{ "abstract": "Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reproducibility and comparability, limiting integration with other omics data. We here present a community-developed reporting checklist tailored to the specific needs of metaproteomics. We also outline current efforts to enable structured and interoperable metadata capture, drawing on standards from proteomics and microbiome research wherever possible. By promoting transparent reporting and advancing metadata practices, our recommendations aim to align metaproteomics more closely with FAIR principles and support reproducible and interoperable research practices. Video Abstract.", "abstract_shown": true, "affiliations": [ "CompOmics, VIB-UGent Center for Medical Biotechnology, Ghent, Belgium", "Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium", "Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, Bielefeld, Germany", "Multidimensional Omics Analyses Group, Faculty of Technology, Bielefeld University, Bielefeld, Germany", "Département Médicaments Et Technologies Pour La Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-Sur-Cèze, France", "Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway", "Applied Biosciences and Process Engineering, Anhalt University of Applied Science, Köthen, Germany", "Faculty of Medicine, University of Ottawa, Ottawa, Canada", "Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, USA", "Wellcome Trust Genome Campus, European Bioinformatics Institute, Cambridge, UK", "Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, USA", "Department of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany", "Department of Plant and Microbial Biology, North Carolina State University, Raleigh, USA", "Department of Cancer Research, Multiomics Data Science Research Group, Luxembourg Institute of Health, Strassen, Luxembourg", "State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, Beijing, China", "Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, USA", "Department of Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium", "National Institute of Standards and Technology, Charleston, USA", "Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, Lausanne, Switzerland", "Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany", "HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany", "Department of Biomedical Sciences, University of Sassari, Sassari, Italy", "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, Luxembourg", "Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany. robert.heyer@isas.de", "Multidimensional Omics Analyses Group, Faculty of Technology, Bielefeld University, Bielefeld, Germany. robert.heyer@isas.de" ], "article_type": null, "arxiv": null, "author_total": 29, "authors": [ { "affs": [ 0, 1 ], "name": "Tim Van Den Bossche", "orcid": "0000-0002-5916-2587" }, { "affs": [ 2, 3 ], "name": "Maximilian Wolf", "orcid": "0000-0002-8770-8399" }, { "affs": [ 4 ], "name": "Jean Armengaud", "orcid": "0000-0003-1589-445X" }, { "affs": [ 5 ], "name": "Magnus Ø. Arntzen", "orcid": "0000-0002-1803-727X" }, { "affs": [ 6 ], "name": "Dirk Benndorf", "orcid": "0000-0003-4021-8525" }, { "affs": [ 7 ], "name": "Daniel Figeys", "orcid": "0000-0002-5373-7546" }, { "affs": [ 4 ], "name": "Lucia Grenga", "orcid": "0000-0001-5560-1717" }, { "affs": [ 8 ], "name": "Robert L. Hettich", "orcid": "0000-0001-7708-786X" }, { "affs": [ 9 ], "name": "Nithu Sara John", "orcid": "0000-0002-4823-6210" }, { "affs": [ 10 ], "name": "Pratik Jagtap" }, { "affs": [ 11 ], "name": "Nico Jehmlich", "orcid": "0000-0002-5638-6868" }, { "affs": [ 12 ], "name": "Manuel Kleiner", "orcid": "0000-0001-6904-0287" }, { "affs": [ 13 ], "name": "Benoit Josef Kunath", "orcid": "0000-0002-3356-8562" }, { "affs": [ 14 ], "name": "Leyuan Li", "orcid": "0000-0003-2063-4441" }, { "affs": [ 15 ], "name": "Mary S. Weir Lipton", "orcid": "0000-0001-7749-0077" }, { "affs": [ 16 ], "name": "Bart Mesuere", "orcid": "0000-0003-0610-3441" }, { "affs": [ 17 ], "name": "Benjamin A. Neely", "orcid": "0000-0001-6120-7695" }, { "affs": [ 7 ], "name": "Zhibin Ning", "orcid": "0000-0003-2045-7596" }, { "affs": [ 18 ], "name": "Ane Laura Pedersen", "orcid": "0009-0009-2297-3448" }, { "affs": [ 9 ], "name": "Yasset Pérez‐Riverol", "orcid": "0000-0001-6579-6941" }, { "affs": [ 9 ], "name": "Jeena Rajan", "orcid": "0000-0002-3613-0013" }, { "affs": [ 19 ], "name": "Kay Schallert", "orcid": "0000-0002-1683-7222" }, { "affs": [ 20 ], "name": "Jana Seifert", "orcid": "0000-0002-7690-8539" }, { "affs": [ 21 ], "name": "Sergio Uzzau", "orcid": "0000-0001-6246-2794" }, { "affs": [ 0, 1 ], "name": "Pieter Verschaffelt", "orcid": "0000-0002-6675-1048" }, { "affs": [ 22 ], "name": "Paul Wilmes", "orcid": "0000-0002-6478-2924" }, { "affs": [ 9 ], "name": "Juan Antonio Vizcaíno", "orcid": "0000-0002-3905-4335" }, { "affs": [ 1 ], "name": "Lennart Martens", "orcid": "0000-0003-4277-658X" }, { "affs": [ 23, 24 ], "name": "Robert Heyer", "orcid": "0000-0001-7840-8899" } ], "bibtex": "https://research.draconitic.com/paper/4c2vqes6yf4k6.bib", "cited_by": 6, "doi": "10.1186/s40168-026-02455-0", "fulltext_url": null, "id": "4c2vqes6yf4k6", "issns": [ "2049-2618" ], "landing_url": "https://doi.org/10.1186/s40168-026-02455-0", "language": "en", "licence": "CC-BY", "licence_label": "CC BY", "licence_source": "journal", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "1607|Advanced Proteomics Techniques and Applications" ] ], "openalex": "W7170133120", "pdf_url": "https://link.springer.com/content/pdf/10.1186/s40168-026-02455-0.pdf", "pmcid": "PMC13393928", "pmid": "42493800", "published": "2026-07-23", "publisher": "BioMed Central", "ris": "https://research.draconitic.com/paper/4c2vqes6yf4k6.ris", "sources": [ { "first_seen": "2026-11-04T13:21:03Z", "native_id": "W7170133120", "source": "openalex", "url": "https://doi.org/10.1186/s40168-026-02455-0" } ], "subjects": [ { "field": "chemistry", "origin": "openalex:1607|Advanced Proteomics Techniques and Applications", "subfield": "physical" } ], "title": "The need for standardization and improved open (meta)data practices in metaproteomics", "title_text": "The need for standardization and improved open (meta)data practices in metaproteomics", "type": "peer-reviewed", "updated_at": "2026-11-08T13:20:39Z", "url": "https://research.draconitic.com/paper/4c2vqes6yf4k6", "venue": "Microbiome", "versions": [] }