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.
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows / Van Den Bossche, T.; Kunath, B. J.; Schallert, K.; Schape, S. S.; Abraham, P. E.; Armengaud, J.; Arntzen, M. O.; Bassignani, A.; Benndorf, D.; Fuchs, S.; Giannone, R. J.; Griffin, T. J.; Hagen, L. H.; Halder, R.; Henry, C.; Hettich, R. L.; Heyer, R.; Jagtap, P.; Jehmlich, N.; Jensen, M.; Juste, C.; Kleiner, M.; Langella, O.; Lehmann, T.; Leith, E.; May, P.; Mesuere, B.; Miotello, G.; Peters, S. L.; Pible, O.; Queiros, P. T.; Reichl, U.; Renard, B. Y.; Schiebenhoefer, H.; Sczyrba, A.; Tanca, A.; Trappe, K.; Trezzi, J. -P.; Uzzau, S.; Verschaffelt, P.; von Bergen, M.; Wilmes, P.; Wolf, M.; Martens, L.; Muth, T.. - In: NATURE COMMUNICATIONS. - ISSN 2041-1723. - 12:1(2021), p. 7305. [10.1038/s41467-021-27542-8]
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
Tanca A.;Uzzau S.;
2021-01-01
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.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
