%0 Journal Article %A Tim Van Den Bossche %A Benoit J. Kunath %A Kay Schallert %A Stephanie S. Schäpe %A Paul E. Abraham %A Jean Armengaud %A Magnus Ø. Arntzen %A Ariane Bassignani %A Dirk Benndorf %A Stephan Fuchs %A Richard J. Giannone %A Timothy J. Griffin %A Live H. Hagen %A Rashi Halder %A Céline Henry %A Robert L. Hettich %A Robert Heyer %A Pratik Jagtap %A Nico Jehmlich %A Marlene Jensen %A Catherine Juste %A Manuel Kleiner %A Olivier Langella %A Theresa Lehmann %A Emma Leith %A Patrick May %A Bart Mesuere %A Guylaine Miotello %A Samantha L. Peters %A Olivier Pible %A Pedro T. Queiros %A Udo Reichl %A Bernhard Y. Renard %A Henning Schiebenhoefer %A Alexander Sczyrba %A Alessandro Tanca %A Kathrin Trappe %A Jean-Pierre Trezzi %A Sergio Uzzau %A Pieter Verschaffelt %A Martin von Bergen %A Paul Wilmes %A Maximilian Wolf %A Lennart Martens %A Thilo Muth %T Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows %D 2021 %R 10.1101/2021.03.05.433915 %J bioRxiv %P 2021.03.05.433915 %X 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 carried out the first community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluated 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 observed that variability at the peptide level was predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappeared at the protein group level. While differences were observed for predicted community composition, similar functional profiles were 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.Competing Interest StatementThe authors have declared no competing interest. %U https://www.biorxiv.org/content/biorxiv/early/2021/08/17/2021.03.05.433915.full.pdf