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

Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen MØ, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, et al. (2021)
Nature Communications 12(1): 7305.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
Van Den Bossche, Tim; Kunath, Benoit J.; Schallert, Kay; Schäpe, Stephanie S.; Abraham, Paul E.; Armengaud, Jean; Arntzen, Magnus Ø.; Bassignani, Ariane; Benndorf, Dirk; Fuchs, Stephan; Giannone, Richard J.; Griffin, Timothy J.
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Abstract / Bemerkung
**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.
Erscheinungsjahr
2021
Zeitschriftentitel
Nature Communications
Band
12
Ausgabe
1
Art.-Nr.
7305
eISSN
2041-1723
Page URI
https://pub.uni-bielefeld.de/record/2960171

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Van Den Bossche T, Kunath BJ, Schallert K, et al. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications. 2021;12(1): 7305.
Van Den Bossche, T., Kunath, B. J., Schallert, K., Schäpe, S. S., Abraham, P. E., Armengaud, J., Arntzen, M. Ø., et al. (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
Van Den Bossche, Tim, Kunath, Benoit J., Schallert, Kay, Schäpe, Stephanie S., Abraham, Paul E., Armengaud, Jean, Arntzen, Magnus Ø., et al. 2021. “Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows”. Nature Communications 12 (1): 7305.
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., et al. (2021). Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications 12:7305.
Van Den Bossche, T., et al., 2021. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications, 12(1): 7305.
T. Van Den Bossche, et al., “Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows”, Nature Communications, vol. 12, 2021, : 7305.
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., Jensen, M., Juste, C., Kleiner, M., Langella, O., Lehmann, T., Leith, E., May, P., Mesuere, B., Miotello, G., Peters, S.L., Pible, O., Queiros, P.T., Reichl, U., Renard, B.Y., 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.: Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications. 12, : 7305 (2021).
Van Den Bossche, Tim, Kunath, Benoit J., Schallert, Kay, Schäpe, Stephanie S., Abraham, Paul E., Armengaud, Jean, Arntzen, Magnus Ø., Bassignani, Ariane, Benndorf, Dirk, Fuchs, Stephan, Giannone, Richard J., Griffin, Timothy J., Hagen, Live H., Halder, Rashi, Henry, Céline, Hettich, Robert L., Heyer, Robert, Jagtap, Pratik, Jehmlich, Nico, Jensen, Marlene, Juste, Catherine, Kleiner, Manuel, Langella, Olivier, Lehmann, Theresa, Leith, Emma, May, Patrick, Mesuere, Bart, Miotello, Guylaine, Peters, Samantha L., Pible, Olivier, Queiros, Pedro T., Reichl, Udo, Renard, Bernhard Y., Schiebenhoefer, Henning, Sczyrba, Alexander, Tanca, Alessandro, Trappe, Kathrin, Trezzi, Jean-Pierre, Uzzau, Sergio, Verschaffelt, Pieter, von Bergen, Martin, Wilmes, Paul, Wolf, Maximilian, Martens, Lennart, and Muth, Thilo. “Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows”. Nature Communications 12.1 (2021): 7305.
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