Cargando…

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

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:...

Descripción completa

Detalles Bibliográficos
Autores principales: 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, Juste, Catherine, Kleiner, Manuel, Langella, Olivier, Lehmann, Theresa, Leith, Emma, May, Patrick, Mesuere, Bart, Miotello, Guylaine, Peters, Samantha L., Pible, Olivier, Queiros, Pedro T., Reichl, Udo, Renard, Bernhard Y., Schiebenhoefer, Henning, Sczyrba, Alexander, Tanca, Alessandro, Trappe, Kathrin, Trezzi, Jean-Pierre, Uzzau, Sergio, Verschaffelt, Pieter, von Bergen, Martin, Wilmes, Paul, Wolf, Maximilian, Martens, Lennart, Muth, Thilo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8674281/
https://www.ncbi.nlm.nih.gov/pubmed/34911965
http://dx.doi.org/10.1038/s41467-021-27542-8
_version_ 1784615613829742592
author 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
Juste, Catherine
Kleiner, Manuel
Langella, Olivier
Lehmann, Theresa
Leith, Emma
May, Patrick
Mesuere, Bart
Miotello, Guylaine
Peters, Samantha L.
Pible, Olivier
Queiros, Pedro T.
Reichl, Udo
Renard, Bernhard Y.
Schiebenhoefer, Henning
Sczyrba, Alexander
Tanca, Alessandro
Trappe, Kathrin
Trezzi, Jean-Pierre
Uzzau, Sergio
Verschaffelt, Pieter
von Bergen, Martin
Wilmes, Paul
Wolf, Maximilian
Martens, Lennart
Muth, Thilo
author_facet 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
Juste, Catherine
Kleiner, Manuel
Langella, Olivier
Lehmann, Theresa
Leith, Emma
May, Patrick
Mesuere, Bart
Miotello, Guylaine
Peters, Samantha L.
Pible, Olivier
Queiros, Pedro T.
Reichl, Udo
Renard, Bernhard Y.
Schiebenhoefer, Henning
Sczyrba, Alexander
Tanca, Alessandro
Trappe, Kathrin
Trezzi, Jean-Pierre
Uzzau, Sergio
Verschaffelt, Pieter
von Bergen, Martin
Wilmes, Paul
Wolf, Maximilian
Martens, Lennart
Muth, Thilo
author_sort Van Den Bossche, Tim
collection PubMed
description 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.
format Online
Article
Text
id pubmed-8674281
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-86742812022-01-04 Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows 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 Juste, Catherine Kleiner, Manuel Langella, Olivier Lehmann, Theresa Leith, Emma May, Patrick Mesuere, Bart Miotello, Guylaine Peters, Samantha L. Pible, Olivier Queiros, Pedro T. Reichl, Udo Renard, Bernhard Y. Schiebenhoefer, Henning Sczyrba, Alexander Tanca, Alessandro Trappe, Kathrin Trezzi, Jean-Pierre Uzzau, Sergio Verschaffelt, Pieter von Bergen, Martin Wilmes, Paul Wolf, Maximilian Martens, Lennart Muth, Thilo Nat Commun Article 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. Nature Publishing Group UK 2021-12-15 /pmc/articles/PMC8674281/ /pubmed/34911965 http://dx.doi.org/10.1038/s41467-021-27542-8 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
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
Juste, Catherine
Kleiner, Manuel
Langella, Olivier
Lehmann, Theresa
Leith, Emma
May, Patrick
Mesuere, Bart
Miotello, Guylaine
Peters, Samantha L.
Pible, Olivier
Queiros, Pedro T.
Reichl, Udo
Renard, Bernhard Y.
Schiebenhoefer, Henning
Sczyrba, Alexander
Tanca, Alessandro
Trappe, Kathrin
Trezzi, Jean-Pierre
Uzzau, Sergio
Verschaffelt, Pieter
von Bergen, Martin
Wilmes, Paul
Wolf, Maximilian
Martens, Lennart
Muth, Thilo
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
title Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
title_full Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
title_fullStr Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
title_full_unstemmed Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
title_short Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
title_sort critical assessment of metaproteome investigation (campi): a multi-laboratory comparison of established workflows
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8674281/
https://www.ncbi.nlm.nih.gov/pubmed/34911965
http://dx.doi.org/10.1038/s41467-021-27542-8
work_keys_str_mv AT vandenbosschetim criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT kunathbenoitj criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT schallertkay criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT schapestephanies criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT abrahampaule criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT armengaudjean criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT arntzenmagnusø criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT bassignaniariane criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT benndorfdirk criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT fuchsstephan criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT giannonerichardj criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT griffintimothyj criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT hagenliveh criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT halderrashi criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT henryceline criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT hettichrobertl criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT heyerrobert criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT jagtappratik criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT jehmlichnico criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT jensenmarlene criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT justecatherine criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT kleinermanuel criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT langellaolivier criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT lehmanntheresa criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT leithemma criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT maypatrick criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT mesuerebart criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT miotelloguylaine criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT peterssamanthal criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT pibleolivier criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT queirospedrot criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT reichludo criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT renardbernhardy criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT schiebenhoeferhenning criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT sczyrbaalexander criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT tancaalessandro criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT trappekathrin criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT trezzijeanpierre criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT uzzausergio criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT verschaffeltpieter criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT vonbergenmartin criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT wilmespaul criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT wolfmaximilian criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT martenslennart criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows
AT muththilo criticalassessmentofmetaproteomeinvestigationcampiamultilaboratorycomparisonofestablishedworkflows