microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data

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

doi:10.1038/s41564-023-01575-9

microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data

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

^*Corresponding author af dette arbejde

Ernæring og Sundhed

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

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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.

Originalsprog	Engelsk
Tidsskrift	Nature Microbiology
Vol/bind	9
Udgave nummer	2
Sider (fra-til)	336-345
ISSN	2058-5276
DOI	https://doi.org/10.1038/s41564-023-01575-9
Status	Udgivet - 2024

Bibliografisk note

Funding Information:
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. We thank T. Adkins and L. McCormick from the USDA ARS Culture Collection for assistance in selecting and providing microbial strains used in this research. 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. We thank Shimadzu South Africa Ltd. for analytical support, and J. MacRae, head of The Metabolomics STP at the Francis Crick Institute, for guidance. J.-L.W. is supported by the Swiss National Science Foundation (SNSF) Bridge – Discovery 40B2-0_211759 for studies on fungal metabolomics.

Funding Information:
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. We thank T. Adkins and L. McCormick from the USDA ARS Culture Collection for assistance in selecting and providing microbial strains used in this research. 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. We thank Shimadzu South Africa Ltd. for analytical support, and J. MacRae, head of The Metabolomics STP at the Francis Crick Institute, for guidance. J.-L.W. is supported by the Swiss National Science Foundation (SNSF) Bridge – Discovery 40B2-0_211759 for studies on fungal metabolomics.

Publisher Copyright:
© The Author(s) 2024.

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10.1038/s41564-023-01575-9

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Citationsformater

Zuffa, S., Schmid, R., Bauermeister, A., Paulo, P. W., 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. Y., 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), 336-345. https://doi.org/10.1038/s41564-023-01575-9

Zuffa, S, Schmid, R, Bauermeister, A, Paulo, PW, Caraballo-Rodriguez, AM, El Abiead, Y, 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, Pessotti, RDC, 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, Silva dos Santos, M, Pérez-Lorente, AI, Molina-Santiago, C, Romero, D, Franke, R, Brönstrup, M, Vera Ponce de León, A, Pope, PB, La Rosa, SL, La 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 & Dorrestein, PC 2024, 'microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data', Nature Microbiology, bind 9, nr. 2, s. 336-345. https://doi.org/10.1038/s41564-023-01575-9

@article{afeaf7b021b74317b875ea4ce98e2071,

title = "microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data",

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{\textquoteright} role in ecology and human health.",

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

note = "Publisher Copyright: {\textcopyright} The Author(s) 2024.",

year = "2024",

doi = "10.1038/s41564-023-01575-9",

language = "English",

volume = "9",

pages = "336--345",

journal = "Nature Microbiology",

issn = "2058-5276",

publisher = "nature publishing group",

number = "2",

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TY - JOUR

T1 - microbeMASST

T2 - a taxonomically informed mass spectrometry search tool for microbial metabolomics data

AU - Zuffa, Simone

AU - Schmid, Robin

AU - Bauermeister, Anelize

AU - Paulo, Paulo Wender

AU - Caraballo-Rodriguez, Andres M.

AU - El Abiead, Yasin

AU - Aron, Allegra T.

AU - Gentry, Emily C.

AU - Zemlin, Jasmine

AU - Meehan, Michael J.

AU - Avalon, Nicole E.

AU - Cichewicz, Robert H.

AU - Buzun, Ekaterina

AU - Terrazas, Marvic Carrillo

AU - Hsu, Chia Yun

AU - Oles, Renee

AU - Ayala, Adriana Vasquez

AU - Zhao, Jiaqi

AU - Chu, Hiutung

AU - Kuijpers, Mirte C.M.

AU - Jackrel, Sara L.

AU - Tugizimana, Fidele

AU - Nephali, Lerato Pertunia

AU - Dubery, Ian A.

AU - Madala, Ntakadzeni Edwin

AU - Moreira, Eduarda Antunes

AU - Costa-Lotufo, Leticia Veras

AU - Lopes, Norberto Peporine

AU - Rezende-Teixeira, Paula

AU - Jimenez, Paula C.

AU - Rimal, Bipin

AU - Patterson, Andrew D.

AU - Traxler, Matthew F.

AU - Pessotti, Rita de Cassia

AU - Alvarado-Villalobos, Daniel

AU - Tamayo-Castillo, Giselle

AU - Chaverri, Priscila

AU - Escudero-Leyva, Efrain

AU - Quiros-Guerrero, Luis Manuel

AU - Bory, Alexandre Jean

AU - Joubert, Juliette

AU - Rutz, Adriano

AU - Wolfender, Jean Luc

AU - Allard, Pierre Marie

AU - Sichert, Andreas

AU - Pontrelli, Sammy

AU - Pullman, Benjamin S.

AU - Bandeira, Nuno

AU - Gerwick, William H.

AU - Gindro, Katia

AU - Massana-Codina, Josep

AU - Wagner, Berenike C.

AU - Forchhammer, Karl

AU - Petras, Daniel

AU - Aiosa, Nicole

AU - Garg, Neha

AU - Liebeke, Manuel

AU - Bourceau, Patric

AU - Kang, Kyo Bin

AU - Gadhavi, Henna

AU - de Carvalho, Luiz Pedro Sorio

AU - Silva dos Santos, Mariana

AU - Pérez-Lorente, Alicia Isabel

AU - Molina-Santiago, Carlos

AU - Romero, Diego

AU - Franke, Raimo

AU - Brönstrup, Mark

AU - Vera Ponce de León, Arturo

AU - Pope, Phillip Byron

AU - La Rosa, Sabina Leanti

AU - La Barbera, Giorgia

AU - Roager, Henrik M.

AU - Laursen, Martin Frederik

AU - Hammerle, Fabian

AU - Siewert, Bianka

AU - Peintner, Ursula

AU - Licona-Cassani, Cuauhtemoc

AU - Rodriguez-Orduña, Lorena

AU - Rampler, Evelyn

AU - Hildebrand, Felina

AU - Koellensperger, Gunda

AU - Schoeny, Harald

AU - Hohenwallner, Katharina

AU - Panzenboeck, Lisa

AU - Gregor, Rachel

AU - O’Neill, Ellis Charles

AU - Roxborough, Eve Tallulah

AU - Odoi, Jane

AU - Bale, Nicole J.

AU - Ding, Su

AU - Sinninghe Damsté, Jaap S.

AU - Guan, Xue Li

AU - Cui, Jerry J.

AU - Ju, Kou San

AU - Silva, Denise Brentan

AU - Silva, Fernanda Motta Ribeiro

AU - da Silva, Gilvan Ferreira

AU - Koolen, Hector H.F.

AU - Grundmann, Carlismari

AU - Clement, Jason A.

AU - Mohimani, Hosein

AU - Broders, Kirk

AU - McPhail, Kerry L.

AU - Ober-Singleton, Sidnee E.

AU - Rath, Christopher M.

AU - McDonald, Daniel

AU - Knight, Rob

AU - Wang, Mingxun

AU - Dorrestein, Pieter C.

PY - 2024

Y1 - 2024

N2 - 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.

AB - 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.

U2 - 10.1038/s41564-023-01575-9

DO - 10.1038/s41564-023-01575-9

M3 - Journal article

C2 - 38316926

AN - SCOPUS:85184262772

SN - 2058-5276

VL - 9

SP - 336

EP - 345

JO - Nature Microbiology

JF - Nature Microbiology

IS - 2

ER -