Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows.

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 d

SUBMITTER: Van Den Bossche T 

PROVIDER: S-EPMC8674281 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature