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26 results on '"Gomes, Paulo Wender P."'

1. Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data

Author

Pakkir Shah, Abzer K., Walter, Axel, Ottosson, Filip, Russo, Francesco, Navarro-Diaz, Marcelo, Boldt, Judith, Kalinski, Jarmo-Charles J., Kontou, Eftychia Eva, Elofson, James, Polyzois, Alexandros, González-Marín, Carolina, Farrell, Shane, Aggerbeck, Marie R., Pruksatrakul, Thapanee, Chan, Nathan, Wang, Yunshu, Pöchhacker, Magdalena, Brungs, Corinna, Cámara, Beatriz, Caraballo-Rodríguez, Andrés Mauricio, Cumsille, Andres, de Oliveira, Fernanda, Dührkop, Kai, El Abiead, Yasin, Geibel, Christian, Graves, Lana G., Hansen, Martin, Heuckeroth, Steffen, Knoblauch, Simon, Kostenko, Anastasiia, Kuijpers, Mirte C. M., Mildau, Kevin, Papadopoulos Lambidis, Stilianos, Portal Gomes, Paulo Wender, Schramm, Tilman, Steuer-Lodd, Karoline, Stincone, Paolo, Tayyab, Sibgha, Vitale, Giovanni Andrea, Wagner, Berenike C., Xing, Shipei, Yazzie, Marquis T., Zuffa, Simone, de Kruijff, Martinus, Beemelmanns, Christine, Link, Hannes, Mayer, Christoph, van der Hooft, Justin J. J., Damiani, Tito, Pluskal, Tomáš, Dorrestein, Pieter, Stanstrup, Jan, Schmid, Robin, Wang, Mingxun, Aron, Allegra, Ernst, Madeleine, and Petras, Daniel

Published
2025
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2. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data

Author

Zuffa, Simone, Schmid, Robin, Bauermeister, Anelize, P. Gomes, Paulo Wender, Caraballo-Rodriguez, Andres M, El Abiead, Yasin, Aron, Allegra T, Gentry, Emily C, Zemlin, Jasmine, Meehan, Michael J, Avalon, Nicole E, Cichewicz, Robert H, Buzun, Ekaterina, Terrazas, Marvic Carrillo, Hsu, Chia-Yun, Oles, Renee, Ayala, Adriana Vasquez, Zhao, Jiaqi, Chu, Hiutung, Kuijpers, Mirte CM, Jackrel, Sara L, Tugizimana, Fidele, Nephali, Lerato Pertunia, Dubery, Ian A, Madala, Ntakadzeni Edwin, Moreira, Eduarda Antunes, Costa-Lotufo, Leticia Veras, Lopes, Norberto Peporine, Rezende-Teixeira, Paula, Jimenez, Paula C, Rimal, Bipin, Patterson, Andrew D, Traxler, Matthew F, Pessotti, Rita de Cassia, Alvarado-Villalobos, Daniel, Tamayo-Castillo, Giselle, Chaverri, Priscila, Escudero-Leyva, Efrain, Quiros-Guerrero, Luis-Manuel, Bory, Alexandre Jean, Joubert, Juliette, Rutz, Adriano, Wolfender, Jean-Luc, Allard, Pierre-Marie, Sichert, Andreas, Pontrelli, Sammy, Pullman, Benjamin S, Bandeira, Nuno, Gerwick, William H, Gindro, Katia, Massana-Codina, Josep, Wagner, Berenike C, Forchhammer, Karl, Petras, Daniel, Aiosa, Nicole, Garg, Neha, Liebeke, Manuel, Bourceau, Patric, Kang, Kyo Bin, Gadhavi, Henna, de Carvalho, Luiz Pedro Sorio, Silva dos Santos, Mariana, Pérez-Lorente, Alicia Isabel, Molina-Santiago, Carlos, Romero, Diego, Franke, Raimo, Brönstrup, Mark, Vera Ponce de León, Arturo, Pope, Phillip Byron, La Rosa, Sabina Leanti, La Barbera, Giorgia, Roager, Henrik M, Laursen, Martin Frederik, Hammerle, Fabian, Siewert, Bianka, Peintner, Ursula, Licona-Cassani, Cuauhtemoc, Rodriguez-Orduña, Lorena, Rampler, Evelyn, Hildebrand, Felina, Koellensperger, Gunda, Schoeny, Harald, Hohenwallner, Katharina, Panzenboeck, Lisa, Gregor, Rachel, O’Neill, Ellis Charles, Roxborough, Eve Tallulah, Odoi, Jane, Bale, Nicole J, Ding, Su, Sinninghe Damsté, Jaap S, Guan, Xue Li, Cui, Jerry J, Ju, Kou-San, Silva, Denise Brentan, Silva, Fernanda Motta Ribeiro, da Silva, Gilvan Ferreira, Koolen, Hector HF, Grundmann, Carlismari, and Clement, Jason A

