The need for standardization and improved open (meta)data practices in metaproteomics
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.
Authors
- Manuel Kleiner (ORCID: https://orcid.org/0000-0001-6904-0287)
- Robert L. Hettich (ORCID: https://orcid.org/0000-0001-7708-786X)
- Dirk Benndorf (ORCID: https://orcid.org/0000-0003-4021-8525)
- Bart Mesuere (ORCID: https://orcid.org/0000-0003-0610-3441)
- Nico Jehmlich (ORCID: https://orcid.org/0000-0002-5638-6868)
- Lucia Grenga (ORCID: https://orcid.org/0000-0001-5560-1717)
- Maximilian Wolf (ORCID: https://orcid.org/0000-0002-8770-8399)
- Jana Seifert (ORCID: https://orcid.org/0000-0002-7690-8539)
- Kay Schallert (ORCID: https://orcid.org/0000-0002-1683-7222)
- Lennart Martens (ORCID: https://orcid.org/0000-0003-4277-658X)
- Pieter Verschaffelt (ORCID: https://orcid.org/0000-0002-6675-1048)
- Leyuan Li (ORCID: https://orcid.org/0000-0003-2063-4441)
- Jean Armengaud (ORCID: https://orcid.org/0000-0003-1589-445X)
- Zhibin Ning (ORCID: https://orcid.org/0000-0003-2045-7596)
- Nithu Sara John (ORCID: https://orcid.org/0000-0002-4823-6210)
- Sergio Uzzau (ORCID: https://orcid.org/0000-0001-6246-2794)
- Tim Van Den Bossche (ORCID: https://orcid.org/0000-0002-5916-2587)
- Jeena Rajan (ORCID: https://orcid.org/0000-0002-3613-0013)
- Mary Lipton
- Robert Heyer
- Ane Laura Pedersen (ORCID: https://orcid.org/0009-0009-2297-3448)
- Daniel Figeys
- Benjamin A. Neely (ORCID: https://orcid.org/0000-0001-6120-7695)
- Pratik Jagtap
- Yasset Perez-Riverol
- Juan Antonio Vizcaíno
- Magnus Ø. Arntzen
- Paul Wilmes
- Benoit J. Kunath
Institutions
- University of Hohenheim (DE)
- Oak Ridge National Laboratory (US)
- European Bioinformatics Institute (GB)
- National Institute of Standards and Technology (US)
- Helmholtz Centre for Environmental Research (DE)
- North Carolina State University (US)
- Pacific Northwest National Laboratory (US)
- University of Ottawa (CA)
- University of Sassari (IT)
- University of Luxembourg (LU)
- Bielefeld University (DE)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- Université Paris-Saclay (FR)
- Ghent University (BE)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Anhalt University of Applied Sciences (DE)
- Luxembourg Institute of Health (LU)
- Nestlé (Switzerland) (CH)
- Leibniz Institute for Analytical Sciences - ISAS (DE)
- CEA Paris-Saclay (FR)
- Bioinformatics Institute (RU)
- Beijing Proteome Research Center (CN)
- Institute of Molecular Biology and Biophysics (RU)
- VIB-UGent Center for Medical Biotechnology (BE)
- Norwegian University of Life Sciences (NO)
Publication Details
- Journal
- Microbiome
- Published
- 2026-07-23
- DOI
- https://doi.org/10.1186/s40168-026-02455-0
- Primary Topic
- Advanced Proteomics Techniques and Applications
- Type
- article
- Field-Weighted Citation Impact
- 0.00