TY - JOUR T1 - Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows JF - bioRxiv DO - 10.1101/2021.03.05.433915 SP - 2021.03.05.433915 AU - Tim Van Den Bossche AU - Benoit J. Kunath AU - Kay Schallert AU - Stephanie S. Schäpe AU - Paul E. Abraham AU - Jean Armengaud AU - Magnus Ø. Arntzen AU - Ariane Bassignani AU - Dirk Benndorf AU - Stephan Fuchs AU - Richard J. Giannone AU - Timothy J. Griffin AU - Live H. Hagen AU - Rashi Halder AU - Céline Henry AU - Robert L. Hettich AU - Robert Heyer AU - Pratik Jagtap AU - Nico Jehmlich AU - Marlene Jensen AU - Catherine Juste AU - Manuel Kleiner AU - Olivier Langella AU - Theresa Lehmann AU - Emma Leith AU - Patrick May AU - Bart Mesuere AU - Guylaine Miotello AU - Samantha L. Peters AU - Olivier Pible AU - Pedro T. Queiros AU - Udo Reichl AU - Bernhard Y. Renard AU - Henning Schiebenhoefer AU - Alexander Sczyrba AU - Alessandro Tanca AU - Kathrin Trappe AU - Jean-Pierre Trezzi AU - Sergio Uzzau AU - Pieter Verschaffelt AU - Martin von Bergen AU - Paul Wilmes AU - Maximilian Wolf AU - Lennart Martens AU - Thilo Muth Y1 - 2021/01/01 UR - http://biorxiv.org/content/early/2021/08/17/2021.03.05.433915.abstract N2 - 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. ER -