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

December 15, 2021 By:
  • Van Den Bossche T
  • Kunath BJ
  • Schallert K
  • Schäpe SS
  • Abraham PE
  • Armengaud J
  • Arntzen MO
  • Bassignani A
  • Benndorf D
  • Fuchs S
  • Giannone RJ
  • Griffin TJ
  • Hagen LH
  • Halder R
  • Henry C
  • Hettich RL
  • Heyer R
  • Jagtap P
  • Jehmlich N
  • Jensen M
  • Juste C
  • Kleiner M
  • Langella O
  • Lehmann T
  • Leith E
  • May P
  • Mesuere B
  • Miotello G
  • Peters SL
  • Pible O
  • Queiros PT
  • Reichl U
  • Renard BY
  • Schiebenhoefer H
  • Sczyrba A
  • Tanca A
  • Trappe K
  • Trezzi JP
  • Uzzau S
  • Verschaffelt P
  • von Bergen M
  • Wilmes P
  • Wolf M
  • Martens L
  • Muth T.

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.

2021 Dec. Nat Commun.12(1):7305.
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