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

Tim Van Den Bossche, Benoit J Kunath, Kay Schallert, Stephanie S Schäpe, Paul E Abraham, Jean Armengaud, Magnus Ø Arntzen, Ariane Bassignani, Dirk Benndorf, Stephan Fuchs, Richard J Giannone, Timothy J Griffin, Live H Hagen, Rashi Halder, Céline Henry, Robert L Hettich, Robert Heyer, Pratik Jagtap, Nico Jehmlich, Marlene JensenCatherine Juste, Manuel Kleiner, Olivier Langella, Theresa Lehmann, Emma Leith, Patrick May, Bart Mesuere, Guylaine Miotello, Samantha L Peters, Olivier Pible, Pedro T Queiros, Udo Reichl, Bernhard Y Renard, Henning Schiebenhoefer, Alexander Sczyrba, Alessandro Tanca, Kathrin Trappe, Jean-Pierre Trezzi, Sergio Uzzau, Pieter Verschaffelt, Martin von Bergen, Paul Wilmes, Maximilian Wolf, Lennart Martens, Thilo Muth

Research output: Contribution to journalArticleResearchpeer-review

4 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)7305
JournalNature Communications
Volume12
Issue number1
DOIs
Publication statusPublished - 15 Dec 2021

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