Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement
Pré-Publication, Document De Travail Année : 2021

Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows

Tim van den Bossche (1, 2) , Benoit Kunath (3) , Kay Schallert (4) , Stephanie Schäpe (5) , Paul Abraham (6) , Jean Armengaud (7, 8) , Magnus Ø. Arntzen (9) , Ariane Bassignani (10) , Dirk Benndorf (11, 12) , Stephan Fuchs (13) , Richard Giannone (6) , Timothy Griffin (14) , Live Hagen (9) , Rashi Halder (3) , Céline Henry (10) , Robert Hettich (6) , Robert Heyer (4) , Pratik Jagtap (14) , Nico Jehmlich (5) , Marlene Jensen (15) , Catherine Juste (10) , Manuel Kleiner , Olivier Langella (16) , Theresa Lehmann , Emma Leith , Patrick May , Bart Mesuere , Guylaine Miotello (7, 8) , Samantha Peters , Olivier Pible (7, 8) , Pedro Queiros , Udo Reichl , Bernhard Renard , Henning Schiebenhoefer , Alexander Sczyrba , Alessandro Tanca , Kathrin Trappe , Jean-Pierre Trezzi , Sergio Uzzau , Pieter Verschaffelt , Martin von Bergen (5) , Paul Wilmes (17) , Maximilian Wolf (4) , Lennart Martens (18, 2) , Thilo Muth (19)
1 UGENT - Universiteit Gent = Ghent University = Université de Gand
2 VIB-UGent Center for Medical Biotechnology
3 LCSB - Luxembourg Centre For Systems Biomedicine
4 OVGU - Otto-von-Guericke-Universität Magdeburg = Otto-von-Guericke University [Magdeburg]
5 UFZ - Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research
6 ORNL - Oak Ridge National Laboratory [Oak Ridge]
7 MTS - Médicaments et Technologies pour la Santé
8 SPI - Service de Pharmacologie et Immunoanalyse
9 NMBU - Norwegian University of Life Sciences
10 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
11 Anhalt University of Applied Sciences
12 Max Planck Institute for Dynamics of Complex Technical Systems
13 RKI - Robert Koch Institute [Berlin]
14 UMN - University of Minnesota [Twin Cities]
15 NC State - North Carolina State University [Raleigh]
16 GQE-Le Moulon - Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale)
17 uni.lu - Université du Luxembourg = University of Luxembourg = Universität Luxemburg
18 Ghent University Hospital
19 BAM Federal Institute for Materials Research and Testing
Tim van den Bossche
Universiteit Gent = Ghent University = Université de Gand
VIB-UGent Center for Medical Biotechnology
Benoit Kunath
Luxembourg Centre For Systems Biomedicine
Kay Schallert
Otto-von-Guericke-Universität Magdeburg = Otto-von-Guericke University [Magdeburg]
Stephanie Schäpe
Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research
Paul Abraham
Oak Ridge National Laboratory [Oak Ridge]
Jean Armengaud
Médicaments et Technologies pour la Santé
Service de Pharmacologie et Immunoanalyse
Magnus Ø. Arntzen
Norwegian University of Life Sciences
Ariane Bassignani
MICrobiologie de l'ALImentation au Service de la Santé
Dirk Benndorf
Anhalt University of Applied Sciences
Max Planck Institute for Dynamics of Complex Technical Systems
Stephan Fuchs
Robert Koch Institute [Berlin]
Richard Giannone
Oak Ridge National Laboratory [Oak Ridge]
Timothy Griffin
University of Minnesota [Twin Cities]
Live Hagen
Norwegian University of Life Sciences
Rashi Halder
Luxembourg Centre For Systems Biomedicine
Céline Henry
MICrobiologie de l'ALImentation au Service de la Santé
Robert Hettich
Oak Ridge National Laboratory [Oak Ridge]
Robert Heyer
  • Fonction : Auteur
Otto-von-Guericke-Universität Magdeburg = Otto-von-Guericke University [Magdeburg]
Pratik Jagtap
University of Minnesota [Twin Cities]
Nico Jehmlich
Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research
Marlene Jensen
  • Fonction : Auteur
North Carolina State University [Raleigh]
Catherine Juste
MICrobiologie de l'ALImentation au Service de la Santé
CV
Manuel Kleiner
Olivier Langella
Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale)
CV
Theresa Lehmann
  • Fonction : Auteur
Emma Leith
  • Fonction : Auteur
Patrick May
Bart Mesuere
Guylaine Miotello
Médicaments et Technologies pour la Santé
Service de Pharmacologie et Immunoanalyse
Samantha Peters
Olivier Pible
Médicaments et Technologies pour la Santé
Service de Pharmacologie et Immunoanalyse
Pedro Queiros
Udo Reichl
Bernhard Renard
Henning Schiebenhoefer
Alexander Sczyrba
Alessandro Tanca
Kathrin Trappe
Jean-Pierre Trezzi
Sergio Uzzau
Pieter Verschaffelt
Martin von Bergen
  • Fonction : Auteur
Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research
Paul Wilmes
Université du Luxembourg = University of Luxembourg = Universität Luxemburg
Maximilian Wolf
  • Fonction : Auteur
Otto-von-Guericke-Universität Magdeburg = Otto-von-Guericke University [Magdeburg]
Lennart Martens
Ghent University Hospital
VIB-UGent Center for Medical Biotechnology
Thilo Muth
BAM Federal Institute for Materials Research and Testing

Résumé

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 carried out the first community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluated 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 observed that variability at the peptide level was predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappeared at the protein group level. While differences were observed for predicted community composition, similar functional profiles were 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.

Domaines

Sciences du Vivant [q-bio]

Jean Armengaud  : Connectez-vous pour contacter le contributeur

https://hal.inrae.fr/hal-04468173

Soumis le : mardi 20 février 2024-13:38:45

Dernière modification le : lundi 16 décembre 2024-12:12:04

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Dates et versions

hal-04468173 , version 1 (20-02-2024)

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Tim van den Bossche, Benoit Kunath, Kay Schallert, Stephanie Schäpe, Paul Abraham, et al.. Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows. 2024. ⟨hal-04468173⟩

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