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As primary catalytic and structural components, proteins reveal active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can understand microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative, provides principles, state-of-the-art methods, and analytical workflows spanning experimental design, sample preparation, mass spectrometry, data analysis, and statistics.",{"@graph":63,"@context":118},[64,80,101],{"@type":65,"itemListElement":66},"BreadcrumbList",[67,71,74,77],{"item":68,"name":69,"@type":70,"position":9},"https://docshare.wps.com","Home","ListItem",{"item":72,"name":10,"@type":70,"position":73},"https://docshare.wps.com/template/",2,{"item":75,"name":11,"@type":70,"position":76},"https://docshare.wps.com/template/presentations/",3,{"item":78,"name":59,"@type":70,"position":79},"https://docshare.wps.com/template/the-microbiologists-guide-to-metaproteomics-review-article-practical-guide/573276/",4,{"url":78,"name":59,"@type":81,"image":82,"author":87,"headline":59,"publisher":90,"fileFormat":93,"inLanguage":57,"description":61,"dateModified":94,"datePublished":95,"encodingFormat":93,"isAccessibleForFree":96,"interactionStatistic":97},"DigitalDocument",{"url":83,"@type":84,"width":85,"height":86},"https://docshare.wps.com/thumbnails/the-microbiologists-guide-to-metaproteomics-review-article-practical-guide/573276.png","ImageObject",442,249,{"name":88,"@type":89},"Jasmine","Person",{"url":68,"name":91,"@type":92},"DocShare","Organization","application/pdf","2026-10-17","2026-10-14",true,{"@type":98,"interactionType":99,"userInteractionCount":9},"InteractionCounter",{"@type":100},"ViewAction",{"@type":102,"mainEntity":103},"FAQPage",[104,110,114],{"name":105,"@type":106,"acceptedAnswer":107},"What is metaproteomics used for in microbiome studies?","Question",{"text":108,"@type":109},"Metaproteomics characterizes proteins that underpin microbial functionality within diverse ecosystems, providing insights into active processes and ecological roles.","Answer",{"name":111,"@type":106,"acceptedAnswer":112},"How does the review position metaproteomics alongside other omics approaches?",{"text":113,"@type":109},"It emphasizes that integrating metaproteomics with other omics disciplines supports a comprehensive understanding of microbial ecology, interactions, and functional dynamics.",{"name":115,"@type":106,"acceptedAnswer":116},"What topics and workflows does the guide cover?",{"text":117,"@type":109},"The review covers experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches necessary for metaproteomics.","https://schema.org",{"og:url":78,"og:type":120,"og:title":59,"og:site_name":91,"og:description":61},"article",{"robots":122,"canonical":78},"index,follow",{"doc_id":124,"site_id":56},573276,1792255348,{"code":4,"msg":5,"data":127},{"doc_id":124,"user_id":128,"nickname":88,"user_avatar":129,"doc_module":9,"category_id":8,"category_name":11,"doc_title":59,"doc_description":61,"doc_content":130,"file_id":131,"file_url":132,"file_type":133,"file_size":134,"view_count":9,"is_deleted":4,"is_public":9,"is_downloadable":9,"audit_status":9,"page_count":135,"language":136,"language_code":57,"site_id":56,"html_lang":57,"table_of_contents":137,"faqs":138,"seo_title":139,"seo_description":61,"update_tm":140,"read_time":141},2336478487870,"https://ap-avatar.wpscdn.com/davatar_085a072bc5b1113ac321206ff7593b45","Received: 21 December 2024  \nRevised: 26 March 2025  \nAccepted: 28 March 2025  \n\n| DOI: 10.1002/imt2.70031 |  |  |\n| --- | --- | --- |\n| REV I EW ARTICLE\u003Cbr>| | |\n| The microbiologist's guide to metaproteomics\u003Cbr>Tim Van Den Bossche1,2  | Jean Armengaud3  | Dirk Benndorf4,5,6  |\u003Cbr>Jose Alfredo Blakeley‐Ruiz7  | Madita