Subjects
Microbiology, Biological Sciences, Good Health and Well Being, Humans, Tandem Mass Spectrometry, Metabolomics, Databases, Factual, Medical Microbiology
Abstract

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.

Published
2024

3. NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters

Author

Leão, Tiago F, Wang, Mingxun, da Silva, Ricardo, Gurevich, Alexey, Bauermeister, Anelize, Gomes, Paulo Wender P, Brejnrod, Asker, Glukhov, Evgenia, Aron, Allegra T, Louwen, Joris JR, Kim, Hyun Woo, Reher, Raphael, Fiore, Marli F, van der Hooft, Justin JJ, Gerwick, Lena, Gerwick, William H, Bandeira, Nuno, and Dorrestein, Pieter C

Subjects
Analytical Chemistry, Biological Sciences, Biomedical and Clinical Sciences, Chemical Sciences, Medical Biochemistry and Metabolomics, Biotechnology, Genetics, Bioengineering, biosynthetic gene clusters, genomics, machine learning, mass spectrometry, specialized metabolites
Abstract

Microbial specialized metabolites are an important source of and inspiration for many pharmaceuticals, biotechnological products and play key roles in ecological processes. Untargeted metabolomics using liquid chromatography coupled with tandem mass spectrometry is an efficient technique to access metabolites from fractions and even environmental crude extracts. Nevertheless, metabolomics is limited in predicting structures or bioactivities for cryptic metabolites. Efficiently linking the biosynthetic potential inferred from (meta)genomics to the specialized metabolome would accelerate drug discovery programs by allowing metabolomics to make use of genetic predictions. Here, we present a k-nearest neighbor classifier to systematically connect mass spectrometry fragmentation spectra to their corresponding biosynthetic gene clusters (independent of their chemical class). Our new pattern-based genome mining pipeline links biosynthetic genes to metabolites that they encode for, as detected via mass spectrometry from bacterial cultures or environmental microbiomes. Using paired datasets that include validated genes-mass spectral links from the Paired Omics Data Platform, we demonstrate this approach by automatically linking 18 previously known mass spectra (17 for which the biosynthesis gene clusters can be found at the MIBiG database plus palmyramide A) to their corresponding previously experimentally validated biosynthetic genes (e.g., via nuclear magnetic resonance or genetic engineering). We illustrated a computational example of how to use our Natural Products Mixed Omics (NPOmix) tool for siderophore mining that can be reproduced by the users. We conclude that NPOmix minimizes the need for culturing (it worked well on microbiomes) and facilitates specialized metabolite prioritization based on integrative omics mining.

Published
2022

4. Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics

Author

Bittremieux, Wout, Avalon, Nicole E., Thomas, Sydney P., Kakhkhorov, Sarvar A., Aksenov, Alexander A., Gomes, Paulo Wender P., Aceves, Christine M., Caraballo-Rodríguez, Andrés Mauricio, Gauglitz, Julia M., Gerwick, William H., Huan, Tao, Jarmusch, Alan K., Kaddurah-Daouk, Rima F., Kang, Kyo Bin, Kim, Hyun Woo, Kondić, Todor, Mannochio-Russo, Helena, Meehan, Michael J., Melnik, Alexey V., Nothias, Louis-Felix, O’Donovan, Claire, Panitchpakdi, Morgan, Petras, Daniel, Schmid, Robin, Schymanski, Emma L., van der Hooft, Justin J. J., Weldon, Kelly C., Yang, Heejung, Xing, Shipei, Zemlin, Jasmine, Wang, Mingxun, and Dorrestein, Pieter C.

