1
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Plancade S, Berland M, Blein-Nicolas M, Langella O, Bassignani A, Juste C. A combined test for feature selection on sparse metaproteomics data-an alternative to missing value imputation. PeerJ 2022; 10:e13525. [PMID: 35769140 PMCID: PMC9235818 DOI: 10.7717/peerj.13525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 05/11/2022] [Indexed: 01/18/2023] Open
Abstract
One of the difficulties encountered in the statistical analysis of metaproteomics data is the high proportion of missing values, which are usually treated by imputation. Nevertheless, imputation methods are based on restrictive assumptions regarding missingness mechanisms, namely "at random" or "not at random". To circumvent these limitations in the context of feature selection in a multi-class comparison, we propose a univariate selection method that combines a test of association between missingness and classes, and a test for difference of observed intensities between classes. This approach implicitly handles both missingness mechanisms. We performed a quantitative and qualitative comparison of our procedure with imputation-based feature selection methods on two experimental data sets, as well as simulated data with various scenarios regarding the missingness mechanisms and the nature of the difference of expression (differential intensity or differential presence). Whereas we observed similar performances in terms of prediction on the experimental data set, the feature ranking and selection from various imputation-based methods were strongly divergent. We showed that the combined test reaches a compromise by correlating reasonably with other methods, and remains efficient in all simulated scenarios unlike imputation-based feature selection methods.
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Affiliation(s)
- Sandra Plancade
- UR875 MIAT, Université fédérale de Toulouse, INRAE, Castanet-Tolosan, France
| | - Magali Berland
- Université Paris-Saclay, INRAE, MGP, Jouy en Josas, France
| | - Mélisande Blein-Nicolas
- Université Paris-Saclay, CNRS, INRAE, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France,Université Paris-Saclay, CNRS, INRAE, AgroParisTech, PAPPSO, Gif-sur-Yvette, France
| | - Olivier Langella
- Université Paris-Saclay, CNRS, INRAE, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France,Université Paris-Saclay, CNRS, INRAE, AgroParisTech, PAPPSO, Gif-sur-Yvette, France
| | - Ariane Bassignani
- Université Paris-Saclay, INRAE, MGP, Jouy en Josas, France,Université Paris-Saclay, CNRS, INRAE, AgroParisTech, PAPPSO, Gif-sur-Yvette, France
| | - Catherine Juste
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParis Tech, Jouy-en-Josas, France
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2
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Henry C, Bassignani A, Berland M, Langella O, Sokol H, Juste C. Modern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers—Example of Crohn’s Disease and Ulcerative Colitis Flare-Ups. Cells 2022; 11:cells11081340. [PMID: 35456018 PMCID: PMC9028112 DOI: 10.3390/cells11081340] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 11/16/2022] Open
Abstract
Thanks to the latest developments in mass spectrometry, software and standards, metaproteomics is emerging as the vital complement of metagenomics, to make headway in understanding the actual functioning of living and active microbial communities. Modern metaproteomics offers new possibilities in the area of clinical diagnosis. This is illustrated here, for the still highly challenging diagnosis of intestinal bowel diseases (IBDs). Using bottom-up proteomics, we analyzed the gut metaproteomes of the same twenty faecal specimens processed either fresh or after a two-month freezing period. We focused on metaproteomes of microbial cell envelopes since it is an outstanding way of capturing host and host–microbe interaction signals. The protein profiles of pairs of fresh and frozen-thawed samples were closely related, making feasible deferred analysis in a distant diagnosis centre. The taxonomic and functional landscape of microbes in diverse IBD phenotypes—active ulcerative colitis, or active Crohn’s disease either with ileo-colonic or exclusive colonic localization—differed from each other and from the controls. Based on their specific peptides, we could identify proteins that were either strictly overrepresented or underrepresented in all samples of one clinical group compared to all samples of another group, paving the road for promising additional diagnostic tool for IBDs.
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Affiliation(s)
- Céline Henry
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.H.); (A.B.)
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
| | - Ariane Bassignani
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.H.); (A.B.)
