Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment
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Publication Date: | 2021 |
Other Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Article |
Language: | eng |
Source: | Repositório Institucional da UNESP |
Download full: | http://dx.doi.org/10.1038/s41467-021-23953-9 http://hdl.handle.net/11449/221817 |
Summary: | 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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Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environmentMolecular 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.National Institute of General Medical SciencesInstitute of Inorganic and Analytical Chemistry University of MünsterSkaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La JollaScripps Institution of Oceanography University of California San DiegoCMFI Cluster of Excellence Interfaculty Institute of Microbiology and Medicine University of TübingenInstitute of Food Chemistry University of MünsterRIKEN Center for Sustainable Resource ScienceRIKEN Center for Integrative Medical SciencesDepartment of Biotechnology and Life Science Tokyo University of Agriculture and TechnologyInstitute for Biomedicine Eurac Research Affiliated Institute of the University of LübeckChair for Bioinformatics Friedrich-Schiller-UniversityInstitute of Organic Chemistry and Biochemistry Czech Academy of SciencesInstitute of Microbiology Czech Academy of SciencesCollaborative Mass Spectrometry Innovation Center University of California San Diego La JollaInstitute of Biomedical Sciences Universidade de São PauloIRNASUS Universidad Católica de Córdoba CONICET Facultad de Ciencias AgropecuariasSchool of Pharmaceutical Sciences of Ribeirão Preto Universidade de São PauloDepartment of Pharmaceutical Sciences College of Pharmacy Oregon State UniversityUniv. Grenoble Alpes CNRS Grenoble INP CHU Grenoble Alpes TIMC-IMAGDepartment of Psychiatry University of California San DiegoNuBBE Institute of Chemistry São Paulo State University (UNESP)Division of Host-Microbe Systems & Therapeutics Department of Pediatrics University of California San DiegoChiba University-UC San Diego Center for Mucosal Immunology Allergy and Vaccines (CU-UCSD cMAV)NuBBE Institute of Chemistry São Paulo State University (UNESP)National Institute of General Medical Sciences: P41 GM103484National Institute of General Medical Sciences: R01 GM107550National Institute of General Medical Sciences: R03 CA211211University of MünsterLa JollaUniversity of California San DiegoUniversity of TübingenRIKEN Center for Sustainable Resource ScienceRIKEN Center for Integrative Medical SciencesTokyo University of Agriculture and TechnologyAffiliated Institute of the University of LübeckFriedrich-Schiller-UniversityCzech Academy of SciencesUniversidade de São Paulo (USP)Facultad de Ciencias AgropecuariasOregon State UniversityTIMC-IMAGUniversidade Estadual Paulista (UNESP)Allergy and Vaccines (CU-UCSD cMAV)Schmid, RobinPetras, DanielNothias, Louis-FélixWang, MingxunAron, Allegra T.Jagels, AnnikaTsugawa, HiroshiRainer, JohannesGarcia-Aloy, MarDührkop, KaiKorf, AnsgarPluskal, TomášKameník, ZdeněkJarmusch, Alan K.Caraballo-Rodríguez, Andrés MauricioWeldon, Kelly C.Nothias-Esposito, MelissaAksenov, Alexander A.Bauermeister, AnelizeAlbarracin Orio, AndreaGrundmann, Carlismari O.Vargas, FernandoKoester, IrinaGauglitz, Julia M.Gentry, Emily C.Hövelmann, YannickKalinina, Svetlana A.Pendergraft, Matthew A.Panitchpakdi, MorganTehan, RichardLe Gouellec, AudreyAleti, GajenderMannochio Russo, Helena [UNESP]Arndt, BirgitHübner, FlorianHayen, HeikoZhi, HuiRaffatellu, ManuelaPrather, Kimberly A.Aluwihare, Lihini I.Böcker, SebastianMcPhail, Kerry L.Humpf, Hans-UlrichKarst, UweDorrestein, Pieter C.2022-04-28T19:40:47Z2022-04-28T19:40:47Z2021-12-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1038/s41467-021-23953-9Nature Communications, v. 12, n. 1, 2021.2041-1723http://hdl.handle.net/11449/22181710.1038/s41467-021-23953-92-s2.0-85108366538Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengNature Communicationsinfo:eu-repo/semantics/openAccess2022-04-28T19:40:48Zoai:repositorio.unesp.br:11449/221817Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462022-04-28T19:40:48Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment |
title |
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment |
spellingShingle |
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment Schmid, Robin |
