microbeMASST: A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms’ role in ecology and human health

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms’ role in ecology and human health

Ion Identity Molecular Networking in the GNPS Environment

Molecular networking connects tandem 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. To connect ion species of the same molecule, we developed Ion Identity Molecular Networking. These new relationships improve network connectivity, are shown to reveal novel ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral libraries.Fil: Schmid, Robin. University Of Munster; AlemaniaFil: Petras, Daniel. University Of California At San Diego. Skaggs School Of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center.; Estados UnidosFil: Nothias, Louis Félix. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Wang, Mingxun. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Aron, Allegra T.. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Jagels, Annika. University of Munster; AlemaniaFil: Tsugawa, Hiroshi. RIKEN Center for Sustainable Resource Science; JapónFil: Rainer, Johannes. University of Lübeck; ItaliaFil: Garcia-Aloy, Mar. University of Lübeck; ItaliaFil: Dührkop, Kai. Universitat Jena; AlemaniaFil: Korf, Ansgar. University of Munster; AlemaniaFil: Pluskal, Tomáš. Czech Academy of Sciences; República ChecaFil: Kameník, Zdeněk. Czech Academy of Sciences; República ChecaFil: Jarmusch, Alan K.. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Caraballo Rodríguez, Andrés Mauricio. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Weldon, Kelly. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Nothias Esposito, Melissa. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Aksenov, Alexander A.. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Bauermeister, Anelize. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Albarracín Orio, Andrea Georgina. Universidad Católica de Córdoba. Instituto de Investigaciones en Recursos Naturales y Sustentabilidad José Sanchez Labrador S. J. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Recursos Naturales y Sustentabilidad José Sanchez Labrador S. J.; ArgentinaFil: Grundmann, Carlismari O.. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Vargas, Fernando. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Koester, Irina. University of California at San Diego; Estados UnidosFil: Gauglitz, Julia M.. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Gentry, Emily C.. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Hövelmann, Yannick. University of Munster; AlemaniaFil: Kalinina, Svetlana A.. University of Munster; AlemaniaFil: Pendergraft, Matthew A.. University of California at San Diego; Estados UnidosFil: Panitchpakdi, Morgan W.. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Tehan, Richard. Oregon State University; Estados UnidosFil: Le Gouellec, Audrey. Universite Grenoble Alpes; Francia. Centre National de la Recherche Scientifique; FranciaFil: Aleti, Gajender. University of California at San Diego; Estados UnidosFil: Mannochio Russo, Helena. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados UnidosFil: Arndt, Birgit. University of Munster; AlemaniaFil: Hübner, Florian. University of Munster; AlemaniaFil: Hayen, Heiko. University of Munster; AlemaniaFil: Zhi, Hui. University of California at San Diego; Estados UnidosFil: Raffatellu, Manuela. University of California at San Diego; Estados UnidosFil: Prather, Kimberly A.. University of California at San Diego; Estados UnidosFil: Aluwihare, Lihini I.. University of California at San Diego; Estados UnidosFil: Böcker, Sebastian. Friedrich-Schiller-University, Jena; AlemaniaFil: McPhail, Kerry L.. State University of Oregon; Estados UnidosFil: Humpf, Hans-Ulrich. University of Munster; AlemaniaFil: Karst, Uwe. University of Munster; FranciaFil: Dorrestein, Pieter. University of California at San Diego. Skaggs School of Pharmacy & Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unido

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

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