RT Journal Article
SR Electronic
T1 Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.03.05.433915
DO 10.1101/2021.03.05.433915
A1 Tim Van Den Bossche
A1 Benoit J. Kunath
A1 Kay Schallert
A1 Stephanie S. Schäpe
A1 Paul E. Abraham
A1 Jean Armengaud
A1 Magnus Ø. Arntzen
A1 Ariane Bassignani
A1 Dirk Benndorf
A1 Stephan Fuchs
A1 Richard J. Giannone
A1 Timothy J. Griffin
A1 Live H. Hagen
A1 Rashi Halder
A1 Céline Henry
A1 Robert L. Hettich
A1 Robert Heyer
A1 Pratik Jagtap
A1 Nico Jehmlich
A1 Marlene Jensen
A1 Catherine Juste
A1 Manuel Kleiner
A1 Olivier Langella
A1 Theresa Lehmann
A1 Emma Leith
A1 Patrick May
A1 Bart Mesuere
A1 Guylaine Miotello
A1 Samantha L. Peters
A1 Olivier Pible
A1 Pedro T. Queiros
A1 Udo Reichl
A1 Bernhard Y. Renard
A1 Henning Schiebenhoefer
A1 Alexander Sczyrba
A1 Alessandro Tanca
A1 Kathrin Trappe
A1 Jean-Pierre Trezzi
A1 Sergio Uzzau
A1 Pieter Verschaffelt
A1 Martin von Bergen
A1 Paul Wilmes
A1 Maximilian Wolf
A1 Lennart Martens
A1 Thilo Muth
YR 2021
UL http://biorxiv.org/content/early/2021/08/17/2021.03.05.433915.abstract
AB 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.