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

Tim Van Den Bossche; Benoit J. Kunath; Kay Schallert; Stephanie S. Schäpe; Paul E. Abraham; Jean Armengaud; Magnus Arntzen; Ariane Bassignani; Dirk Benndorf; Stephan Fuchs; Richard J. Giannone; Timothy J. Griffin; Live H. Hagen; Rashi Halder; Céline Henry; Robert L. Hettich; Robert Heyer; Pratik Jagtap; Nico Jehmlich; Marlene Jensen; Catherine Juste; Manuel Kleiner; Olivier Langella; Theresa Lehmann; Emma Leith; Patrick May; Bart Mesuere; Guylaine Miotello; Samantha L. Peters; Olivier Pible; Pedro T. Queiros; Udo Reichl; Bernhard Y. Renard; Henning Schiebenhoefer; Alexander Sczyrba; Alessandro Tanca; Kathrin Trappe; Jean Pierre Trezzi; Sergio Uzzau; Pieter Verschaffelt; Martin von Bergen; Paul Wilmes; Maximilian Wolf; Lennart Martens; Thilo Muth

doi:10.1038/s41467-021-27542-8

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

Tim Van Den Bossche, Benoit J. Kunath, Kay Schallert, Stephanie S. Schäpe, Paul E. Abraham, Jean Armengaud, Magnus Arntzen, Ariane Bassignani, Dirk Benndorf, Stephan Fuchs, Richard J. Giannone, Timothy J. Griffin, Live H. Hagen, Rashi Halder, Céline Henry, Robert L. Hettich, Robert Heyer, Pratik Jagtap, Nico Jehmlich, Marlene JensenCatherine Juste, Manuel Kleiner, Olivier Langella, Theresa Lehmann, Emma Leith, Patrick May, Bart Mesuere, Guylaine Miotello, Samantha L. Peters, Olivier Pible, Pedro T. Queiros, Udo Reichl, Bernhard Y. Renard, Henning Schiebenhoefer, Alexander Sczyrba, Alessandro Tanca, Kathrin Trappe, Jean Pierre Trezzi, Sergio Uzzau, Pieter Verschaffelt, Martin von Bergen, Paul Wilmes, Maximilian Wolf, Lennart Martens, Thilo Muth

Bioanalytical Mass Spectrometry

Research output: Contribution to journal › Article › peer-review

43 Scopus citations

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.

Original language	English
Article number	7305
Journal	Nature Communications
Volume	12
Issue number	1
DOIs	https://doi.org/10.1038/s41467-021-27542-8
State	Published - Dec 2021

Funding

This work has benefited from collaborations facilitated by the Metaproteomics Initiative (https://metaproteomics.org/) whose goals are to promote, improve and standardize metaproteomics. Part of the LC–MS/MS measurements were made in the Molecular Education, Technology, and Research Innovation Center (METRIC) at North Carolina State University, the ProGénoMIX platform at CEA-Marcoule supported by the IBISA network. Parts of the bioinformatics analysis were carried out using the high-performance computing facilities of the University of Luxembourg (https://hpc.uni.lu). This work was supported by the Research Foundation - Flanders (FWO) [grant no. 1S90918N (S.B.) to T.V.D.B.; 12I5217N to B.M.; G042518N to L.M.]; by a FEBS Summer Fellowship [to T.V.D.B.]; by the European Union’s Horizon 2020 Program (H2020-INFRAIA-2018-1) [823839 to L.M.]; by the FEMS [R.T.G. to S.S.S.]; by the Norwegian Centennial Chair program [to T.J.G., P.D.J., and M.A.]; the Novo Nordisk Foundation grant NNF20OC0061313 to M.A.; the USDA National Institute of Food and Agriculture Hatch project [1014212 to M.K.]; the U.S. National Science Foundation [OIA 1934844 and IOS 2003107 to M.K.]; the Foundation for Food and Agriculture Research [Grant ID: 593607 to M.K.]; the Agence Nationale de la Recherche [ANR-17-CE18-0023-01 to G.M., O.P., J.A.]; Deutsche Forschungsgemeinschaft (DFG) [RE3474/5-1 and RE3474/2-2 to S.F., T.M., B.Y.R.]. Research by T.J.G., P.D.J, E.L was funded by National Cancer Institute-Informatics Technology for Cancer Research (NCI-ITCR) grant 1U24CA199347 and National Science Foundation (U.S.) grant 1458524 to T.J.G.; and the National Institutes of Health R01-DK70977 to RLH. The European Galaxy server that was used for some calculations is in part funded by Collaborative Research Centre 992 Medical Epigenetics (DFG grant SFB 992/1 2012) and the German Federal Ministry of Education and Research (BMBF grants 031 A538A/A538C RBC, 031L0101B/031L0101C de.NBI-epi, 031L0106 de.STAIR, 031L0103 MetaProtServ (de.NBI)). This work was supported by the Luxembourg National Research Fund (FNR) under grants PRIDE/ 11823097 and CORE-INTER/13684739 to B.J.K., P.M. and P.W, and the European Research Council (ERC-CoG 863664) to P.W.

