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 the...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | English |
| Published: |
2024
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/178726 |
| _version_ | 1826110605725007872 |
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| author | Zuffa, Simone Schmid, Robin Bauermeister, Anelize Gomes, Paulo Wender P. 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 C. M. 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 de León, Arturo Vera Ponce 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 H. F. Grundmann, Carlismari Clement, Jason A. Mohimani, Hosein Broders, Kirk McPhail, Kerry L. Ober-Singleton, Sidnee E. Rath, Christopher M. McDonald, Daniel Knight, Rob Wang, Mingxun Dorrestein, Pieter C. |
| author2 | Lee Kong Chian School of Medicine (LKCMedicine) |
| author_facet | Lee Kong Chian School of Medicine (LKCMedicine) Zuffa, Simone Schmid, Robin Bauermeister, Anelize Gomes, Paulo Wender P. 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 C. M. 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 de León, Arturo Vera Ponce 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 H. F. Grundmann, Carlismari Clement, Jason A. Mohimani, Hosein Broders, Kirk McPhail, Kerry L. Ober-Singleton, Sidnee E. Rath, Christopher M. McDonald, Daniel Knight, Rob Wang, Mingxun Dorrestein, Pieter C. |
| author_sort | Zuffa, Simone |
| collection | NTU |
| description | 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. |
| first_indexed | 2024-10-01T02:37:16Z |
| format | Journal Article |
| id | ntu-10356/178726 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T02:37:16Z |
| publishDate | 2024 |
| record_format | dspace |
| spelling | ntu-10356/1787262024-07-07T15:37:50Z microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data Zuffa, Simone Schmid, Robin Bauermeister, Anelize Gomes, Paulo Wender P. 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 C. M. 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 de León, Arturo Vera Ponce 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 H. F. Grundmann, Carlismari Clement, Jason A. Mohimani, Hosein Broders, Kirk McPhail, Kerry L. Ober-Singleton, Sidnee E. Rath, Christopher M. McDonald, Daniel Knight, Rob Wang, Mingxun Dorrestein, Pieter C. Lee Kong Chian School of Medicine (LKCMedicine) Medicine, Health and Life Sciences Mass spectrometry Metabolite 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. Nanyang Technological University Published version This work was carried out through the collaborative microbial metabolite centre, which is supported by the National Institutes of Health (NIH) grant U24DK133658, the Alzheimer’s gut project U19AG063744 and BBSRC-NSF award 2152526. This project was supported in part by the US Department of Agriculture, Agricultural Research Service. A.M.C.-R. and H.M. were supported by NIH grant 1DP2GM137413. Research reported in this publication was supported in part by the National Center for Complementary and Integrative Health of the NIH under award number F32AT011475 to N.E.A. K.B.K. was supported by National Research Foundation of Korea (NRF) grants funded by the Korean Government (MSIT) (NRF-2020R1C1C1004046, 2022R1A5A2021216 and 2022M3H9A2096191). B.S. was supported by the Austrian Science Fund (FWF) P31915 and K.H. was financed by the FWF research group programme (grant FG3). D.P. was supported by the German Research Foundation (DFG) CMFI Cluster of Excellence (EXC 2124) and Collaborative Research Center CellMap (TRR 261). A.B., E.A.M., P.C.J., L.V.C.-L. and N.P.L. were supported by The São Paulo Research Foundation (FAPESP #2018/24865-4, #2019/03008-9, #2020/06430-0, #2022/12654-4, #2015/17177-6, #2020/02207-5, #2021/10603-0) and CNPq. C.L.-C. received financial support from StrainBiotech and the FEMSA Biotechnology Center from Tecnológico de Monterrey. L.R.-O. received a scholarship from the Mexican National Council of Science and Technology (CONACYT). W.H.G. was supported by NIH R01 GM107550. N.G. was supported by the NSF CAREER Award #2047235. N.J.B., S.D. and J.S.S.D. were supported by ERC Horizon 2020 (grant agreement no. 694569) and by a Spinoza award (to J.S.S.D. from NWO). B.C.W. was supported by CMFI Cluster of Excellence (EXC 2124). M.B. was supported by DZIF (Grant no. TTU 09.722). A.V.P.d.L., S.L.L.R. and P.B.P. were supported by ERA-Net Cofund project BlueBio (grant agreement no. 311913), Research Council of Norway (300846). H.M.R., M.F.L. and G.L.B. were supported by Novo Nordisk Foundation (grant NNF19OC0056246; PRIMA—toward Personalized dietary Recommendations based on the Interaction between diet, Microbiome and Abiotic conditions in the gut). H.M.R. was supported by the Independent Research Fund Denmark (MOTILITY; grant no. 0171-00006B). E.C.O.N. was supported by a Nottingham Research Fellowship. A.I.P.