Dataset Information

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]

PMID: 34911965

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Dataset Information

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

Publications

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

Similar Datasets

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