Article (Scientific journals)
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
Van Den Bossche, Tim; Kunath, Benoît; Schallert, Kay et al.
2021In Nature Communications, 12 (1), p. 7305
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Keywords :
Bacteria; Metaproteomics; Mass spectronomy; Microbiome
Abstract :
[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.
Disciplines :
Biochemistry, biophysics & molecular biology
Microbiology
Author, co-author :
Van Den Bossche, Tim
Kunath, Benoît ;  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 ;  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  ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core
Mesuere, Bart
Miotello, Guylaine
Peters, Samantha L.
Pible, Olivier
Teixeira Queiros, Pedro ;  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 ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
Wolf, Maximilian
Martens, Lennart
Muth, Thilo
More authors (35 more) Less
External co-authors :
yes
Language :
English
Title :
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
Publication date :
2021
Journal title :
Nature Communications
ISSN :
2041-1723
Publisher :
Nature Publishing Group, London, United Kingdom
Volume :
12
Issue :
1
Pages :
7305
Peer reviewed :
Peer Reviewed verified by ORBi
Focus Area :
Systems Biomedicine
FnR Project :
FNR13684739 - The Dark Metaproteome: Identifying Proteins Of Unknown Function In The Human Gut Microbiome, 2019 (01/04/2020-31/03/2022) - Paul Wilmes
Funders :
FNR - Fonds National de la Recherche [LU]
ERC-CoG 863664
Available on ORBilu :
since 16 January 2022

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