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<p>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.</p><p><MediaObject ID="MOESM1"> <VideoObject FileRef="MediaObjects/40168_2026_2455_MOESM1_ESM.mp4" VideoID="AKqcSWMLpN1xDKxGK6XHvB"> <Caption Language="En" xml:lang="en"> <CaptionContent> <p>Video Abstract</p> </CaptionContent> </Caption> </VideoObject> </MediaObject></p>

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

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年7月23日

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  • 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,
  • Nico Jehmlich,
  • Manuel Kleiner,
  • Benoit J. Kunath,
  • Leyuan Li,
  • Mary Lipton,
  • Bart Mesuere,
  • Benjamin A. Neely,
  • Zhibin Ning,
  • Ane Laura Pedersen,
  • Yasset Perez-Riverol,
  • Jeena Rajan,
  • Kay Schallert,
  • Jana Seifert,
  • Sergio Uzzau,
  • Pieter Verschaffelt,
  • Paul Wilmes,
  • Juan Antonio Vizcaíno,
  • Lennart Martens,
  • Robert Heyer

摘要

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