Critical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows

• Published in: bioRxiv
• Main Authors: Van Den Bossche, Tim, Kunath, Benoit J, Schallert, Kay, Schäpe, Stephanie S, Abraham, Paul E, Armengaud, Jean, Arntzen, Magnus Ø, Bassignani, Ariane, Benndorf, Dirk, Fuchs, Stephan, Giannone, Richard J, Griffin, Timothy J, Hagen, Live H, Halder, Rashi, Henry, Céline, Hettich, Robert L, Heyer, Robert, Jagtap, Pratik, Jehmlich, Nico, Jensen, Marlene, Juste, Catherine, Kleiner, Manuel, Langella, Olivier, Lehmann, Theresa, Leith, Emma, May, Patrick, Mesuere, Bart, Miotello, Guylaine, Peters, Samantha L, Pible, Olivier, Pedro Teixeira Queiros, Reichl, Udo, Renard, Bernhard Y, Schiebenhoefer, Henning, Sczyrba, Alexander, Tanca, Alessandro, Trappe, Kathrin, Trezzi, Jean-Pierre, Uzzau, Sergio, Verschaffelt, Pieter, Martin Von Bergen, Wilmes, Paul, Wolf, Maximilian, Martens, Lennart, Muth, Thilo
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 17.08.2021
• Subjects: Community composition; Intestine; Mass spectroscopy; Peptides
• DOI: 10.1101/2021.03.05.433915

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-lab 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, lab-assembled human intestinal model and a human fecal sample. We observed that variability at the peptide level was predominantly due to wet-lab workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappeared at 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-lab studies in metaproteomics, and provides publicly available data sets for benchmarking future developments. Competing Interest Statement The authors have declared no competing interest.