Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
15 12 2021
15 12 2021
Historique:
received:
02
04
2021
accepted:
24
11
2021
entrez:
16
12
2021
pubmed:
17
12
2021
medline:
19
1
2022
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 34911965
doi: 10.1038/s41467-021-27542-8
pii: 10.1038/s41467-021-27542-8
pmc: PMC8674281
doi:
Substances chimiques
Bacterial Proteins
0
Peptides
0
Types de publication
Comparative Study
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
7305Subventions
Organisme : NIDDK NIH HHS
ID : R01 DK070977
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA199347
Pays : United States
Informations de copyright
© 2021. The Author(s).
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