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

by Neely, Benjamin A. , Seifert, Jana , Wolf, Maximilian , Perez-Riverol, Yasset , Kunath, Benoit J. , Mesuere, Bart , Jagtap, Pratik , Heyer, Robert , Figeys, Daniel , Lipton, Mary , Verschaffelt, Pieter , Rajan, Jeena , Grenga, Lucia , Martens, Lennart , Hettich, Robert L. , Arntzen, Magnus Ø. , Li, Leyuan , Kleiner, Manuel , Vizcaíno, Juan Antonio , Armengaud, Jean , Uzzau, Sergio , Ning, Zhibin , Pedersen, Ane Laura , John, Nithu Sara , Wilmes, Paul , Van Den Bossche, Tim , Benndorf, Dirk , Jehmlich, Nico , Schallert, Kay

in Adaptation / Bioinformatics / Biomedical and Life Sciences / Biomedicine / Computational Biology - methods / Design of experiments / Genomes / Genomics / Humans / Information sharing / Mass spectrometry / Medical Microbiology / Metadata / Microbial Ecology / Microbial Genetics and Genomics / Microbiology / Microbiomes / Microbiota / Multiomics / Organisms / Peptides / Proteins / Proteomics / Proteomics - methods / Proteomics - standards / Reproducibility / Reproducibility of Results / Scientific imaging / Standardization / Taxonomy / Virology

2026

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2026

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2026

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Journal Article

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

Neely, Benjamin A.,

Seifert, Jana,

Wolf, Maximilian,

Perez-Riverol, Yasset,

Kunath, Benoit J.,

Mesuere, Bart,

Jagtap, Pratik,

Heyer, Robert,

Figeys, Daniel,

Lipton, Mary,

Verschaffelt, Pieter,

Rajan, Jeena,

Grenga, Lucia,

Martens, Lennart,

Hettich, Robert L.,

Arntzen, Magnus Ø.,

Li, Leyuan,

Kleiner, Manuel,

Vizcaíno, Juan Antonio,

Armengaud, Jean,

Uzzau, Sergio,

Ning, Zhibin,

Pedersen, Ane Laura,

John, Nithu Sara,

Wilmes, Paul,

Van Den Bossche, Tim,

Benndorf, Dirk,

Jehmlich, Nico,

Schallert, Kay

2026

Overview

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. AKqcSWMLpN1xDKxGK6XHvB Video Abstract

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Publisher

BioMed Central,Springer Nature B.V,BMC

Subject

Adaptation

/ Bioinformatics

/ Biomedical and Life Sciences

/ Biomedicine

/ Computational Biology - methods

/ Design of experiments

/ Genomes