Reproducible molecular networking of untargeted mass spectrometry data using GNPS

Autor: Daniel Petras, Aldo Moreno Ulloa, Cristopher A. Boya P., Fernando Vargas, Randy Mojica-Flores, Alan K. Jarmusch, Kunyang Sun, Marcelino Gutiérrez, Kyo Bin Kang, Richard M. Tehan, Mingxun Wang, Robert A. Keyzers, Alexander A. Aksenov, Justin J. J. van der Hooft, Christine M. Aceves, Fidele Tugizimana, Andrew W. Truman, Martin H. Christian, Angela I. Calderón, Javier Andres Tejeda Mora, Johant Lakey-Beitia, Nicole Tayler, Nicole Sikora, Andrés Mauricio Caraballo-Rodríguez, Kelly C. Weldon, Julia M. Gauglitz, Emily C. Gentry, Pieter C. Dorrestein, Yilue Zhang, Nuno Bandeira, Louis-Félix Nothias, Mélissa Nothias-Esposito, Nombuso Ndlovu, Irina Koester, Samuel Bertrand, Allegra T. Aron, Victor Vásquez-Chaves, Robin Schmid, Kerry L. McPhail, Madeleine Ernst, Catherine Roullier, Amina Bouslimani

Publikováno v: Nature protocols, 15, 1954-1991
Nature protocols 15 (2020)
Nature Protocols
Nature Protocols, Nature Publishing Group, 2020, 15 (6), pp.1954-1991. ⟨10.1038/s41596-020-0317-5⟩
Nature Protocols volume 15, pages1954–1991(2020)
Kérwá
Universidad de Costa Rica
instacron:UCR

Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule–focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5146b3910a36ac060ac30de7833fdc12
https://doi.org/10.1038/s41596-020-0317-5

Multi-omics profiling of Earth’s biomes reveals patterns of diversity and co-occurrence in microbial and metabolite composition across environments

Autor: Rodolfo A. Salido, Ashley Shade, Mads Albertsen, Daniel McDonald, Anupriya Tripathi, Rob Knight, Daniel Petras, Kai Dührkop, Se Jin Song, Cameron Martino, Thomas O. Metz, James T. Morton, Mélissa Nothias-Esposito, A. Gonzalez, Louis-Félix Nothias, Justin P. Shaffer, Promi Das, Alexander A. Aksenov, Karenina Sanders, Torsten Thomas, Hyun-Woo Kim, Jeremiah J. Minich, Vásquez-Baeza Y, Tara Schwartz, Smruthi Karthikeyan, Janet K. Jansson, James C. Stegen, Jeff DeReus, Jack A. Gilbert, Søren Michael Karst, Bryant Mm, Sneha P. Couvillion, Sebastian Böcker, Jon G. Sanders, Gail Ackermann, Franck Lejzerowicz, Pieter C. Dorrestein, Qiyun Zhu, Greg Humphrey, Niina Haiminen, Serina Huang, Anna Paola Carrieri, Luke R. Thompson, Laxmi Parida, Clarisse Marotz, Kristen L. Beck, Asker Daniel Brejnrod, Wout Bittremieux, Austin D. Swafford, Holly L. Lutz

As our understanding of the structure and diversity of the microbial world grows, interpreting its function is of critical interest for understanding and managing the many systems microbes influence. Despite advances in sequencing, lack of standardiz

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::0b557d6325dcfbe12e382bd698224582
https://doi.org/10.1101/2021.06.04.446988

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data

Autor: Ilaria Belluomo, Morgan Panitchpakdi, Aleksandr Smirnov, Mélissa Nothias-Esposito, Alexey V. Melnik, Gaud Dervilly, Rachel J. Dutton, Adolfo Amézquita, Vasilis Vasiliou, Zheng Zhang, Daniel Petras, Carrie D. Nicora, Audrey Poirier, James T. Morton, Ivan Laponogov, George B. Hanna, Sneha P. Couvillion, Biswapriya B. Misra, Robin Schmid, Wout Bittremieux, Raphaël Lugan, Brooke A. Anderson, Yann Guitton, Chris Callewaert, Kenneth L. Jones, Robert A. Quinn, Rob Knight, Larisa N. Kulikova, Itzhak Mizrahi, Erika M. Zink, Mabel Gonzalez, Sophie L. F. Doran, Rachel Gregor, Pauline Le Boulch, Kelem Gashu, Xiuxia Du, Michael M. Meijler, Kirill Veselkov, Chao Song, Elizabeth Humston-Fulmer, Noga Sikron Persi, Justin J. J. van der Hooft, Dennis Veselkov, Monica Guma, Kathleen Dorrestein, Saleh Alseekh, Roxana Coras, Chiara Carazzone, Thomas O. Metz, Aaron Fait, Andrea Georgina Albarracín Orio, Alexander A. Aksenov, Jose U. Scher, Andrea M. Smania, Bruno Le Bizec, Stav Eyal, Dinesh Kumar Barupal, Pieter C. Dorrestein, Alisdair R. Fernie, Reza Mirnezami, S. Prévost, Louis-Félix Nothias, Meagan C. Burnet, Viatcheslav B. Artaev, Mingxun Wang, Katherine N. Maloney, Julia Manasson, Madeleine Ernst, Roman S. Borisov, Amina Bouslimani