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
- MGP, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
| | - Magali Berland
- MGP, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
| | - Olivier Langella
- PAPPSO, GQE-Le Moulon, AgroParisTech, CNRS, INRAE, Université Paris-Saclay, 91190 Gif-sur-Yvette, France;
| | - Harry Sokol
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
- Gastroenterology Department, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Sorbonne Université, 75012 Paris, France
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, Service de Gastro-Entérologie et Nutrition, Hôpital Saint-Antoine, Direction de la Recherche Clinique et de l’Innovation (DRCI) de l’AP-HP, CEDEX 12, 75571 Paris, France
| | - Catherine Juste
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
- Correspondence: ; Tel.: +33-67-72-82-035
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3
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Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen MØ, 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. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nat Commun 2021; 12:7305. [PMID: 34911965 PMCID: PMC8674281 DOI: 10.1038/s41467-021-27542-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022] Open
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.
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Affiliation(s)
- Tim Van Den Bossche
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Benoit J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Kay Schallert
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Stephanie S Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ariane Bassignani
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Dirk Benndorf
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Microbiology, Department of Applied Biosciences and Process Technology, Anhalt University of Applied Sciences, Köthen, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Stephan Fuchs
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | | | - Timothy J Griffin
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Céline Henry
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Robert Heyer
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Pratik Jagtap
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Marlene Jensen
- Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA
| | - Catherine Juste
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Manuel Kleiner
- Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA
| | - Olivier Langella
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Theresa Lehmann
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Emma Leith
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bart Mesuere
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Guylaine Miotello
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Samantha L Peters
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Pedro T Queiros
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Udo Reichl
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Bernhard Y Renard
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
| | - Henning Schiebenhoefer
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
| | | | - Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Kathrin Trappe
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Jean-Pierre Trezzi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Integrated Biobank of Luxembourg, Luxembourg Institute of Health, 1, rue Louis Rech, L-3555, Dudelange, Luxembourg
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Pieter Verschaffelt
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6 avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Maximilian Wolf
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Lennart Martens
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
| | - Thilo Muth
- Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany
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4
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Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen MØ, 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. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nat Commun 2021; 12:7305. [PMID: 34911965 DOI: 10.1101/2021.03.05.433915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 11/24/2021] [Indexed: 05/21/2023] Open
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.
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Affiliation(s)
- Tim Van Den Bossche
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Benoit J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Kay Schallert
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Stephanie S Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ariane Bassignani
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Dirk Benndorf
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Microbiology, Department of Applied Biosciences and Process Technology, Anhalt University of Applied Sciences, Köthen, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Stephan Fuchs
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | | | - Timothy J Griffin
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Céline Henry
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Robert Heyer
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Pratik Jagtap
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Marlene Jensen
- Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA
| | - Catherine Juste
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Manuel Kleiner
- Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA
| | - Olivier Langella
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Theresa Lehmann
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Emma Leith
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bart Mesuere
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Guylaine Miotello
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Samantha L Peters
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Pedro T Queiros
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Udo Reichl
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Bernhard Y Renard
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
| | - Henning Schiebenhoefer
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
| | | | - Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Kathrin Trappe
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Jean-Pierre Trezzi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Integrated Biobank of Luxembourg, Luxembourg Institute of Health, 1, rue Louis Rech, L-3555, Dudelange, Luxembourg
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Pieter Verschaffelt
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6 avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Maximilian Wolf
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Lennart Martens
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
| | - Thilo Muth
- Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany
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5
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Bassignani A, Plancade S, Berland M, Blein-Nicolas M, Guillot A, Chevret D, Moritz C, Huet S, Rizkalla S, Clément K, Doré J, Langella O, Juste C. Benefits of Iterative Searches of Large Databases to Interpret Large Human Gut Metaproteomic Data Sets. J Proteome Res 2021; 20:1522-1534. [PMID: 33528260 DOI: 10.1021/acs.jproteome.0c00669] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The gut microbiota are increasingly considered as a main partner of human health. Metaproteomics enables us to move from the functional potential revealed by metagenomics to the functions actually operating in the microbiome. However, metaproteome deciphering remains challenging. In particular, confident interpretation of a myriad of MS/MS spectra can only be pursued with smart database searches. Here, we compare the interpretation of MS/MS data sets from 48 individual human gut microbiomes using three interrogation strategies of the dedicated Integrated nonredundant Gene Catalog (IGC 9.9 million genes from 1267 individual fecal samples) together with the Homo sapiens database: the classical single-step interrogation strategy and two iterative strategies (in either two or three steps) aimed at preselecting a reduced-sized, more targeted search space for the final peptide spectrum matching. Both iterative searches outperformed the single-step classical search in terms of the number of peptides and protein clusters identified and the depth of taxonomic and functional knowledge, and this was the most convincing with the three-step approach. However, iterative searches do not help in reducing variability of repeated analyses, which is inherent to the traditional data-dependent acquisition mode, but this variability did not affect the hierarchical relationship between replicates and all other samples.