Published
2023
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6. Microbial Metabolites Annotation by Mass Spectrometry-Based Metabolomics

Author

Gomes, Paulo Wender P., de Tralia Medeiros, Talita Carla, Maimone, Naydja Moralles, Leão, Tiago F., de Moraes, Luiz Alberto Beraldo, Bauermeister, Anelize, Crusio, Wim E., Series Editor, Dong, Haidong, Series Editor, Radeke, Heinfried H., Series Editor, Rezaei, Nima, Series Editor, Steinlein, Ortrud, Series Editor, Xiao, Junjie, Series Editor, and Pacheco Fill, Taícia, editor

Published
2023
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7. Exploring the antiviral potential of justicidin B and four glycosylated lignans from Phyllanthus brasiliensis against Zika virus: A promising pharmacological approach

Author

Ferraz, Ariane Coelho, Gomes, Paulo Wender P., Menegatto, Marília Bueno da Silva, Lima, Rafaela Lameira Souza, Guimarães, Pedro Henrique, Reis, José Diogo Evangelista, Carvalho, Alice Rhelly Veloso, Pamplona, Sônia das Graças Santa Rosa, Muribeca, Abraão de Jesus Barbosa, de Magalhães, José Carlos, Yoshioka e Silva, Consuelo Yumiko, da Silva, Milton Nascimento, and Magalhães, Cintia Lopes de Brito

Published
2024
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9. plantMASST - Community-driven chemotaxonomic digitization of plants

Author

Gomes, Paulo Wender P., primary, Mannochio-Russo, Helena, additional, Schmid, Robin, additional, Zuffa, Simone, additional, Damiani, Tito, additional, Quiros-Guerrero, Luis-Manuel, additional, Caraballo-Rodriguez, Andres Mauricio, additional, Zhao, Haoqi Nina, additional, Yang, Heejung, additional, Xing, Shipei, additional, Charron-Lamoureux, Vincent, additional, Chigumba, Desnor N., additional, Sedio, Brian E., additional, Myers, Jonathan A., additional, Allard, Pierre-Marie, additional, Harwood, Thomas V., additional, Tamayo-Castillo, Giselle, additional, Kang, Kyo Bin, additional, Defossez, Emmanuel, additional, Koolen, Hector H. F., additional, da Silva, Milton Nascimento, additional, e Silva, Consuelo Yumiko Yoshioka, additional, Rasmann, Sergio, additional, Walker, Tom W. N., additional, Glauser, Gaetan, additional, Chaves-Fallas, Jose Miguel, additional, David, Bruno, additional, Kim, Hyunwoo, additional, Lee, Kyu Hyeong, additional, Kim, Myeong Ji, additional, Choi, Won Jun, additional, Keum, Young-Sam, additional, de Lima, Emilly J. S. P., additional, de Medeiros, Livia Soman, additional, Bataglion, Giovana A., additional, Costa, Emmanoel V., additional, da Silva, Felipe M. A., additional, Carvalho, Alice Rhelly V., additional, Reis, Jose Diogo E., additional, Pamplona, Sonia, additional, Jeong, Eunah, additional, Lee, Kyungha, additional, Kim, Geum Jin, additional, Kil, Yun-Seo, additional, Nam, Joo-Won, additional, Choi, Hyukjae, additional, Han, Yoo Kyong, additional, Park, Si Young, additional, Lee, Ki Yong, additional, Hu, Changling, additional, Dong, Yilun, additional, Sang, Shengmin, additional, Morrison, Colin R., additional, Borges, Ricardo Moreira, additional, Teixeira, Andrew Magno, additional, Lee, Seo Yoon, additional, Lee, Bum Soo, additional, Jeong, Se Yun, additional, Kim, Ki Hyun, additional, Rutz, Adriano, additional, Gaudry, Arnaud, additional, Bruelhart, Edouard, additional, Kappers, Iris F., additional, Karlova, Rumyana, additional, Meisenburg, Mara, additional, Berdaguer, Roland, additional, Tello, J. Sebastian, additional, Henderson, David, additional, Cayola, Leslie, additional, Wright, S. Joseph, additional, Allen, David N., additional, Anderson-Teixeira, Kristina J., additional, Baltzer, Jennifer L., additional, Lutz, James A., additional, McMahon, Sean M., additional, Parker, Geoffrey G., additional, Parker, John D., additional, Northen, Trent R., additional, Bowen, Benjamin P., additional, Pluskal, Tomas, additional, van der Hooft, Justin J. J., additional, Carver, Jeremy J., additional, Bandeira, Nuno, additional, Pullman, Benjamin S., additional, Wolfender, Jean-Luc, additional, Kersten, Roland D., additional, Wang, Mingxun, additional, and Dorrestein, Pieter C., additional

