Evidence map›Paper›PMID 42493800›Full record

ArticleMicrobiome2026

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

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 and 19 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbiome, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

29 authors.

Tim Van Den BosscheCompOmics, VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.
Maximilian WolfMultidimensional Omics Analyses Group, Faculty of Technology, Bielefeld University, Bielefeld, Germany.
Jean ArmengaudDépartement Médicaments Et Technologies Pour La Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-Sur-Cèze, France.
Magnus Ø ArntzenFaculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
Dirk BenndorfApplied Biosciences and Process Engineering, Anhalt University of Applied Science, Köthen, Germany.
Daniel FigeysFaculty of Medicine, University of Ottawa, Ottawa, Canada.
Lucia GrengaDépartement Médicaments Et Technologies Pour La Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-Sur-Cèze, France.
Robert L HettichBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, USA.
Nithu Sara JohnWellcome Trust Genome Campus, European Bioinformatics Institute, Cambridge, UK.
Pratik JagtapDepartment of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, USA.
Nico JehmlichDepartment of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany.
Manuel KleinerDepartment of Plant and Microbial Biology, North Carolina State University, Raleigh, USA.
Benoit J KunathDepartment of Cancer Research, Multiomics Data Science Research Group, Luxembourg Institute of Health, Strassen, Luxembourg.
Leyuan LiState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, Beijing, China.
Mary LiptonEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, USA.
Bart MesuereDepartment of Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.
Benjamin A NeelyNational Institute of Standards and Technology, Charleston, USA.
Zhibin NingFaculty of Medicine, University of Ottawa, Ottawa, Canada.
Ane Laura PedersenNestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, Lausanne, Switzerland.
Yasset Perez-RiverolWellcome Trust Genome Campus, European Bioinformatics Institute, Cambridge, UK.
Jeena RajanWellcome Trust Genome Campus, European Bioinformatics Institute, Cambridge, UK.
Kay SchallertLeibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany.
Jana SeifertHoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany.
Sergio UzzauDepartment of Biomedical Sciences, University of Sassari, Sassari, Italy.
Pieter VerschaffeltCompOmics, VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.
Paul WilmesLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, Luxembourg.
Juan Antonio VizcaínoWellcome Trust Genome Campus, European Bioinformatics Institute, Cambridge, UK.
Lennart Martens *Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
Robert Heyer *Multidimensional Omics Analyses Group, Faculty of Technology, Bielefeld University, Bielefeld, Germany. robert.heyer@isas.de.

Funding

Metaproteomics to investigate intestinal microbiota-host and -diet interactionsR35GM138362 · NIGMS · NORTH CAROLINA STATE UNIVERSITY RALEIGH · PI KLEINER, MANUEL · 2020 to 2024
$1.9M
NIGMS NIH HHS R35 GM138362NIH HHS R35GM138362
6 · The paper itself

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.

Indexed as

MicrobiotaProteomicsComputational BiologyHumansMetadataMultiomicsReproducibility of Results

Identifiers

PMID42493800
PMCPMC13393928

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.