The microbiologist's guide to metaproteomics
Abstract Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active...
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| Format: | Article |
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Wiley
2025-06-01
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| Online Access: | https://doi.org/10.1002/imt2.70031 |
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| author | Tim Van Den Bossche Jean Armengaud Dirk Benndorf Jose Alfredo Blakeley‐Ruiz Madita Brauer Kai Cheng Marybeth Creskey Daniel Figeys Lucia Grenga Timothy J. Griffin Céline Henry Robert L. Hettich Tanja Holstein Pratik D. Jagtap Nico Jehmlich Jonghyun Kim Manuel Kleiner Benoit J. Kunath Xuxa Malliet Lennart Martens Subina Mehta Bart Mesuere Zhibin Ning Alessandro Tanca Sergio Uzzau Pieter Verschaffelt Jing Wang Paul Wilmes Xu Zhang Xin Zhang Leyuan Li The Metaproteomics Initiative |
| author_facet | Tim Van Den Bossche Jean Armengaud Dirk Benndorf Jose Alfredo Blakeley‐Ruiz Madita Brauer Kai Cheng Marybeth Creskey Daniel Figeys Lucia Grenga Timothy J. Griffin Céline Henry Robert L. Hettich Tanja Holstein Pratik D. Jagtap Nico Jehmlich Jonghyun Kim Manuel Kleiner Benoit J. Kunath Xuxa Malliet Lennart Martens Subina Mehta Bart Mesuere Zhibin Ning Alessandro Tanca Sergio Uzzau Pieter Verschaffelt Jing Wang Paul Wilmes Xu Zhang Xin Zhang Leyuan Li The Metaproteomics Initiative |
| author_sort | Tim Van Den Bossche |
| collection | DOAJ |
| description | Abstract Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state‐of‐the‐art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches. |
| format | Article |
| id | doaj-art-55003dfd9c85466f9681d02b7f2bc176 |
| institution | OA Journals |
| issn | 2770-596X |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Wiley |
| record_format | Article |
| series | iMeta |
| spelling | doaj-art-55003dfd9c85466f9681d02b7f2bc1762025-08-20T02:24:23ZengWileyiMeta2770-596X2025-06-0143n/an/a10.1002/imt2.70031The microbiologist's guide to metaproteomicsTim Van Den Bossche0Jean Armengaud1Dirk Benndorf2Jose Alfredo Blakeley‐Ruiz3Madita Brauer4Kai Cheng5Marybeth Creskey6Daniel Figeys7Lucia Grenga8Timothy J. Griffin9Céline Henry10Robert L. Hettich11Tanja Holstein12Pratik D. Jagtap13Nico Jehmlich14Jonghyun Kim15Manuel Kleiner16Benoit J. Kunath17Xuxa Malliet18Lennart Martens19Subina Mehta20Bart Mesuere21Zhibin Ning22Alessandro Tanca23Sergio Uzzau24Pieter Verschaffelt25Jing Wang26Paul Wilmes27Xu Zhang28Xin Zhang29Leyuan Li30The Metaproteomics InitiativeDepartment of Biomolecular Medicine, Faculty of Medicine and Health Sciences Ghent University Ghent BelgiumDépartement Médicaments Et Technologies Pour La Santé (DMTS) Université Paris‐Saclay, CEA, INRAE, SPI, Bagnols‐Sur‐Cèze FranceApplied Biosciences and Process Engineering Anhalt University of Applied Sciences Köthen GermanyDepartment of Plant and Microbial Biology North Carolina State University Raleigh North Carolina USAMolecular Disease Mechanisms Group, Department of Life Sciences and Medicine University of Luxembourg Esch‐sur‐Alzette LuxembourgSchool of Pharmaceutical Sciences, Faculty of Medicine University of Ottawa Ottawa Ontario CanadaBiologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch Health Canada Ottawa Ontario CanadaSchool of Pharmaceutical Sciences, Faculty of Medicine University of Ottawa Ottawa Ontario CanadaDépartement Médicaments Et Technologies Pour La Santé (DMTS) Université Paris‐Saclay, CEA, INRAE, SPI, Bagnols‐Sur‐Cèze FranceDepartment of Biochemistry, Molecular Biology, and Biophysics University of Minnesota, Minneapolis Minnesota USAUniversité Paris‐Saclay, INRAE, AgroParisTech, Micalis Institute PAPPSO Jouy‐en‐Josas FranceBiosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USADepartment of Biomolecular Medicine, Faculty of Medicine and Health Sciences Ghent University Ghent BelgiumDepartment of Biochemistry, Molecular Biology, and Biophysics University of Minnesota, Minneapolis Minnesota USADepartment of Molecular Toxicology Helmholtz‐Centre for Environmental Research ‐ UFZ GmbH Leipzig GermanyBiosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USADepartment of Plant and Microbial Biology North Carolina State University Raleigh North Carolina USADepartment of Plant and Microbial Biology North Carolina State University Raleigh North Carolina USADepartment of Biomolecular Medicine, Faculty of Medicine and Health Sciences Ghent University Ghent BelgiumDepartment of Biomolecular Medicine, Faculty of Medicine and Health Sciences Ghent University Ghent BelgiumDepartment of Biochemistry, Molecular Biology, and Biophysics University of Minnesota, Minneapolis Minnesota USADepartment of Mathematics, Statistics and Computer Science, Faculty of Sciences Ghent University Ghent BelgiumSchool of Pharmaceutical Sciences, Faculty of Medicine University of Ottawa Ottawa Ontario CanadaDepartment of Biomedical Sciences University of Sassari Sassari ItalyDepartment of Biomedical Sciences University of Sassari Sassari ItalyDepartment of Biomolecular Medicine, Faculty of Medicine and Health Sciences Ghent University Ghent BelgiumState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics Beijing ChinaLuxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette LuxembourgBiologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch Health Canada Ottawa Ontario CanadaState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics Beijing ChinaState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) Beijing Institute of Lifeomics Beijing ChinaAbstract Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state‐of‐the‐art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.https://doi.org/10.1002/imt2.70031bioinformaticsfunctional dynamicsmass spectrometrymetaproteomicsmicrobiome |
| spellingShingle | Tim Van Den Bossche Jean Armengaud Dirk Benndorf Jose Alfredo Blakeley‐Ruiz Madita Brauer Kai Cheng Marybeth Creskey Daniel Figeys Lucia Grenga Timothy J. Griffin Céline Henry Robert L. Hettich Tanja Holstein Pratik D. Jagtap Nico Jehmlich Jonghyun Kim Manuel Kleiner Benoit J. Kunath Xuxa Malliet Lennart Martens Subina Mehta Bart Mesuere Zhibin Ning Alessandro Tanca Sergio Uzzau Pieter Verschaffelt Jing Wang Paul Wilmes Xu Zhang Xin Zhang Leyuan Li The Metaproteomics Initiative The microbiologist's guide to metaproteomics iMeta bioinformatics functional dynamics mass spectrometry metaproteomics microbiome |
| title | The microbiologist's guide to metaproteomics |
| title_full | The microbiologist's guide to metaproteomics |
| title_fullStr | The microbiologist's guide to metaproteomics |
| title_full_unstemmed | The microbiologist's guide to metaproteomics |
| title_short | The microbiologist's guide to metaproteomics |
| title_sort | microbiologist s guide to metaproteomics |
| topic | bioinformatics functional dynamics mass spectrometry metaproteomics microbiome |
| url | https://doi.org/10.1002/imt2.70031 |
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