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PUBLICATIONS

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

Published

Author(s)

Tim Van Den Bossche, Kay Schallert, Jean Armengaud, Zhibin Ning, Daniel Figeys, Pratik Jagtap, Benoît Kunath, Lucia Grenga, Juan Antonio Vizcaino, Benjamin Neely, Leyuan Li, Drik Benndorf, Nico Jehmlich, Paul Wilmes, Robert Hettich, Jana Seifert, Sergio Uzzau, Mary Lipton, Manuel Kleiner, Magnus Arntzen, Lennart Martens, Robert Heyer

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.
Citation
BMC Microbiome
Volume
14
Pub Type
Journals

Download Paper

https://doi.org/10.1186/s40168-026-02455-0
Local Download

Keywords

metaproteomics, reporting, FAIR, microbiome
Proteomics, Microbial measurements and Biotechnology

Citation

Van Den Bossche, T. , Schallert, K. , Armengaud, J. , Ning, Z. , Figeys, D. , Jagtap, P. , Kunath, B. , Grenga, L. , Vizcaino, J. , Neely, B. , Li, L. , Benndorf, D. , Jehmlich, N. , Wilmes, P. , Hettich, R. , Seifert, J. , Uzzau, S. , Lipton, M. , Kleiner, M. , Arntzen, M. , Martens, L. and Heyer, R. (2026), The need for standardization and improved open (meta)data practices in metaproteomics, BMC Microbiome, [online], https://doi.org/10.1186/s40168-026-02455-0, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=960111 (Accessed August 13, 2026)
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Created July 26, 2026, Updated August 12, 2026
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