Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1038/s41467-021-27542-8
Licence creative commons licence
Title (Primary) Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
Author Van Den Bossche, T.; Kunath, B.J.; Schallert, K.; Schäpe, S.S.; Abraham, P.E.; Armengaud, J.; Arntzen, M.Ø.; 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. ORCID logo ; 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.
Source Titel Nature Communications
Year 2021
Department MOLSYB
Volume 12
Page From art. 7305
Language englisch
Topic T9 Healthy Planet
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.
Persistent UFZ Identifier
Van Den Bossche, T., Kunath, B.J., Schallert, K., Schäpe, S.S., Abraham, P.E., Armengaud, J., Arntzen, M.Ø., 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. (2021):
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
Nat. Commun. 12 , art. 7305 10.1038/s41467-021-27542-8