Funders	Funder number
Collaborative Research Centre 992 Medical Epigenetics	SFB 992/1 2012
National Cancer Institute-Informatics Technology for Cancer Research
USDA National Institute of Food and Agriculture Hatch project
National Science Foundation	OIA 1934844, 1458524, IOS 2003107
National Science Foundation
National Institutes of Health	R01-DK70977
National Institutes of Health
Foundation for the National Institutes of Health
National Cancer Institute	U24CA199347
National Cancer Institute
National Institute of Food and Agriculture	1014212
National Institute of Food and Agriculture
Horizon 2020 Framework Programme
H2020 European Research Council
Foundation for Food and Agriculture Research	593607
Foundation for Food and Agriculture Research
Federation of European Biochemical Societies
Federation of European Microbiological Societies
European Research Council	ERC-CoG 863664
European Research Council
Deutsche Forschungsgemeinschaft	RE3474/2-2, RE3474/5-1
Deutsche Forschungsgemeinschaft
Agence Nationale de la Recherche	ANR-17-CE18-0023-01
Agence Nationale de la Recherche
Fonds National de la Recherche Luxembourg	PRIDE/ 11823097, CORE-INTER/13684739
Fonds National de la Recherche Luxembourg
Bundesministerium für Bildung und Forschung	031 A538A/A538C RBC, 031L0106 de.STAIR, 031L0103
Bundesministerium für Bildung und Forschung
Fonds Wetenschappelijk Onderzoek	1S90918N, 12I5217N, G042518N
Fonds Wetenschappelijk Onderzoek
Vlaams Instituut voor Biotechnologie
Horizon 2020	823839, H2020-INFRAIA-2018-1
Horizon 2020
Novo Nordisk Fonden	NNF20OC0061313
Novo Nordisk Fonden

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Van Den Bossche, T., Kunath, B. J., Schallert, K., Schäpe, S. S., Abraham, P. E., Armengaud, J., Arntzen, M., 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., ... Muth, T. (2021). Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications, 12(1), Article 7305. https://doi.org/10.1038/s41467-021-27542-8

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title = "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 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.",

author = "{Van Den Bossche}, Tim and Kunath, {Benoit J.} and Kay Schallert and Sch{\"a}pe, {Stephanie S.} and Abraham, {Paul E.} and Jean Armengaud and Magnus Arntzen and Ariane Bassignani and Dirk Benndorf and Stephan Fuchs and Giannone, {Richard J.} and Griffin, {Timothy J.} and Hagen, {Live H.} and Rashi Halder and C{\'e}line Henry and Hettich, {Robert L.} and Robert Heyer and Pratik Jagtap and Nico Jehmlich and Marlene Jensen and Catherine Juste and Manuel Kleiner and Olivier Langella and Theresa Lehmann and Emma Leith and Patrick May and Bart Mesuere and Guylaine Miotello and Peters, {Samantha L.} and Olivier Pible and Queiros, {Pedro T.} and Udo Reichl and Renard, {Bernhard Y.} and Henning Schiebenhoefer and Alexander Sczyrba and Alessandro Tanca and Kathrin Trappe and Trezzi, {Jean Pierre} and Sergio Uzzau and Pieter Verschaffelt and {von Bergen}, Martin and Paul Wilmes and Maximilian Wolf and Lennart Martens and Thilo Muth",

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Van Den Bossche, T, Kunath, BJ, Schallert, K, Schäpe, SS, Abraham, PE, Armengaud, J, Arntzen, M, Bassignani, A, Benndorf, D, Fuchs, S, Giannone, RJ, Griffin, TJ, Hagen, LH, Halder, R, Henry, C, Hettich, RL, 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, SL, Pible, O, Queiros, PT, Reichl, U, Renard, BY, Schiebenhoefer, H, Sczyrba, A, Tanca, A, Trappe, K, Trezzi, JP, 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', Nature Communications, vol. 12, no. 1, 7305. https://doi.org/10.1038/s41467-021-27542-8

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AU - Van Den Bossche, Tim

AU - Kunath, Benoit J.

AU - Schallert, Kay

AU - Schäpe, Stephanie S.

AU - Abraham, Paul E.

AU - Armengaud, Jean

AU - Arntzen, Magnus

AU - Bassignani, Ariane

AU - Benndorf, Dirk

AU - Fuchs, Stephan

AU - Giannone, Richard J.

AU - Griffin, Timothy J.

AU - Hagen, Live H.

AU - Halder, Rashi

AU - Henry, Céline

AU - Hettich, Robert L.

AU - Heyer, Robert

AU - Jagtap, Pratik

AU - Jehmlich, Nico

AU - Jensen, Marlene

AU - Juste, Catherine

AU - Kleiner, Manuel

AU - Langella, Olivier

AU - Lehmann, Theresa

AU - Leith, Emma

AU - May, Patrick

AU - Mesuere, Bart

AU - Miotello, Guylaine

AU - Peters, Samantha L.

AU - Pible, Olivier

AU - Queiros, Pedro T.

AU - Reichl, Udo

AU - Renard, Bernhard Y.

AU - Schiebenhoefer, Henning

AU - Sczyrba, Alexander

AU - Tanca, Alessandro

AU - Trappe, Kathrin

AU - Trezzi, Jean Pierre

AU - Uzzau, Sergio

AU - Verschaffelt, Pieter

AU - von Bergen, Martin

AU - Wilmes, Paul

AU - Wolf, Maximilian

AU - Martens, Lennart

AU - Muth, Thilo

PY - 2021/12

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N2 - 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.

AB - 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.

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VL - 12

JO - Nature Communications

JF - Nature Communications

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

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