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. 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^*

^*Corresponding author for this work

University of California at San Diego
University of Denver
Virginia Polytechnic Institute and State University
University of Oklahoma
University of Johannesburg
University of Venda
Universidade Federal de São Paulo
Pennsylvania State University
University of California at Berkeley
University of Costa Rica
University of Geneva
Agroscope
University of Tübingen
Georgia Institute of Technology
Max Planck Institute for Marine Microbiology
Sookmyung Women's University
The Francis Crick Institute
CSIC - Institute of Subtropical and Mediterranean Horticulture
Helmholtz Centre for Infection Research
Norwegian University of Life Sciences
University of Copenhagen
University of Innsbruck
Instituto Tecnologico de Estudios Superiores de Monterrey
University of Vienna
University of Nottingham
Royal Netherlands Institute for Sea Research - NIOZ
Ohio State University
Universidade Federal de Mato Grosso do Sul
Empresa Brasileira de Pesquisa Agropecuária
Universidade do Estado do Amazonas
Hepatitis B Foundation
Carnegie Mellon University
United States Department of Agriculture
Oregon State University
University of Oregon
University of California at Riverside
Nanyang Technological University
Massachusetts Institute of Technology
Universidade de São Paulo
Swiss Federal Institute of Technology Zurich

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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.

Original language	English
Journal	Nature Microbiology
Volume	9
Pages (from-to)	336-345
Number of pages	13
ISSN	2058-5276
DOIs	https://doi.org/10.1038/s41564-023-01575-9
Publication status	Published - 2024

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SDG 3 Good Health and Well-being

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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, 336-345. https://doi.org/10.1038/s41564-023-01575-9

@article{71b90b22dfc94882940b73337ef525ae,

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 Jean-Luc Wolfender and Pierre-Marie Allard 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} 2024, The Author(s).",

year = "2024",

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

language = "English",

volume = "9",

pages = "336--345",

journal = "Nature Microbiology",

issn = "2058-5276",

publisher = "Nature Research",

}

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, J-L, Allard, P-M, 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, vol. 9, pp. 336-345. https://doi.org/10.1038/s41564-023-01575-9

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 - Letter

C2 - 38316926

AN - SCOPUS:85184262772

SN - 2058-5276

VL - 9

SP - 336

EP - 345

JO - Nature Microbiology

JF - Nature Microbiology

ER -

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

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