Published
2024
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11. Characterization of a tetrameric proanthocyanidin in Stryphnodendron pulcherrimum and an overview on potential health benefits of condensed tannins via interaction with gut microbiota

Author

Gomes, Paulo Wender P., primary, Gomes, Emilli Roberta S., additional, Carvalho, Alice R.V., additional, Mannochio-Russo, Helena, additional, Leão, Tiago F., additional, Reis, José Diogo E., additional, de Sarges, Maria Rosilda V., additional, Mardegan, Horrana A., additional, Pamplona, Sônia das G.S.R., additional, Y. e Silva, Consuelo Yumiko, additional, and da Silva, Milton N., additional

Published
2023
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12. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

Author

Zuffa, Simone, primary, Schmid, Robin, additional, Bauermeister, Anelize, additional, Gomes, Paulo Wender P., additional, Caraballo-Rodriguez, Andres M., additional, Abiead, Yasin El, additional, Aron, Allegra T., additional, Gentry, Emily C., additional, Zemlin, Jasmine, additional, Meehan, Michael J., additional, Avalon, Nicole E., additional, Cichewicz, Robert H., additional, Buzun, Ekaterina, additional, Terrazas, Marvic Carrillo, additional, Hsu, Chia-Yun, additional, Oles, Renee, additional, Ayala, Adriana Vasquez, additional, Zhao, Jiaqi, additional, Chu, Hiutung, additional, Kuijpers, Mirte C. M., additional, Jackrel, Sara L., additional, Tugizimana, Fidele, additional, Nephali, Lerato Pertunia, additional, Dubery, Ian A., additional, Madala, Ntakadzeni Edwin, additional, Moreira, Eduarda Antunes, additional, Costa-Lotufo, Leticia Veras, additional, Lopes, Norberto Peporine, additional, Rezende-Teixeira, Paula, additional, Jimenez, Paula C., additional, Rimal, Bipin, additional, Patterson, Andrew D., additional, Traxler, Matthew F., additional, de Cassia Pessotti, Rita, additional, Alvarado-Villalobos, Daniel, additional, Tamayo-Castillo, Giselle, additional, Chaverri, Priscila, additional, Escudero-Leyva, Efrain, additional, Quiros-Guerrero, Luis-Manuel, additional, Bory, Alexandre Jean, additional, Joubert, Juliette, additional, Rutz, Adriano, additional, Wolfender, Jean-Luc, additional, Allard, Pierre-Marie, additional, Sichert, Andreas, additional, Pontrelli, Sammy, additional, Pullman, Benjamin S, additional, Bandeira, Nuno, additional, Gerwick, William H., additional, Gindro, Katia, additional, Massana-Codina, Josep, additional, Wagner, Berenike C., additional, Forchhammer, Karl, additional, Petras, Daniel, additional, Aiosa, Nicole, additional, Garg, Neha, additional, Liebeke, Manuel, additional, Bourceau, Patric, additional, Kang, Kyo Bin, additional, Gadhavi, Henna, additional, de Carvalho, Luiz Pedro Sorio, additional, dos Santos, Mariana Silva, additional, Pérez-Lorente, Alicia Isabel, additional, Molina-Santiago, Carlos, additional, Romero, Diego, additional, Franke, Raimo, additional, Brönstrup, Mark, additional, de León, Arturo Vera Ponce, additional, Pope, Phillip Byron, additional, La Rosa, Sabina Leanti, additional, Barbera, Giorgia La, additional, Roager, Henrik M., additional, Laursen, Martin Frederik, additional, Hammerle, Fabian, additional, Siewert, Bianka, additional, Peintner, Ursula, additional, Licona-Cassani, Cuauhtemoc, additional, Rodriguez-Orduña, Lorena, additional, Rampler, Evelyn, additional, Hildebrand, Felina, additional, Koellensperger, Gunda, additional, Schoeny, Harald, additional, Hohenwallner, Katharina, additional, Panzenboeck, Lisa, additional, Gregor, Rachel, additional, O’Neill, Ellis Charles, additional, Roxborough, Eve Tallulah, additional, Odoi, Jane, additional, Bale, Nicole J., additional, Ding, Su, additional, Sinninghe Damsté, Jaap S., additional, Guan, Xueli Li, additional, Cui, Jerry J., additional, Ju, Kou-San, additional, Silva, Denise Brentan, additional, Ribeiro Silva, Fernanda Motta, additional, da Silva, Gilvan Ferreira, additional, Koolen, Hector H. F., additional, Grundmann, Carlismari, additional, Clement, Jason A., additional, Mohimani, Hosein, additional, Broders, Kirk, additional, McPhail, Kerry L., additional, Ober-Singleton, Sidnee E., additional, Rath, Christopher M., additional, McDonald, Daniel, additional, Knight, Rob, additional, Wang, Mingxun, additional, and Dorrestein, Pieter C., additional