Brauer8,9  | Kai Cheng10  | Marybeth Creskey11  | Daniel Figeys10,12,13  | Lucia Grenga3  | Timothy J. Griffin14  | Céline Henry15  | Robert L. Hettich16  | Tanja Holstein1,2,17  | Pratik D. Jagtap14  | Nico Jehmlich18  | Jonghyun Kim16  | Manuel Kleiner7  | Benoit J. Kunath7,19  | Xuxa Malliet1,2  | Lennart Martens1,2,20  | Subina Mehta14  | Bart Mesuere21  | Zhibin Ning10  | Alessandro Tanca22,23  | Sergio Uzzau22,23  | Pieter Verschaffelt1,2,21  | Jing Wang24  |\u003Cbr>Paul Wilmes19,25  | Xu Zhang11  | Xin Zhang24  | Leyuan Li24  | The |  |  |\n| Metaproteomics Initiative\u003Cbr>Correspondence\u003Cbr>Leyuan Li, State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.\u003Cbr>Email: [lileyuan@ncpsb.org.cn](lileyuan@ncpsb.org.cn)\u003Cbr>Funding information\u003Cbr>European Research Council (ERC) under the European Union's Horizon 2020\u003Cbr>research and innovation program, Grant/Award Number: 863664 (P.W.); National Institute of General Medical Sciences of the National Institutes of Health, Grant/Award Number:\u003Cbr>R35GM138362 (J.A.B.R.); Minnesota Ovarian Cancer Alliance, the National Institutes of Health/National Cancer Institute, Grant/Award Number:\u003Cbr>1R21CA267707 (P.D.J. and T.J.G.) and 5R01CA262153 (A.P.N.S.); United States | \u003Cbr>Abstract\u003Cbr>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](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 tometaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches. |  |\n| For affiliations refer to page 37 . |  |  |\n| This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.\u003Cbr>© 2025 The Author(s) . iMeta published by John Wiley & Sons Australia, Ltd on behalf of iMeta Science. |  |  |\n\niMeta. 2025;4:e70031 .  \n[https://doi.org/10.1002/imt2.70031](https://doi.org/10.1002/imt2.70031)  \n[wileyonlinelibrary.com/journal/imeta](wileyonlinelibrary.com/journal/imeta)  \n1 of 53  \n2 of 53  \nVAN DEN BOSSCHE ET AL.  \nDepartment of Energy, Biologcal and Environmental Research Program (R.L.H.); FNR INTERMOBILITY/2022/BM/ 16965254 (B.K.); The National Institutes of Health/National Cancer Institute,  \nGrant/Award Number: P30CA077598 (P.D.J. and T.J.G.); Next Generation EU, Grant/Award Number: PNRR‐MAD‐2022‐ 12376416 (A.T. and S.U.); Research Foundation Flanders (FWO),  \nGrant/Award Numbers: 1286824N (T.V.D.B), G010023N (L.M.), G028821N (L.M.); French National Agency for Research and Occitanie Région, Agence Nationale de la Recherche,  \nGrant/Award Number: ANR‐20‐CE34‐0012 (J.A.) and 21023526‐DeepMicro (J.A.);  \nGhent University (BOF), Grant/Award Number: BOF/ 01P10623 (P.V.)  \nKEYW OR DS  \nbioinformatics, functional dynamics, mass spectrometry, metaproteomics, micro","cbCaicsE2c5hVFHX","https://ap.wps.com/l/cbCaicsE2c5hVFHX","pdf",5679266,53,"English","# Abstract\n## Metaproteomics and microbiome functionality\n## Integration with multi-omics\n## Review scope and included workflows","[{\"question\":\"What is metaproteomics used for in microbiome studies?\",\"answer\":\"Metaproteomics characterizes proteins that underpin microbial functionality within diverse ecosystems, providing insights into active processes and ecological roles.\"},{\"question\":\"How does the review position metaproteomics alongside other omics approaches?\",\"answer\":\"It emphasizes that integrating metaproteomics with other omics disciplines supports a comprehensive understanding of microbial ecology, interactions, and functional dynamics.\"},{\"question\":\"What topics and workflows does the guide cover?\",\"answer\":\"The review covers experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches necessary for metaproteomics.\"}]","The microbiologist's guide to metaproteomics - Review article - Practical guide | PDF",1791936310,19]