Peer-reviewedCC BYMicrobiome
The need for standardization and improved open (meta)data practices in metaproteomics
25 affiliations
- 1CompOmics, VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- 2Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- 3Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, Bielefeld, Germany
- 4Multidimensional Omics Analyses Group, Faculty of Technology, Bielefeld University, Bielefeld, Germany
- 5Département Médicaments Et Technologies Pour La Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-Sur-Cèze, France
- 6Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- 7Applied Biosciences and Process Engineering, Anhalt University of Applied Science, Köthen, Germany
- 8Faculty of Medicine, University of Ottawa, Ottawa, Canada
- 9Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, USA
- 10Wellcome Trust Genome Campus, European Bioinformatics Institute, Cambridge, UK
- 11Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, USA
- 12Department of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
- 13Department of Plant and Microbial Biology, North Carolina State University, Raleigh, USA
- 14Department of Cancer Research, Multiomics Data Science Research Group, Luxembourg Institute of Health, Strassen, Luxembourg
- 15State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, Beijing, China
- 16Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, USA
- 17Department of Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- 18National Institute of Standards and Technology, Charleston, USA
- 19Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, Lausanne, Switzerland
- 20Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
- 21HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- 22Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- 23Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, Luxembourg
- 24Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany. [email protected]
- 25Multidimensional Omics Analyses Group, Faculty of Technology, Bielefeld University, Bielefeld, Germany. [email protected]
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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BibTeX
@article{bossche2026need,
title = {{The need for standardization and improved open (meta)data practices in metaproteomics}},
author = {Tim Van Den Bossche and Maximilian Wolf and Jean Armengaud and Magnus Ø. Arntzen and Dirk Benndorf and Daniel Figeys and Lucia Grenga and Robert L. Hettich and Nithu Sara John and Pratik Jagtap and Nico Jehmlich and Manuel Kleiner and Benoit Josef Kunath and Leyuan Li and Mary S. Weir Lipton and Bart Mesuere and Benjamin A. Neely and Zhibin Ning and Ane Laura Pedersen and Yasset Pérez‐Riverol and Jeena Rajan and Kay Schallert and Jana Seifert and Sergio Uzzau and Pieter Verschaffelt and Paul Wilmes and Juan Antonio Vizcaíno and Lennart Martens and Robert Heyer},
journal = {Microbiome},
year = {2026},
month = jul,
doi = {10.1186/s40168-026-02455-0},
url = {https://doi.org/10.1186/s40168-026-02455-0},
note = {CC BY},
}
RIS
TY - JOUR
TI - The need for standardization and improved open (meta)data practices in metaproteomics
AU - Tim Van Den Bossche
AU - Maximilian Wolf
AU - Jean Armengaud
AU - Magnus Ø. Arntzen
AU - Dirk Benndorf
AU - Daniel Figeys
AU - Lucia Grenga
AU - Robert L. Hettich
AU - Nithu Sara John
AU - Pratik Jagtap
AU - Nico Jehmlich
AU - Manuel Kleiner
AU - Benoit Josef Kunath
AU - Leyuan Li
AU - Mary S. Weir Lipton
AU - Bart Mesuere
AU - Benjamin A. Neely
AU - Zhibin Ning
AU - Ane Laura Pedersen
AU - Yasset Pérez‐Riverol
AU - Jeena Rajan
AU - Kay Schallert
AU - Jana Seifert
AU - Sergio Uzzau
AU - Pieter Verschaffelt
AU - Paul Wilmes
AU - Juan Antonio Vizcaíno
AU - Lennart Martens
AU - Robert Heyer
PY - 2026
DA - 2026/07/23
JO - Microbiome
DO - 10.1186/s40168-026-02455-0
UR - https://doi.org/10.1186/s40168-026-02455-0
AB - 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.
SN - 2049-2618
ER -