehanDepartment of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USAAudrey Le GouëllecUniv. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, FranceGajender AletiDepartment of Psychiatry, University of California San Diego, San Diego, CA, USAHelena Mannochio-RussoNuBBE, Institute of Chemistry, , São Paulo State University (UNESP), Araraquara, SP, BrazilBirgit ArndtInstitute of Food Chemistry, University of Münster, Münster, GermanyFlorian HübnerInstitute of Food Chemistry, University of Münster, Münster, GermanyHeiko HayenInstitute of Inorganic and Analytical Chemistry, University of Münster, Münster, GermanyHui ZhiDivision of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, USAManuela RaffatelluChiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (CU-UCSD cMAV), La Jolla, CA, USAKimberly A. PratherScripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USALihini I. AluwihareScripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USASebastian BöckerChair for Bioinformatics, Friedrich-Schiller-University, Jena, GermanyKerry L. McPhailDepartment of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USAHans‐Ulrich HumpfInstitute of Food Chemistry, University of Münster, Münster, GermanyUwe KärstInstitute of Inorganic and Analytical Chemistry, University of Münster, Münster, GermanyPieter C. DorresteinCollaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, San Diego, CA, USA. [email protected]
2021en
ABI
Аннотация
Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes. To overcome this bottleneck, we develop Ion Identity Molecular Networking (IIMN) that integrates chromatographic peak shape correlation analysis into molecular networks to connect and collapse different ion species of the same molecule. The new feature relationships improve network connectivity for structurally related molecules, can be used to reveal unknown ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral reference libraries. IIMN is integrated into various open source feature finding tools and the GNPS environment. Moreover, IIMN-based spectral libraries with a broad coverage of ion species are publicly available.
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