The need for standardization and improved open (meta)data practices in metaproteomics.

Tim Van Den Bossche; Maximilian Wolf; Jean Armengaud; Magnus &#xd8; Arntzen; Dirk Benndorf; Daniel Figeys; Lucia Grenga; Robert L Hettich; Nithu Sara John; Pratik Jagtap; Nico Jehmlich; Manuel Kleiner; Benoit J Kunath; Leyuan Li; Mary Lipton; Bart Mesuere; Benjamin A Neely; Zhibin Ning; Ane Laura Pedersen; Yasset Perez-Riverol; Jeena Rajan; Kay Schallert; Jana Seifert; Sergio Uzzau; Pieter Verschaffelt; Paul Wilmes; Juan Antonio Vizca&#xed;no; Lennart Martens; Robert Heyer

doi:10.1186/s40168-026-02455-0

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The need for standardization and improved open (meta)data practices in metaproteomics.

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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.

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Proteomics Computational Biology Microbiota Metadata Humans Multiomics Reproducibility of Results Journal Article Research Support, Non-U.S. Gov't Research Support, N.I.H., Extramural

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Tim Van Den Bossche, Maximilian Wolf, Jean Armengaud, Magnus Ø Arntzen, Dirk Benndorf, Daniel Figeys, Lucia Grenga, Robert L Hettich, Nithu Sara John, Pratik Jagtap, Nico Jehmlich, Manuel Kleiner, Benoit J Kunath, Leyuan Li, Mary Lipton, Bart Mesuere, Benjamin A Neely, Zhibin Ning, Ane Laura Pedersen, Yasset Perez-Riverol, Jeena Rajan, Kay Schallert, Jana Seifert, Sergio Uzzau, Pieter Verschaffelt, Paul Wilmes, Juan Antonio Vizcaíno, Lennart Martens, Robert Heyer. 2026-07-23. The need for standardization and improved open (meta)data practices in metaproteomics.. https://doi.org/10.1186/s40168-026-02455-0

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