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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 (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.metaproteomics.org\">www.metaproteomics.org<\/jats:ext-link>\n                    ), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state\u2010of\u2010the\u2010art methodologies, and analytical workflows essential to metaproteomics. 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