Published
2023
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13. Untargeted‐based metabolomics analysis and in vitro/in silico antiviral activity of extracts from Phyllanthus brasiliensis (Aubl.) Poir

Author

Carvalho, Alice Rhelly V., primary, Reis, José Diogo E., additional, Gomes, Paulo Wender P., additional, Ferraz, Ariane Coelho, additional, Mardegan, Horrana A., additional, Menegatto, Marília Bueno da Silva, additional, Souza Lima, Rafaela Lameira, additional, de Sarges, Maria Rosilda V., additional, Pamplona, Sônia das G. S. R., additional, Jeunon Gontijo, Karen Sartori, additional, de Magalhães, José Carlos, additional, da Silva, Milton N., additional, Magalhães, Cintia Lopes de Brito, additional, and Silva, Consuelo Yumiko Yoshioka e, additional

Published
2023
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14. Putative Identification of New Phragmaline-Type Limonoids from the Leaves of Swietenia macrophylla King: A Case Study Using Mass Spectrometry-Based Molecular Networking.

Author

Reis, José Diogo E., Gomes, Paulo Wender P., Sá, Paulo R. da C., Pamplona, Sônia das G. S. R., Silva, Consuelo Yumiko Y. e, da Silva, Maria Fátima das G. F., Bishayee, Anupam, and da Silva, Milton Nascimento

Subjects
*LIMONOIDS, *MOLECULAR weights, *MASS spectrometry, *SOCIAL networks, *NATURAL products
Abstract

Swietenia macrophylla King is a plant commonly known as Brazilian mahogany. The wood from its stem is highly prized for its exceptional quality, while its leaves are valued for their high content of phragmalin-type limonoids, a subclass of compounds known for their significant biological activities, including antimalarial, antitumor, antiviral, and anti-inflammatory properties. In this context, twelve isolated limonoids from S. macrophylla leaves were employed as standards in mass spectrometry-based molecular networking to unveil new potential mass spectrometry signatures for phragmalin-type limonoids. Consequently, ultra-performance liquid chromatography coupled with high-resolution mass spectrometry was utilized for data acquisition. Subsequently, the obtained data were analyzed using the Global Natural Products Social Molecular Networking platform based on spectral similarity. In summary, this study identified 24 new putative phragmalin-type limonoids for the first time in S. macrophylla. These compounds may prove valuable in guiding future drug development efforts, leveraging the already established biological activities associated with limonoids. [ABSTRACT FROM AUTHOR]

Published
2023
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15. The Roots of Deguelia nitidula as a Natural Antibacterial Source against Staphylococcus aureus Strains

Author

Nogueira-Lima, Suzana Helena Campelo, primary, Gomes, Paulo Wender P., additional, Navegantes-Lima, Kely C., additional, Reis, José Diogo E., additional, Carvalho, Alice Rhelly Veloso, additional, Pamplona, Sônia das Graças Santa R., additional, Muribeca, Abraão de Jesus B., additional, da Silva, Milton N., additional, Monteiro, Marta C., additional, and e Silva, Consuelo Yumiko Yoshioka, additional

Published
2022
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16. Antibacterial Activity from Momordica charantia L. Leaves and Flavones Enriched Phase

Author

Muribeca, Abraão de Jesus B., primary, Gomes, Paulo Wender P., additional, Paes, Steven Souza, additional, da Costa, Ana Paula Alves, additional, Gomes, Paulo Weslem Portal, additional, Viana, Jéssica de Souza, additional, Reis, José Diogo E., additional, Pamplona, Sônia das Graças Santa R., additional, Silva, Consuelo, additional, Bauermeister, Anelize, additional, Santos, Lourivaldo da Silva, additional, and da Silva, Milton Nascimento, additional

Published
2022
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17. A Universal Language for Finding Mass Spectrometry Data Patterns

