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
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
N1 - Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12
Y1 - 2021/12
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 - http://www.scopus.com/inward/record.url?scp=85121394798&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85121394798&partnerID=8YFLogxK
U2 - 10.1038/s41467-021-27542-8
DO - 10.1038/s41467-021-27542-8
M3 - Article
C2 - 34911965
AN - SCOPUS:85121394798
SN - 2041-1723
VL - 12
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 7305
ER -