Reference : Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory compari...
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
Life sciences : Microbiology
Systems Biomedicine
http://hdl.handle.net/10993/49679
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
English
Van Den Bossche, Tim [> >]
Kunath, Benoît mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
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 mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Scientific Central Services]
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 mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core]
Mesuere, Bart [> >]
Miotello, Guylaine [> >]
Peters, Samantha L. [> >]
Pible, Olivier [> >]
Teixeira Queiros, Pedro mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology >]
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 mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology]
Wolf, Maximilian [> >]
Martens, Lennart [> >]
Muth, Thilo [> >]
2021
Nature Communications
12
1
7305
Yes (verified by ORBilu)
International
2041-1723
[en] Bacteria ; Metaproteomics ; Mass spectronomy ; Microbiome
[en] 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.
Fonds National de la Recherche - FnR ; ERC-CoG 863664
Researchers ; Professionals
http://hdl.handle.net/10993/49679
10.1038/s41467-021-27542-8
https://www.nature.com/articles/s41467-021-27542-8
FnR ; FNR13684739 > Paul Wilmes > metaPUF > The Dark Metaproteome: Identifying Proteins Of Unknown Function In The Human Gut Microbiome > 01/04/2020 > 31/03/2022 > 2019

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