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; Thilo Muth

doi:10.1038/s41467-021-27542-8

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 JensenCatherine 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

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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 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.

Original language	English
Pages (from-to)	7305
Journal	Nature Communications
Volume	12
Issue number	1
DOIs	https://doi.org/10.1038/s41467-021-27542-8
Publication status	Published - 15 Dec 2021

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Van Den Bossche, T., Kunath, B. J., Schallert, K., Schäpe, S. S., Abraham, P. E., Armengaud, J., Arntzen, M. Ø., Bassignani, A., Benndorf, D., Fuchs, S., Giannone, R. J., Griffin, T. J., Hagen, L. H., Halder, R., Henry, C., Hettich, R. L., Heyer, R., Jagtap, P., Jehmlich, N., ... Muth, T. (2021). Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications, 12(1), 7305. https://doi.org/10.1038/s41467-021-27542-8

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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 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.",

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Van Den Bossche, T, Kunath, BJ, Schallert, K, Schäpe, SS, Abraham, PE, Armengaud, J, Arntzen, MØ, Bassignani, A, Benndorf, D, Fuchs, S, Giannone, RJ, Griffin, TJ, Hagen, LH, Halder, R, Henry, C, Hettich, RL, Heyer, R, Jagtap, P, Jehmlich, N, Jensen, M, Juste, C, Kleiner, M, Langella, O, Lehmann, T, Leith, E, May, P, Mesuere, B, Miotello, G, Peters, SL, Pible, O, Queiros, PT, Reichl, U, Renard, BY, Schiebenhoefer, H, Sczyrba, A, Tanca, A, Trappe, K, Trezzi, J-P, Uzzau, S, Verschaffelt, P, von Bergen, M, Wilmes, P, Wolf, M, Martens, L & Muth, T 2021, 'Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows', Nature Communications, vol. 12, no. 1, pp. 7305. https://doi.org/10.1038/s41467-021-27542-8

TY - JOUR

T1 - Critical Assessment of MetaProteome Investigation (CAMPI)

T2 - a multi-laboratory comparison of established workflows

AU - Van Den Bossche, Tim

AU - Kunath, Benoit J

AU - Schallert, Kay

AU - Schäpe, Stephanie S

AU - Abraham, Paul E

AU - Armengaud, Jean

AU - Arntzen, Magnus Ø

AU - Bassignani, Ariane

AU - Benndorf, Dirk

AU - Fuchs, Stephan

AU - Giannone, Richard J

AU - Griffin, Timothy J

AU - Hagen, Live H

AU - Halder, Rashi

AU - Henry, Céline

AU - Hettich, Robert L

AU - Heyer, Robert

AU - Jagtap, Pratik

AU - Jehmlich, Nico

AU - Jensen, Marlene

AU - Juste, Catherine

AU - Kleiner, Manuel

AU - Langella, Olivier

AU - Lehmann, Theresa

AU - Leith, Emma

AU - May, Patrick

AU - Mesuere, Bart

AU - Miotello, Guylaine

AU - Peters, Samantha L

AU - Pible, Olivier

AU - Queiros, Pedro T

AU - Reichl, Udo

AU - Renard, Bernhard Y

AU - Schiebenhoefer, Henning

AU - Sczyrba, Alexander

AU - Tanca, Alessandro

AU - Trappe, Kathrin

AU - Trezzi, Jean-Pierre

AU - Uzzau, Sergio

AU - Verschaffelt, Pieter

AU - von Bergen, Martin

AU - Wilmes, Paul

AU - Wolf, Maximilian

AU - Martens, Lennart

AU - Muth, Thilo

PY - 2021/12/15

Y1 - 2021/12/15

N2 - 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.

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 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.

UR - https://www.ncbi.nlm.nih.gov/pubmed/34911965

U2 - 10.1038/s41467-021-27542-8

DO - 10.1038/s41467-021-27542-8

M3 - Article

C2 - 34911965

SN - 2041-1723

VL - 12

SP - 7305

JO - Nature Communications

JF - Nature Communications

IS - 1

ER -

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

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