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

View ORCID ProfileTim Van Den Bossche, View ORCID ProfileBenoit J. Kunath, View ORCID ProfileKay Schallert, View ORCID ProfileStephanie S. Schäpe, View ORCID ProfilePaul E. Abraham, View ORCID ProfileJean Armengaud, View ORCID ProfileMagnus Ø. Arntzen, View ORCID ProfileAriane Bassignani, View ORCID ProfileDirk Benndorf, View ORCID ProfileStephan Fuchs, View ORCID ProfileRichard J. Giannone, View ORCID ProfileTimothy J. Griffin, View ORCID ProfileLive H. Hagen, View ORCID ProfileRashi Halder, View ORCID ProfileCéline Henry, View ORCID ProfileRobert L. Hettich, Robert Heyer, View ORCID ProfilePratik Jagtap, View ORCID ProfileNico Jehmlich, Marlene Jensen, View ORCID ProfileCatherine Juste, View ORCID ProfileManuel Kleiner, View ORCID ProfileOlivier Langella, Theresa Lehmann, Emma Leith, View ORCID ProfilePatrick May, View ORCID ProfileBart Mesuere, View ORCID ProfileGuylaine Miotello, View ORCID ProfileSamantha L. Peters, View ORCID ProfileOlivier Pible, View ORCID ProfilePedro T. Queiros, View ORCID ProfileUdo Reichl, View ORCID ProfileBernhard Y. Renard, View ORCID ProfileHenning Schiebenhoefer, View ORCID ProfileAlexander Sczyrba, View ORCID ProfileAlessandro Tanca, View ORCID ProfileKathrin Trappe, View ORCID ProfileJean-Pierre Trezzi, View ORCID ProfileSergio Uzzau, View ORCID ProfilePieter Verschaffelt, Martin von Bergen, View ORCID ProfilePaul Wilmes, Maximilian Wolf, View ORCID ProfileLennart Martens, View ORCID ProfileThilo Muth
doi: https://doi.org/10.1101/2021.03.05.433915
Tim Van Den Bossche
1VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
2Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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Benoit J. Kunath
3Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg
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  • ORCID record for Benoit J. Kunath
Kay Schallert
4Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
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  • ORCID record for Kay Schallert
Stephanie S. Schäpe
5Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Systems Biology, Leipzig, Germany
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Paul E. Abraham
6Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Jean Armengaud
7Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols- sur-Cèze, France
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Magnus Ø. Arntzen
8Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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Ariane Bassignani
9Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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Dirk Benndorf
4Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
10Microbiology,Department of Applied Biosciences and Process Technology, Anhalt University of Applied Sciences, Köthen, Germany
11Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
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Stephan Fuchs
12Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
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Richard J. Giannone
6Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Timothy J. Griffin
13Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
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Live H. Hagen
8Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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Rashi Halder
3Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg
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Céline Henry
9Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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Robert L. Hettich
6Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Robert Heyer
4Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
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Pratik Jagtap
13Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
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Nico Jehmlich
5Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Systems Biology, Leipzig, Germany
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Marlene Jensen
14Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA
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Catherine Juste
9Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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Manuel Kleiner
14Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA
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  • ORCID record for Manuel Kleiner
Olivier Langella
15Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, 91190, Gif-sur-Yvette, France
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Theresa Lehmann
4Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
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Emma Leith
13Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
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Patrick May
3Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg
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Bart Mesuere
1VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
16Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
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Guylaine Miotello
7Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols- sur-Cèze, France
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Samantha L. Peters
6Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Olivier Pible
7Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols- sur-Cèze, France
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Pedro T. Queiros
3Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg
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  • ORCID record for Pedro T. Queiros
Udo Reichl
4Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
11Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
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Bernhard Y. Renard
12Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
17Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
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Henning Schiebenhoefer
12Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
17Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
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Alexander Sczyrba
18Faculty of Technology, Bielefeld University, Bielefeld, Germany
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Alessandro Tanca
19Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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Kathrin Trappe
12Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
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Jean-Pierre Trezzi
3Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg
20Integrated Biobank of Luxembourg, Luxembourg Institute of Health, 1, rue Louis Rech, L-3555, Dudelange, Luxembourg
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Sergio Uzzau
19Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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Pieter Verschaffelt
1VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
16Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
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Martin von Bergen
5Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Systems Biology, Leipzig, Germany
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Paul Wilmes
3Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg
21Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
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Maximilian Wolf
4Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
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Lennart Martens
1VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
2Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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  • For correspondence: lennart.martens@ugent.be thilo.muth@bam.de
Thilo Muth
22Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany
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  • ORCID record for Thilo Muth
  • For correspondence: lennart.martens@ugent.be thilo.muth@bam.de
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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 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 Statement

The authors have declared no competing interest.

Footnotes

  • ↵* Shared first authors

  • Intermediate authors are listed alphabetically

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab 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, Thilo Muth
bioRxiv 2021.03.05.433915; doi: https://doi.org/10.1101/2021.03.05.433915
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Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab 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, Thilo Muth
bioRxiv 2021.03.05.433915; doi: https://doi.org/10.1101/2021.03.05.433915

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