Author

Jarmusch, Alan K., primary, Aron, Allegra T., additional, Petras, Daniel, additional, Phelan, Vanessa V., additional, Bittremieux, Wout, additional, Acharya, Deepa D., additional, Ahmed, Mohammed M. A., additional, Bauermeister, Anelize, additional, Bertin, Matthew J., additional, Boudreau, Paul D., additional, Borges, Ricardo M., additional, Bowen, Benjamin P., additional, Brown, Christopher J., additional, Chagas, Fernanda O., additional, Clevenger, Kenneth D., additional, Correia, Mario S. P., additional, Crandall, William J., additional, Crüsemann, Max, additional, Damiani, Tito, additional, Fiehn, Oliver, additional, Garg, Neha, additional, Gerwick, William H, additional, Gilbert, Jeffrey R., additional, Globisch, Daniel, additional, Gomes, Paulo Wender P., additional, Heuckeroth, Steffen, additional, James, C. Andrew, additional, Jarmusch, Scott A., additional, Kakhkhorov, Sarvar A., additional, Kang, Kyo Bin, additional, Kersten, Roland D, additional, Kim, Hyunwoo, additional, Kirk, Riley D., additional, Kohlbacher, Oliver, additional, Kontou, Eftychia E., additional, Liu, Ken, additional, Lizama-Chamu, Itzel, additional, Luu, Gordon T., additional, Knaan, Tal Luzzatto, additional, Marty, Michael T., additional, McAvoy, Andrew C., additional, McCall, Laura-Isobel, additional, Mohamed, Osama G., additional, Nahor, Omri, additional, Niedermeyer, Timo H.J., additional, Northen, Trent R., additional, Overdahl, Kirsten E., additional, Pluskal, Tomáš, additional, Rainer, Johannes, additional, Reher, Raphael, additional, Rodriguez, Elys, additional, Sachsenberg, Timo T., additional, Sanchez, Laura M., additional, Schmid, Robin, additional, Stevens, Cole, additional, Tian, Zhenyu, additional, Tripathi, Ashootosh, additional, Tsugawa, Hiroshi, additional, Nishida, Kozo, additional, Matsuzawa, Yuki, additional, van der Hooft, Justin J.J., additional, Vicini, Andrea, additional, Walter, Axel, additional, Weber, Tilmann, additional, Xiong, Quanbo, additional, Xu, Tao, additional, Zhao, Haoqi Nina, additional, Dorrestein, Pieter C., additional, and Wang, Mingxun, additional

Published
2022
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18. Open Access Repository-Scale Propagated Nearest Neighbor Suspect Spectral Library for Untargeted Metabolomics

Author

Bittremieux, Wout, Avalon, Nicole E., Thomas, Sydney P., Kakhkhorov, Sarvar A., Aksenov, Alexander A., Gomes, Paulo Wender P., Aceves, Christine M., Caraballo Rodríguez, Andrés Mauricio, Gauglitz, Julia M., Gerwick, William H., Jarmusch, Alan K., Kaddurah-Daouk, Rima F., Kang, Kyo Bin, Kim, Hyun Woo, Kondic, Todor, Mannochio-Russo, Helena, Meehan, Michael J., Melnik, Alexey V., Nothias, Louis-Felix, O’Donovan, Claire, Panitchpakdi, Morgan, Petras, Daniel, Schmid, Robin, Schymanski, Emma, van der Hooft, Justin J. J., Weldon, Kelly C., Yang, Heejung, Zemlin, Jasmine, Wang, Mingxun, Dorrestein, Pieter C., Bittremieux, Wout, Avalon, Nicole E., Thomas, Sydney P., Kakhkhorov, Sarvar A., Aksenov, Alexander A., Gomes, Paulo Wender P., Aceves, Christine M., Caraballo Rodríguez, Andrés Mauricio, Gauglitz, Julia M., Gerwick, William H., Jarmusch, Alan K., Kaddurah-Daouk, Rima F., Kang, Kyo Bin, Kim, Hyun Woo, Kondic, Todor, Mannochio-Russo, Helena, Meehan, Michael J., Melnik, Alexey V., Nothias, Louis-Felix, O’Donovan, Claire, Panitchpakdi, Morgan, Petras, Daniel, Schmid, Robin, Schymanski, Emma, van der Hooft, Justin J. J., Weldon, Kelly C., Yang, Heejung, Zemlin, Jasmine, Wang, Mingxun, and Dorrestein, Pieter C.

Abstract

Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of public MS/MS spectra. Annotations were propagated based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer’s brain phenotype. The nearest neighbor suspect spectral library is openly available through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.

