Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment

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Schmid, Robin ^{[1, 2]} ; Petras, Daniel ^{[1, 3, 4]} ; Nothias, Louis-Felix ^[1] ; Wang, Mingxun ^[1] ; Aron, Allegra T. ^[1] ; Jagels, Annika ^[5] ; Tsugawa, Hiroshi ^{[6, 7, 8]} ; Rainer, Johannes ^[9] ; Garcia-Aloy, Mar ^[9] ; Duhrkop, Kai ^[10] ; Korf, Ansgar ^[2] ; Pluskal, Tomas ^[11] ; Kamenik, Zdenek ^[12] ; Jarmusch, Alan K. ^[1] ; Caraballo-Rodriguez, Andres Mauricio ^[1] ; Weldon, Kelly C. ^[1] ; Nothias-Esposito, Melissa ^[1] ; Aksenov, Alexander A. ^{[1, 13]} ; Bauermeister, Anelize ^{[1, 14]} ; Orio, Andrea Albarracin ^[15] ; Grundmann, Carlismari O. ^{[1, 16]} ; Vargas, Fernando ^[1] ; Koester, Irina ^[3] ; Gauglitz, Julia M. ^[1] ; Gentry, Emily C. ^[1] ; Hovelmann, Yannick ^[5] ; Kalinina, Svetlana A. ^[5] ; Pendergraft, Matthew A. ^[3] ; Panitchpakdi, Morgan ^[1] ; Tehan, Richard ^[17] ; Le Gouellec, Audrey ^[18] ; Aleti, Gajender ^[19] ; Russo, Helena Mannochio ^{[1, 20]} ; Arndt, Birgit ^[5] ; Hubner, Florian ^[5] ; Hayen, Heiko ^[2] ; Zhi, Hui ^[21] ; Raffatellu, Manuela ^{[21, 22]} ; Prather, Kimberly A. ^[3] ; Aluwihare, I, Lihini ; Bocker, Sebastian ^[10] ; McPhail, Kerry L. ^[17] ; Humpf, Hans-Ulrich ^[5] ; Karst, Uwe ^[2] ; Dorrestein, Pieter C. ^{[1, 13]}

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^[1] Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92093 - USA

^[2] Univ Munster, Inst Inorgan & Analyt Chem, Munster - Germany

^[3] I, Univ Calif San Diego, Scripps Inst Oceanog, La Jolla, CA 92093 - USA

^[4] Univ Tubingen, Interfac Inst Microbiol & Med, CMFI Cluster Excellence, Tubingen - Germany

^[5] Univ Munster, Inst Food Chem, Munster - Germany

^[6] RIKEN Ctr Sustainable Resource Sci, Yokohama, Kanagawa - Japan

^[7] RIKEN Ctr Integrat Med Sci, Yokohama, Kanagawa - Japan

^[8] Tokyo Univ Agr & Technol, Dept Biotechnol & Life Sci, Koganei, Tokyo - Japan

^[9] Univ Lubeck, Affiliated Inst, Eurac Res, Inst Biomed, Bolzano - Italy

^[10] Friedrich Schiller Univ, Chair Bioinformat, Jena - Germany

^[11] Czech Acad Sci, Inst Organ Chem & Biochem, Prague - Czech Republic

^[12] Czech Acad Sci, Inst Microbiol, Prague - Czech Republic

^[13] Univ Calif San Diego, Collaborat Mass Spectrometry Innovat Ctr, La Jolla, CA 92093 - USA

^[14] Univ Sao Paulo, Inst Biomed Sci, Sao Paulo, SP - Brazil

^[15] Univ Catolica Cordoba, IRNASUS, Fac Ciencias Agr, Cordoba - Argentina

^[16] Univ Sao Paulo, Sch Pharmaceut Sci Ribeirao Preto, Ribeirao Preto - Brazil

^[17] Oregon State Univ, Coll Pharm, Dept Pharmaceut Sci, Corvallis, OR 97331 - USA

^[18] Univ Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC IMAG, Grenoble - France

^[19] Univ Calif San Diego, Dept Psychiat, San Diego, CA 92103 - USA

^[20] Sao Paulo State Univ UNESP, Inst Chem, NuBBE, Araraquara, SP - Brazil

^[21] Univ Calif San Diego, Dept Pediat, Div Host Microbe Syst & Therapeut, La Jolla, CA 92093 - USA

^[22] Chiba Univ UC San Diego Ctr Mucosal Immunol Aller, La Jolla, CA - USA

• Tipo de documento: Artigo Científico
• Fonte: NATURE COMMUNICATIONS; v. 12, n. 1 JUN 22 2021.
• Citações Web of Science: 0

Resumo

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. Molecular networking connects molecules based on their fragment ion mass spectra (MS2), but may leave adduct species from the same molecular family separate. To address this issue, the authors develop a networking approach that fuses MS1- and MS2-based networks and integrate it into the GNPS environment. (AU)

• Processo FAPESP: 18/24865-4 - Novas abordagens em metabolomica: Cartografia Molecular 3D de ascídias baseado em dados de LC-MS/MS
• Beneficiário: Anelize Bauermeister
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Pós-Doutorado
• Processo FAPESP: 19/06061-8 - Combinando métodos modernos de espectrometria de massa e genome mining para a análise de interações interespécies de microrganismos de colônias de Trachymyrmex
• Beneficiário: Carlismari Oliveira Grundmann
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Mestrado