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Article Dans Une Revue Nature Communications Année : 2021

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

Stephan Fuchs
Timothy Griffin
Live Hagen
Pratik Jagtap
Manuel Kleiner
Theresa Lehmann
  • Fonction : Auteur
Emma Leith
  • Fonction : Auteur
Patrick May
Bart Mesuere
Samantha Peters
Pedro Queiros
  • Fonction : Auteur
Udo Reichl
  • Fonction : Auteur
Bernhard Renard
Henning Schiebenhoefer
Alexander Sczyrba
Alessandro Tanca

Résumé

Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
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Dates et versions

hal-04460334 , version 1 (06-05-2024)

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Paternité

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Tim van den Bossche, Benoit Kunath, Kay Schallert, Stephanie Schäpe, Paul Abraham, et al.. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications, 2021, 12 (1), pp. 7305. ⟨10.1038/s41467-021-27542-8⟩. ⟨hal-04460334⟩
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