Published
2022

19. NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters

Author

Leão, Tiago F., Wang, Mingxun, da Silva, Ricardo, Gurevich, Alexey, Bauermeister, Anelize, Gomes, Paulo Wender P., Brejnrod, Asker, Glukhov, Evgenia, Aron, Allegra T., Louwen, Joris J.R., Kim, Hyun Woo, Reher, Raphael, Fiore, Marli F., van der Hooft, Justin J.J., Gerwick, Lena, Gerwick, William H., Bandeira, Nuno, Dorrestein, Pieter C., Leão, Tiago F., Wang, Mingxun, da Silva, Ricardo, Gurevich, Alexey, Bauermeister, Anelize, Gomes, Paulo Wender P., Brejnrod, Asker, Glukhov, Evgenia, Aron, Allegra T., Louwen, Joris J.R., Kim, Hyun Woo, Reher, Raphael, Fiore, Marli F., van der Hooft, Justin J.J., Gerwick, Lena, Gerwick, William H., Bandeira, Nuno, and Dorrestein, Pieter C.

Abstract

Microbial specialized metabolites are an important source of and inspiration for many pharmaceuticals, biotechnological products and play key roles in ecological processes. Untargeted metabolomics using liquid chromatography coupled with tandem mass spectrometry is an efficient technique to access metabolites from fractions and even environmental crude extracts. Nevertheless, metabolomics is limited in predicting structures or bioactivities for cryptic metabolites. Efficiently linking the biosynthetic potential inferred from (meta)genomics to the specialized metabolome would accelerate drug discovery programs by allowing metabolomics to make use of genetic predictions. Here, we present a k-nearest neighbor classifier to systematically connect mass spectrometry fragmentation spectra to their corresponding biosynthetic gene clusters (independent of their chemical class). Our new pattern-based genome mining pipeline links biosynthetic genes to metabolites that they encode for, as detected via mass spectrometry from bacterial cultures or environmental microbiomes. Using paired datasets that include validated genes-mass spectral links from the Paired Omics Data Platform, we demonstrate this approach by automatically linking 18 previously known mass spectra (17 for which the biosynthesis gene clusters can be found at the MIBiG database plus palmyramide A) to their corresponding previously experimentally validated biosynthetic genes (e.g., via nuclear magnetic resonance or genetic engineering). We illustrated a computational example of how to use our Natural Products Mixed Omics (NPOmix) tool for siderophore mining that can be reproduced by the users. We conclude that NPOmix minimizes the need for culturing (it worked well on microbiomes) and facilitates specialized metabolite prioritization based on integrative omics mining.

Published
2022

22. NPOmix: a machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters

Author

Leão, Tiago F., primary, Wang, Mingxun, additional, da Silva, Ricardo, additional, Gurevich, Alexey, additional, Bauermeister, Anelize, additional, Gomes, Paulo Wender P., additional, Brejnrod, Asker, additional, Glukhov, Evgenia, additional, Aron, Allegra T., additional, Louwen, Joris J. R., additional, Kim, Hyun Woo, additional, Reher, Raphael, additional, Fiore, Marli F., additional, van der Hooft, Justin J.J., additional, Gerwick, Lena, additional, Gerwick, William H., additional, Bandeira, Nuno, additional, and Dorrestein, Pieter C., additional

Published
2021
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23. Chemical Composition, Toxicity, Antinociceptive, and Anti-Inflammatory Activity of Dry Aqueous Extract of Varronia multispicata (Cham.) Borhidi (Cordiaceae) Leaves

Author

Lopes, Klaylton, primary, Oliveira, Juliana, additional, Sousa-Junior, Fabio J. C., additional, Santos, Túlio da F., additional, Andrade, Débora, additional, Andrade, Sara L., additional, Pereira, Washington L., additional, Gomes, Paulo Wender P., additional, Monteiro, Marta C., additional, e Silva, Consuelo Y. Yoshioka, additional, da Silva, Milton Nascimento, additional, Maia, Cristiane F., additional, and Fontes-Júnior, Enéas A., additional

Published
2019
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24. Empirically establishing drug exposure records directly from untargeted metabolomics data.

