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The microbiologist's guide to metaproteomics

Van Den Bossche, Tim [Ghent Univ. (Belgium)] (ORCID:0000000259162587)·Armengaud, Jean [Univ. Paris-Saclay (France)] (ORCID:000000031589445X)·Benndorf, Dirk [Anhalt Univ. of Applied Sciences, Bernberg (Germany); Max Planck Institute for Dynamics of Complex Technical Systems (Germany); Otto von Guericke University (Germany)] (ORCID:0000000340218525)·Blakeley‐Ruiz, Jose Alfredo [North Carolina State University, Raleigh, NC (United States)] (ORCID:0000000176385849)·Brauer, Madita [Univ. of Luxembourg, Esch-sur-Alzette, (Luxembourg)] (ORCID:0000000197099155)·Cheng, Kai [Univ. of Ottawa, ON (Canada)] (ORCID:0000000260450244)·Creskey, Marybeth [Health Canada, Ottawa, ON (Canada)] (ORCID:0000000258841051)·Figeys, Daniel [Univ. of Ottawa, ON (Canada); Quadram Institute Bioscience (United Kingdom); Univ. of East Anglia, Norwich (United Kingdom)] (ORCID:0000000253737546)·Grenga, Lucia [Univ. Paris-Saclay (France)] (ORCID:0000000155601717)·Griffin, Timothy J. [Univ. of Minnesota, Minneapolis, MN (United States)] (ORCID:0000000168012559)·Henry, Céline [Univ. Paris-Saclay (France)] (ORCID:0000000223551791)·Hettich, Robert L. [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)] (ORCID:000000017708786X)·Holstein, Tanja [Ghent Univ. (Belgium); Robert‐Koch‐Institut (Germany)] (ORCID:0000000215521453)·Jagtap, Pratik D. [Univ. of Minnesota, Minneapolis, MN (United States)] (ORCID:0000000309840973)·Jehmlich, Nico [Helmholtz Centre for Environmental Research (UFZ) (Germany)] (ORCID:0000000256386868)·Kim, Jonghyun [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)] (ORCID:0000000197496169)·Kleiner, Manuel [North Carolina State University, Raleigh, NC (United States)] (ORCID:0000000169040287)·Kunath, Benoit J. [North Carolina State University, Raleigh, NC (United States); Univ. of Luxembourg, Esch-sur-Alzette, (Luxembourg)] (ORCID:0000000233568562)·Malliet, Xuxa [Ghent Univ. (Belgium)] (ORCID:0009000094202655)·Martens, Lennart [Ghent Univ. (Belgium); University of Strasbourg (France)] (ORCID:000000034277658X)·Mehta, Subina [Univ. of Minnesota, Minneapolis, MN (United States)] (ORCID:0000000198180537)·Mesuere, Bart [Ghent Univ. (Belgium)] (ORCID:0000000306103441)·Ning, Zhibin [Univ. of Ottawa, ON (Canada)] (ORCID:0000000320457596)·Tanca, Alessandro [Univ. of Sassari (Italy)] (ORCID:0000000260667048)·Uzzau, Sergio [Univ. of Sassari (Italy)] (ORCID:0000000162462794)·Verschaffelt, Pieter [Ghent Univ. (Belgium)] (ORCID:0000000266751048)·Wang, Jing [Beijing Institute of Lifeomics (China)] (ORCID:0009000582073928)·Wilmes, Paul [Univ. of Luxembourg, Esch-sur-Alzette, (Luxembourg)] (ORCID:0000000264782924)·Zhang, Xu [Health Canada, Ottawa, ON (Canada)] (ORCID:0000000324069478)·Zhang, Xin [Beijing Institute of Lifeomics (China)] (ORCID:0009000191071626)·Li, Leyuan [Beijing Institute of Lifeomics (China)] (ORCID:0000000320634441)
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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.

