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


ABSTRACT: 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.

SUBMITTER: Van Den Bossche T 

PROVIDER: S-EPMC8674281 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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

Van Den Bossche Tim T   Kunath Benoit J BJ   Schallert Kay K   Schäpe Stephanie S SS   Abraham Paul E PE   Armengaud Jean J   Arntzen Magnus Ø MØ   Bassignani Ariane A   Benndorf Dirk D   Fuchs Stephan S   Giannone Richard J RJ   Griffin Timothy J TJ   Hagen Live H LH   Halder Rashi R   Henry Céline C   Hettich Robert L RL   Heyer Robert R   Jagtap Pratik P   Jehmlich Nico N   Jensen Marlene M   Juste Catherine C   Kleiner Manuel M   Langella Olivier O   Lehmann Theresa T   Leith Emma E   May Patrick P   Mesuere Bart B   Miotello Guylaine G   Peters Samantha L SL   Pible Olivier O   Queiros Pedro T PT   Reichl Udo U   Renard Bernhard Y BY   Schiebenhoefer Henning H   Sczyrba Alexander A   Tanca Alessandro A   Trappe Kathrin K   Trezzi Jean-Pierre JP   Uzzau Sergio S   Verschaffelt Pieter P   von Bergen Martin M   Wilmes Paul P   Wolf Maximilian M   Martens Lennart L   Muth Thilo T  

Nature communications 20211215 1


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 us  ...[more]

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