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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, Dorrestein PC. plantMASST - Community-driven chemotaxonomic digitization of plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593988. [PMID: 38798440 PMCID: PMC11118438 DOI: 10.1101/2024.05.13.593988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
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.
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Affiliation(s)
- Paulo Wender P Gomes
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Helena Mannochio-Russo
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Robin Schmid
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Simone Zuffa
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Tito Damiani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Luis-Manuel Quiros-Guerrero
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, 1211 Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, CMU, 1211 Geneva, Switzerland
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Haoqi Nina Zhao
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Heejung Yang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- College of Pharmacy, Kangwon National University, Chuncheon, Republic of Korea
| | - Shipei Xing
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Vincent Charron-Lamoureux
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Desnor N Chigumba
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Brian E Sedio
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
- Smithsonian Tropical Research Institute, Republic of Panama
| | - Jonathan A Myers
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Thomas V Harwood
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, United States
| | - Giselle Tamayo-Castillo
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José 11501-2060, Costa Rica
- Escuela de Química, Universidad de Costa Rica, 2061 San José, Costa Rica
| | - Kyo Bin Kang
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Emmanuel Defossez
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
- Botanical garden of Neuchâtel
| | | | - Milton Nascimento da Silva
- Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil
- Institute of Exact and Natural Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Consuelo Yumiko Yoshioka E Silva
- Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil
- Institute of Health Sciences, Faculty of Pharmacy, Federal University of Pará, Belém 66075-110, Brazil
| | - Sergio Rasmann
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Tom W N Walker
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Gaëtan Glauser
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - José Miguel Chaves-Fallas
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José 11501-2060, Costa Rica
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - Bruno David
- Green Mission Pierre Fabre, Institut de Recherche Pierre Fabre, 3 Avenue Hubert Curien, BP 13562, 31562 Toulouse, France
| | - Hyunwoo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea
| | - Kyu Hyeong Lee
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea
| | - Myeong Ji Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea
| | - Won Jun Choi
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea
| | - Young-Sam Keum
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea
| | | | - Lívia Soman de Medeiros
- Federal University of São Paulo, Diadema, Brazil
- Department of Chemistry, Federal University of São Paulo, Diadema, SP, 09972-270, Brazil
| | | | | | | | - Alice Rhelly V Carvalho
- Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil
- Institute of Health Sciences, Faculty of Pharmacy, Federal University of Pará, Belém 66075-110, Brazil
| | - José Diogo E Reis
- Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil
- Institute of Exact and Natural Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Sônia Pamplona
- Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil
- Institute of Exact and Natural Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Eunah Jeong
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Kyungha Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Geum Jin Kim
- Department of Pharmacology, College of Medicine, Dongguk University, Gyeongju, Gyeongsangbuk-do, Republic of Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, Republic of Korea
| | - Yun-Seo Kil
- College of Pharmacy, Yeungnam University, Gyeongsan, Republic of Korea
- College of Pharmacy and Inje Institute of Pharmaceutical Sciences and Research, Inje University, Gimhae, Gyeongnam 50834, Republic of Korea
| | - Joo-Won Nam
- College of Pharmacy, Yeungnam University, Gyeongsan, Republic of Korea
- Core Research Support Center for Natural Products and Medical Materials, Yeungnam University, Gyeongsan, Republic of Korea
| | - Hyukjae Choi
- College of Pharmacy, Yeungnam University, Gyeongsan, Republic of Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, Republic of Korea
- Core Research Support Center for Natural Products and Medical Materials, Yeungnam University, Gyeongsan, Republic of Korea
| | - Yoo Kyong Han
- College of Pharmacy, Korea University, Sejong, Republic of Korea
| | - Si Young Park
- College of Pharmacy, Korea University, Sejong, Republic of Korea
| | - Ki Yong Lee
- College of Pharmacy, Korea University, Sejong, Republic of Korea
| | - Changling Hu
- Laboratory for Functional Foods and Human Health, Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural and Technical State University, North Carolina Research Campus, Kannapolis, NC, USA
| | - Yilun Dong
- Laboratory for Functional Foods and Human Health, Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural and Technical State University, North Carolina Research Campus, Kannapolis, NC, USA
| | - Shengmin Sang
- Laboratory for Functional Foods and Human Health, Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural and Technical State University, North Carolina Research Campus, Kannapolis, NC, USA
| | - Colin R Morrison
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
- Brackenridge Field Laboratory, University of Texas at Austin, Austin, TX, USA
| | - Ricardo Moreira Borges
- Walter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andrew Magno Teixeira
- Walter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Seo Yoon Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Bum Soo Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Se Yun Jeong
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Adriano Rutz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, 1211 Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, CMU, 1211 Geneva, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Arnaud Gaudry
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, 1211 Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, CMU, 1211 Geneva, Switzerland
| | - Edouard Bruelhart
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Iris F Kappers
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University, Wageningen, The Netherlands
| | - Rumyana Karlova
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University, Wageningen, The Netherlands
| | - Mara Meisenburg
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University, Wageningen, The Netherlands
| | - Roland Berdaguer
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University, Wageningen, The Netherlands
| | - J Sebastián Tello
- Latin America Department, Missouri Botanical Garden, St. Louis, MO, USA
| | - David Henderson
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
- Missouri Botanical Garden, St. Louis, MO, USA
| | - Leslie Cayola
- Herbario Nacional de Bolivia, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - David N Allen
- Department of Biology, Middlebury College, Middlebury, VT, USA
| | | | | | - James A Lutz
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Sean M McMahon
- Smithsonian Environmental Research Center, Edgewater, MD, USA
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Panama City, Panama
| | - Geoffrey G Parker
- Forest Ecology Group, Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - John D Parker
- Forest Ecology Group, Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division and the DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division and the DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Tomáš Pluskal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
- Department of Biochemistry, University of Johannesburg, Johannesburg 2006, South Africa
| | - Jeremy J Carver
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States
| | - Nuno Bandeira
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin S Pullman
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States
| | - Jean-Luc Wolfender
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, 1211 Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, CMU, 1211 Geneva, Switzerland
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Mingxun Wang
- Department of Computer Science, University of California Riverside, Riverside, CA, 92521, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
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