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bioinformaticsfunctional dynamicsmass spectrometrymetaproteomicsmicrobiome

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Van Den Bossche, Tim [Ghent Univ. (Belgium)] (ORCID:0000000259162587), Armengaud, Jean [Univ. Paris-Saclay (France)] (ORCID:000000031589445X), Benndorf, Dirk [Anhalt Univ. of Applied Sciences, Bernberg (Germany); Max Planck Institute for Dynamics of Complex Technical Systems (Germany); Otto von Guericke University (Germany)] (ORCID:0000000340218525), Blakeley‐Ruiz, Jose Alfredo [North Carolina State University, Raleigh, NC (United States)] (ORCID:0000000176385849), Brauer, Madita [Univ. of Luxembourg, Esch-sur-Alzette, (Luxembourg)] (ORCID:0000000197099155), Cheng, Kai [Univ. of Ottawa, ON (Canada)] (ORCID:0000000260450244), Creskey, Marybeth [Health Canada, Ottawa, ON (Canada)] (ORCID:0000000258841051), Figeys, Daniel [Univ. of Ottawa, ON (Canada); Quadram Institute Bioscience (United Kingdom); Univ. of East Anglia, Norwich (United Kingdom)] (ORCID:0000000253737546), Grenga, Lucia [Univ. Paris-Saclay (France)] (ORCID:0000000155601717), Griffin, Timothy J. [Univ. of Minnesota, Minneapolis, MN (United States)] (ORCID:0000000168012559), Henry, Céline [Univ. Paris-Saclay (France)] (ORCID:0000000223551791), Hettich, Robert L. [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)] (ORCID:000000017708786X), Holstein, Tanja [Ghent Univ. (Belgium); Robert‐Koch‐Institut (Germany)] (ORCID:0000000215521453), Jagtap, Pratik D. [Univ. of Minnesota, Minneapolis, MN (United States)] (ORCID:0000000309840973), Jehmlich, Nico [Helmholtz Centre for Environmental Research (UFZ) (Germany)] (ORCID:0000000256386868), Kim, Jonghyun [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)] (ORCID:0000000197496169), Kleiner, Manuel [North Carolina State University, Raleigh, NC (United States)] (ORCID:0000000169040287), Kunath, Benoit J. [North Carolina State University, Raleigh, NC (United States); Univ. of Luxembourg, Esch-sur-Alzette, (Luxembourg)] (ORCID:0000000233568562), Malliet, Xuxa [Ghent Univ. (Belgium)] (ORCID:0009000094202655), Martens, Lennart [Ghent Univ. (Belgium); University of Strasbourg (France)] (ORCID:000000034277658X), Mehta, Subina [Univ. of Minnesota, Minneapolis, MN (United States)] (ORCID:0000000198180537), Mesuere, Bart [Ghent Univ. (Belgium)] (ORCID:0000000306103441), Ning, Zhibin [Univ. of Ottawa, ON (Canada)] (ORCID:0000000320457596), Tanca, Alessandro [Univ. of Sassari (Italy)] (ORCID:0000000260667048), Uzzau, Sergio [Univ. of Sassari (Italy)] (ORCID:0000000162462794), Verschaffelt, Pieter [Ghent Univ. (Belgium)] (ORCID:0000000266751048), Wang, Jing [Beijing Institute of Lifeomics (China)] (ORCID:0009000582073928), Wilmes, Paul [Univ. of Luxembourg, Esch-sur-Alzette, (Luxembourg)] (ORCID:0000000264782924), Zhang, Xu [Health Canada, Ottawa, ON (Canada)] (ORCID:0000000324069478), Zhang, Xin [Beijing Institute of Lifeomics (China)] (ORCID:0009000191071626), Li, Leyuan [Beijing Institute of Lifeomics (China)] (ORCID:0000000320634441). 2025-05-06. The microbiologist's guide to metaproteomics. https://doi.org/10.1002/imt2.70031

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