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Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

Author

Listed:
  • Tim Van Den Bossche

    (VIB - UGent Center for Medical Biotechnology, VIB
    Ghent University)

  • 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
    Anhalt University of Applied Sciences
    Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems)

  • 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
    Ghent University)

  • 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
    Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems)

  • Bernhard Y. Renard

    (Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute
    Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam)

  • Henning Schiebenhoefer

    (Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute
    Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam)

  • 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
    Integrated Biobank of Luxembourg, Luxembourg Institute of Health)

  • Sergio Uzzau

    (University of Sassari)

  • Pieter Verschaffelt

    (VIB - UGent Center for Medical Biotechnology, VIB
    Ghent University)

  • Martin von Bergen

    (Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH)

  • Paul Wilmes

    (University of Luxembourg
    University of Luxembourg)

  • Maximilian Wolf

    (Bioprocess Engineering, Otto-von-Guericke University Magdeburg)

  • Lennart Martens

    (VIB - UGent Center for Medical Biotechnology, VIB
    Ghent University)

  • Thilo Muth

    (Section eScience (S.3), Federal Institute for Materials Research and Testing)

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.

Suggested Citation

  • 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. Gia, 2021. "Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-27542-8
    DOI: 10.1038/s41467-021-27542-8
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