-L. was supported by FPU (FPU19/00289). M.F.T. and R.d.C.P. were supported by R35GM12889. C.M.-S. was supported by Juan de la Cierva-Incorporación (IJC2018-036923-I) and Proyectos dirigidos por jóvenes investigadores de la Universidad de Málaga (B1-2021_21). D.R. was supported by Plan Nacional de I+D+i of the Ministerio de Ciencia e Innovación (PID2019-107724GB-I00) and Junta de Andalucía (P20_00479). X.L.G. was supported by a Nanyang Assistant Professorship. K.-S.J. was supported by NIH R01 GM137135. A.S. was supported by EMBO fellowship ALTF 996-2021. S.P. was supported by ETH Zurich Career Seed Fellowship. R.G. was supported by the Simons Foundation Postdoctoral Fellowship in Marine Microbial Ecology. H.C. was supported by NIH R01AI167860 and CIFAR. M.C.T. was supported by T32 DK007202 (NIDDK), the National Academies of Sciences, Engineering and Medicine through the Predoctoral Fellowship of the Ford Foundation, and the Howard Hughes Medical Institute (HHMI) Graduate Fellowships grant GT15123. E.E.-L. was supported by VI-Universidad de Costa Rica, Grants numbers C1604 and C0469. P.C. was supported by VI-Universidad de Costa Rica, Grants numbers C1604 and C0469; US National Science Foundation DEB-1638976. D.A.-V. and G.T.-C. were supported by VI-Universidad de Costa Rica, Grants numbers C1604 and C0469. K.F. was supported by CMFI Cluster of Excellence (EXC 2124). H.H.F.K. and G.F.d.S. were supported by Fundação de Amparo à Pesquisa do Estado do Amazonas (FAPEAM). D.B.S. was supported by Fundação de Apoio ao Desenvolvimento do Ensino, Ciência e Tecnologia do Estado de Mato Grosso do Sul - FUNDECT (process number: 71/032.390/2022, FUNDECT number: 311/2022). K.L.M. was supported by NIH/1R01GM132649. P.-M.A. was supported by a swissuniversities Open Research Data grant. M.C.M.K. and S.L.J. were supported by NIH R35GM142938. A.D.P. was supported by NIH U01 DK119702 and S10 OD021750. A.T.A. was supported by the Betty and Gordon Moore Foundation. M.L. and P.B. were supported by the Max Planck Society. Omnia Group Ltd. is duly acknowledged for microbial cultures. B.S.P. and N.B. were partially supported by NIH 1R01LM013115 and NSF ABI 1759980. R.K. was supported by NIH DP1AT010885. L.P.N. was supported by Omnia Group Ltd. J.-L.W. is supported by the Swiss National Science Foundation (SNSF) Bridge – Discovery 40B2-0_211759 for studies on fungal metabolomics. 2024-07-03T07:28:40Z 2024-07-03T07:28:40Z 2024 Journal Article Zuffa, S., Schmid, R., Bauermeister, A., Gomes, P. W. P., Caraballo-Rodriguez, A. M., El Abiead, Y., Aron, A. T., Gentry, E. C., Zemlin, J., Meehan, M. J., Avalon, N. E., Cichewicz, R. H., Buzun, E., Terrazas, M. C., Hsu, C., Oles, R., Ayala, A. V., Zhao, J., Chu, H., ...Dorrestein, P. C. (2024). microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nature Microbiology, 9(2), 336-. https://dx.doi.org/10.1038/s41564-023-01575-9 2058-5276 https://hdl.handle.net/10356/178726 10.1038/s41564-023-01575-9 38316926 2-s2.0-85184262772 2 9 336 en NAP Nature Microbiology © 2024 The Author(s). Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons. org/licenses/by/4.0/. application/pdf |
| spellingShingle | Medicine, Health and Life Sciences Mass spectrometry Metabolite Zuffa, Simone Schmid, Robin Bauermeister, Anelize Gomes, Paulo Wender P. 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 C. M. 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 de León, Arturo Vera Ponce 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 H. F. Grundmann, Carlismari Clement, Jason A. Mohimani, Hosein Broders, Kirk McPhail, Kerry L. Ober-Singleton, Sidnee E. Rath, Christopher M. McDonald, Daniel Knight, Rob Wang, Mingxun Dorrestein, Pieter C. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data |
| title | microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data |
| title_full | microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data |
| title_fullStr | microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data |
| title_full_unstemmed | microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data |
| title_short | microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data |
| title_sort | microbemasst a taxonomically informed mass spectrometry search tool for microbial metabolomics data |
| topic | Medicine, Health and Life Sciences Mass spectrometry Metabolite |
| url | https://hdl.handle.net/10356/178726 |
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