title_short |
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment |
title_full |
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment |
title_fullStr |
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment |
title_full_unstemmed |
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment |
title_sort |
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment |
author |
Schmid, Robin |
author_facet |
Schmid, Robin Petras, Daniel Nothias, Louis-Félix Wang, Mingxun Aron, Allegra T. Jagels, Annika Tsugawa, Hiroshi Rainer, Johannes Garcia-Aloy, Mar Dührkop, Kai Korf, Ansgar Pluskal, Tomáš Kameník, Zdeněk Jarmusch, Alan K. Caraballo-Rodríguez, Andrés Mauricio Weldon, Kelly C. Nothias-Esposito, Melissa Aksenov, Alexander A. Bauermeister, Anelize Albarracin Orio, Andrea Grundmann, Carlismari O. Vargas, Fernando Koester, Irina Gauglitz, Julia M. Gentry, Emily C. Hövelmann, Yannick Kalinina, Svetlana A. Pendergraft, Matthew A. Panitchpakdi, Morgan Tehan, Richard Le Gouellec, Audrey Aleti, Gajender Mannochio Russo, Helena [UNESP] Arndt, Birgit Hübner, Florian Hayen, Heiko Zhi, Hui Raffatellu, Manuela Prather, Kimberly A. Aluwihare, Lihini I. Böcker, Sebastian McPhail, Kerry L. Humpf, Hans-Ulrich Karst, Uwe Dorrestein, Pieter C. |
author_role |
author |
author2 |
Petras, Daniel Nothias, Louis-Félix Wang, Mingxun Aron, Allegra T. Jagels, Annika Tsugawa, Hiroshi Rainer, Johannes Garcia-Aloy, Mar Dührkop, Kai Korf, Ansgar Pluskal, Tomáš Kameník, Zdeněk Jarmusch, Alan K. Caraballo-Rodríguez, Andrés Mauricio Weldon, Kelly C. Nothias-Esposito, Melissa Aksenov, Alexander A. Bauermeister, Anelize Albarracin Orio, Andrea Grundmann, Carlismari O. Vargas, Fernando Koester, Irina Gauglitz, Julia M. Gentry, Emily C. Hövelmann, Yannick Kalinina, Svetlana A. Pendergraft, Matthew A. Panitchpakdi, Morgan Tehan, Richard Le Gouellec, Audrey Aleti, Gajender Mannochio Russo, Helena [UNESP] Arndt, Birgit Hübner, Florian Hayen, Heiko Zhi, Hui Raffatellu, Manuela Prather, Kimberly A. Aluwihare, Lihini I. Böcker, Sebastian McPhail, Kerry L. Humpf, Hans-Ulrich Karst, Uwe Dorrestein, Pieter C. |
author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
University of Münster La Jolla University of California San Diego University of Tübingen RIKEN Center for Sustainable Resource Science RIKEN Center for Integrative Medical Sciences Tokyo University of Agriculture and Technology Affiliated Institute of the University of Lübeck Friedrich-Schiller-University Czech Academy of Sciences Universidade de São Paulo (USP) Facultad de Ciencias Agropecuarias Oregon State University TIMC-IMAG Universidade Estadual Paulista (UNESP) Allergy and Vaccines (CU-UCSD cMAV) |
dc.contributor.author.fl_str_mv |
Schmid, Robin Petras, Daniel Nothias, Louis-Félix Wang, Mingxun Aron, Allegra T. Jagels, Annika Tsugawa, Hiroshi Rainer, Johannes Garcia-Aloy, Mar Dührkop, Kai Korf, Ansgar Pluskal, Tomáš Kameník, Zdeněk Jarmusch, Alan K. Caraballo-Rodríguez, Andrés Mauricio Weldon, Kelly C. Nothias-Esposito, Melissa Aksenov, Alexander A. Bauermeister, Anelize Albarracin Orio, Andrea Grundmann, Carlismari O. Vargas, Fernando Koester, Irina Gauglitz, Julia M. Gentry, Emily C. Hövelmann, Yannick Kalinina, Svetlana A. Pendergraft, Matthew A. Panitchpakdi, Morgan Tehan, Richard Le Gouellec, Audrey Aleti, Gajender Mannochio Russo, Helena [UNESP] Arndt, Birgit Hübner, Florian Hayen, Heiko Zhi, Hui Raffatellu, Manuela Prather, Kimberly A. Aluwihare, Lihini I. Böcker, Sebastian McPhail, Kerry L. Humpf, Hans-Ulrich Karst, Uwe Dorrestein, Pieter C. |
description |
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. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-12-01 2022-04-28T19:40:47Z 2022-04-28T19:40:47Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1038/s41467-021-23953-9 Nature Communications, v. 12, n. 1, 2021. 2041-1723 http://hdl.handle.net/11449/221817 10.1038/s41467-021-23953-9 2-s2.0-85108366538 |
url |
http://dx.doi.org/10.1038/s41467-021-23953-9 http://hdl.handle.net/11449/221817 |
identifier_str_mv |
Nature Communications, v. 12, n. 1, 2021. 2041-1723 10.1038/s41467-021-23953-9 2-s2.0-85108366538 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Nature Communications |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
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Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
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