Author

Zhao HN, Kvitne KE, Brungs C, Mohan S, Charron-Lamoureux V, Bittremieux W, Tang R, Schmid R, Lamichhane S, El Abiead Y, Andalibi MS, Mannochio-Russo H, Ambre M, Avalon NE, Bryant M, Caraballo-Rodríguez AM, Maya MC, Chin L, Ellis RJ, Franklin D, Girod S, Gomes PWP, Hansen L, Heaton R, Iudicello JE, Jarmusch AK, Khatib L, Letendre S, Magyari S, McDonald D, Mohanty I, Cumsille A, Moore DJ, Rajkumar P, Ross DH, Sapre H, Shahneh MRZ, Thomas SP, Tribelhorn C, Tubb HM, Walker C, Wang CX, Xing S, Zemlin J, Zuffa S, Wishart DS, Kaddurah-Daouk R, Wang M, Raffatellu M, Zengler K, Pluskal T, Xu L, Knight R, Tsunoda SM, and Dorrestein PC

Abstract

Despite extensive efforts, extracting information on medication exposure from clinical records remains challenging. To complement this approach, we developed the tandem mass spectrometry (MS/MS) based GNPS Drug Library. This resource integrates MS/MS data for drugs and their metabolites/analogs with controlled vocabularies on exposure sources, pharmacologic classes, therapeutic indications, and mechanisms of action. It enables direct analysis of drug exposure and metabolism from untargeted metabolomics data independent of clinical records. Our library facilitates stratification of individuals in clinical studies based on the empirically detected medications, exemplified by drug-dependent microbiota-derived N -acyl lipid changes in a cohort with human immunodeficiency virus. The GNPS Drug Library holds potential for broader applications in drug discovery and precision medicine.

Published
2024
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25. plantMASST - Community-driven chemotaxonomic digitization of plants.

Author

Gomes PWP, Mannochio-Russo H, Schmid R, Zuffa S, Damiani T, Quiros-Guerrero LM, Caraballo-Rodríguez AM, Zhao HN, Yang H, Xing S, Charron-Lamoureux V, Chigumba DN, Sedio BE, Myers JA, Allard PM, Harwood TV, Tamayo-Castillo G, Kang KB, Defossez E, Koolen HHF, da Silva MN, E Silva CYY, Rasmann S, Walker TWN, Glauser G, Chaves-Fallas JM, David B, Kim H, Lee KH, Kim MJ, Choi WJ, Keum YS, de Lima EJSP, de Medeiros LS, Bataglion GA, Costa EV, da Silva FMA, Carvalho ARV, Reis JDE, Pamplona S, Jeong E, Lee K, Kim GJ, Kil YS, Nam JW, Choi H, Han YK, Park SY, Lee KY, Hu C, Dong Y, Sang S, Morrison CR, Borges RM, Teixeira AM, Lee SY, Lee BS, Jeong SY, Kim KH, Rutz A, Gaudry A, Bruelhart E, Kappers IF, Karlova R, Meisenburg M, Berdaguer R, Tello JS, Henderson D, Cayola L, Wright SJ, Allen DN, Anderson-Teixeira KJ, Baltzer JL, Lutz JA, McMahon SM, Parker GG, Parker JD, Northen TR, Bowen BP, Pluskal T, van der Hooft JJJ, Carver JJ, Bandeira N, Pullman BS, Wolfender JL, Kersten RD, Wang M, and Dorrestein PC

Abstract

Understanding the distribution of hundreds of thousands of plant metabolites across the plant kingdom presents a challenge. To address this, we curated publicly available LC-MS/MS data from 19,075 plant extracts and developed the plantMASST reference database encompassing 246 botanical families, 1,469 genera, and 2,793 species. This taxonomically focused database facilitates the exploration of plant-derived molecules using tandem mass spectrometry (MS/MS) spectra. This tool will aid in drug discovery, biosynthesis, (chemo)taxonomy, and the evolutionary ecology of herbivore interactions.

Published
2024
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26. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data.

Author

Zuffa S, Schmid R, Bauermeister A, Gomes PWP, Caraballo-Rodriguez AM, Abiead YE, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, de Cassia Pessotti R, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Dos Santos MS, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, de León AVP, Pope PB, Rosa SL, Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, and Dorrestein PC

Abstract

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., Competing Interests: Disclosures PCD is an advisor to Cybele, consulted for MSD animal health in 2023, and he is a Co-founder and scientific advisor for Ometa Labs, Arome, and Enveda with prior approval by UC San Diego. MW is a Co-founder of Ometa labs. There are no known conflicts of interest in this work by the USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.

Published
2023
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