Publikováno v: Nat Biotechnol
Nature biotechnology
Aksenov, Alexander A., Laponogov, Ivan, Zhang, Zheng, Doran, Sophie L. F., Belluomo, Ilaria, Veselkov, Dennis, Bittremieux, Wout, Nothias, Louis Felix, Nothias-Esposito, Mélissa, Maloney, Katherine N., Misra, Biswapriya B., Melnik, Alexey V., Smirnov, Aleksandr, Du, Xiuxia, Jones, Kenneth L., Dorrestein, Kathleen, Panitchpakdi, Morgan, Ernst, Madeleine, van der Hooft, Justin J. J., Gonzalez, Mabel, Carazzone, Chiara, Amézquita, Adolfo, Callewaert, Chris, Morton, James T., Quinn, Robert A., Bouslimani, Amina, Orio, Andrea Albarracín, Petras, Daniel, Smania, Andrea M., Couvillion, Sneha P., Burnet, Meagan C., Nicora, Carrie D., Zink, Erika, Metz, Thomas O., Artaev, Viatcheslav, Humston-Fulmer, Elizabeth, Gregor, Rachel, Meijler, Michael M., Mizrahi, Itzhak, Eyal, Stav, Anderson, Brooke, Dutton, Rachel, Lugan, Raphaël, Boulch, Pauline Le, Guitton, Yann, Prevost, Stephanie, Poirier, Audrey, Dervilly, Gaud, Le Bizec, Bruno, Fait, Aaron, Persi, Noga Sikron, Song, Chao, Gashu, Kelem, Coras, Roxana, Guma, Monica, Manasson, Julia, Scher, Jose U., Barupal, Dinesh Kumar, Alseekh, Saleh, Fernie, Alisdair R., Mirnezami, Reza, Vasiliou, Vasilis, Schmid, Robin, Borisov, Roman S., Kulikova, Larisa N., Knight, Rob, Wang, Mingxun, Hanna, George B., Dorrestein, Pieter C. and Veselkov, Kirill (2021) Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data. Nature Biotechnology, 39 (2). ISSN 1087-0156
Nature Biotechnology
Nature Biotechnology, 39(2), 169-173
Nature Biotechnology, Nature Publishing Group, 2021, 39 (2), pp.169-173. ⟨10.1038/s41587-020-0700-3⟩
Nature Biotechnology 39 (2021) 2
Nature biotechnology, vol 39, iss 2

We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography–mass spectrometry (GC–MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e1ff89483759269c68c13571b23db181
http://hdl.handle.net/10044/1/84598

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree

Autor: Julia M. Gauglitz, Louis-Félix Nothias, Yoshiki Vázquez-Baeza, Pieter C. Dorrestein, Anupriya Tripathi, Mingxun Wang, Mélissa Nothias-Esposito, Asker Daniel Brejnrod, Jo Handelsman, Daniel McDonald, Deepa D. Acharya, Marcus Ludwig, Justin J. J. van der Hooft, Sebastian Böcker, Madeleine Ernst, Kai Dührkop, Markus Fleischauer, Qiyun Zhu, Antonio Gonzalez, Rob Knight

Publikováno v: Nat Chem Biol
Nature Chemical Biology, 17, 146-151
Nature chemical biology, vol 17, iss 2
Nature Chemical Biology 17 (2021)

Untargeted mass spectrometry is employed to detect small molecules in complex biospecimens, generating data that are difficult to interpret. We developed Qemistree, a data exploration strategy based on the hierarchical organization of molecular finge

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::27a5887b54d7b60f8c6b3aebad8c81d7
https://pubmed.ncbi.nlm.nih.gov/33199911

Investigation of Premyrsinane and Myrsinane Esters in Euphorbia cupanii and Euphobia pithyusa with MS2LDA and Combinatorial Molecular Network Annotation Propagation

Autor: Pieter Leyssen, Zheng Zhang, Fanny Roussi, Julien Paolini, Marc Litaudon, Mélissa Nothias-Esposito, David Touboul, Pascal Retailleau, Pieter C. Dorrestein, Ricardo Silva, Louis-Félix Nothias

Publikováno v: Journal of Natural Products
Journal of Natural Products, American Chemical Society, 2019, ⟨10.1021/acs.jnatprod.8b00916⟩

The species Euphorbia pithyusa and Euphorbia cupanii are two closely related Mediterranean spurges for which their taxonomic relationships are still being debated. Herein, the diterpene ester content of E. cupanii was investigated using liquid chroma

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d54bc408f49a12fd13f8e90783687de1
https://hal.archives-ouvertes.fr/hal-02159546