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 Jensen, Catherine 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 () and Thilo Muth
Additional contact information
Tim Van Den Bossche: VIB - UGent Center for Medical Biotechnology, VIB
Benoit J. Kunath: University of Luxembourg
Kay Schallert: Bioprocess Engineering, Otto-von-Guericke University Magdeburg
Stephanie S. Schäpe: Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH
Paul E. Abraham: Biosciences Division, Oak Ridge National Laboratory
Jean Armengaud: Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI
Magnus Ø. Arntzen: Norwegian University of Life Sciences (NMBU)
Ariane Bassignani: INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay
Dirk Benndorf: Bioprocess Engineering, Otto-von-Guericke University Magdeburg
Stephan Fuchs: Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute
Richard J. Giannone: Biosciences Division, Oak Ridge National Laboratory
Timothy J. Griffin: University of Minnesota
Live H. Hagen: Norwegian University of Life Sciences (NMBU)
Rashi Halder: University of Luxembourg
Céline Henry: INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay
Robert L. Hettich: Biosciences Division, Oak Ridge National Laboratory
Robert Heyer: Bioprocess Engineering, Otto-von-Guericke University Magdeburg
Pratik Jagtap: University of Minnesota
Nico Jehmlich: Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH
Marlene Jensen: North Carolina State University
Catherine Juste: INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay
Manuel Kleiner: North Carolina State University
Olivier Langella: Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon
Theresa Lehmann: Bioprocess Engineering, Otto-von-Guericke University Magdeburg
Emma Leith: University of Minnesota
Patrick May: University of Luxembourg
Bart Mesuere: VIB - UGent Center for Medical Biotechnology, VIB
Guylaine Miotello: Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI
Samantha L. Peters: Biosciences Division, Oak Ridge National Laboratory
Olivier Pible: Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI
Pedro T. Queiros: University of Luxembourg
Udo Reichl: Bioprocess Engineering, Otto-von-Guericke University Magdeburg
Bernhard Y. Renard: Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute
Henning Schiebenhoefer: Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute
Alexander Sczyrba: Bielefeld University
Alessandro Tanca: University of Sassari
Kathrin Trappe: Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute
Jean-Pierre Trezzi: University of Luxembourg
Sergio Uzzau: University of Sassari
Pieter Verschaffelt: VIB - UGent Center for Medical Biotechnology, VIB
Martin von Bergen: Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH
Paul Wilmes: University of Luxembourg
Maximilian Wolf: Bioprocess Engineering, Otto-von-Guericke University Magdeburg
Lennart Martens: VIB - UGent Center for Medical Biotechnology, VIB
Thilo Muth: Section eScience (S.3), Federal Institute for Materials Research and Testing

Nature Communications, 2021, vol. 12, issue 1, 1-15

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-27542-8

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