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- Title
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows.
- Authors
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
- 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. The authors present CAMPI, a large-scale multi-lab comparison of diverse metaproteomics workflows. CAMPI provides insights into the robustness of current methods, suggests further improvements to the field, and may pave the way for future community-driven metaproteomics projects.
- Subjects
MASS spectrometry; MICROBIAL communities; INTESTINES; WORKFLOW management; WORKFLOW; SAMPLING (Process)
- Publication
Nature Communications, 2021, Vol 12, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-021-27542-8