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Affiliation(s)
- Ariane Bassignani
- Université Paris-Saclay, INRAE, MGP, 78350, Jouy-en-Josas, France.,Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.,Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France.,MaIAGE, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Sandra Plancade
- MaIAGE, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France.,INRAE, UR875 MIAT, F-31326 Castanet-Tolosan, France
| | - Magali Berland
- Université Paris-Saclay, INRAE, MGP, 78350, Jouy-en-Josas, France
| | - Melisande Blein-Nicolas
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Alain Guillot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Didier Chevret
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Chloé Moritz
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Sylvie Huet
- MaIAGE, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Salwa Rizkalla
- Sorbonne Université, Inserm, UMRS Nutrition et Obésités; approches systémiques, Paris 75006, France.,Assistance Publique Hôpitaux de Paris, Service de Nutrition, CRNH Ile-de-France, Pitié-Salpêtrière Hospital, Paris 75013, France
| | - Karine Clément
- Sorbonne Université, Inserm, UMRS Nutrition et Obésités; approches systémiques, Paris 75006, France.,Assistance Publique Hôpitaux de Paris, Service de Nutrition, CRNH Ile-de-France, Pitié-Salpêtrière Hospital, Paris 75013, France
| | - Joël Doré
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Olivier Langella
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Catherine Juste
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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6
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Arpesella C, Bam BB, Bassignani A, Cecchini S, Colombo G, Dekhissi H, Fresca Fantoni R, Giacomelli G, Lembo L, Maltoni G, Mandrioli G, Patrizii L, Sartorio C, Serra P, Togo V, Vilela E. Radon measurements in the Gran Sasso Underground Laboratory. Health Phys 1997; 72:629-632. [PMID: 9119689 DOI: 10.1097/00004032-199704000-00016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Systematic radon monitoring in the Gran Sasso Underground Laboratory was performed in order to determine the background radon contribution to the sophisticated experimental apparatus and to check health physics standards for the personnel. As expected, the radon concentrations were found to depend strongly on the ventilation in the three experimental halls. Considerable reductions in the radon concentrations were obtained in 1993, when fresh air was drawn into the laboratory through a pipe and exhaust air was routed into the highway tunnel.
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Affiliation(s)
- C Arpesella
- Laboratori Nazionali del Gran Sasso dell' Istituto Nazionale di Fisica Nucleare (INFN), L'Aquila, Italy
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7
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Bassignani A, Bam B, Colombo G, Dekhissi H, Fresca Fantoni R, Giacomelli G, Maltoni Giacomelli G, Sartorio C. Review of long term radon studies at the gran sasso underground laboratory. RADIAT MEAS 1995. [DOI: 10.1016/1350-4487(95)00183-f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Testa C, Desideri D, Meli MA, Roselli C, Bassignani A, Colombo G, Fantoni RF. Radiation protection and radioactive scales in oil and gas production. Health Phys 1994; 67:34-38. [PMID: 8200799 DOI: 10.1097/00004032-199407000-00004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Low specific-activity scales consisting of alkaline earth metal carbonates and sulfates are often present in some gaseous and liquid hydrocarbon plants. These scales contain a certain concentration of radium, uranium, and thorium which can cause a risk of gamma irradiation and internal radiocontamination when they must be mechanically removed. The gamma dose rates and the 238U, 232Th, 226Ra concentrations were determined in sludges, scales, and waters of some gas and oil hydrocarbon plants located in Italy, Congo, and Tunisia. 238U and 232Th concentrations were were low. The isotopes 238U and 234U resulted in radioactive equilibrium, while 232Th and 228Th were not always equilibrium. A rough correlation was found between the gamma dose rate and the 226Ra concentration. Some considerations and conclusions about radiation protection problems are pointed out.
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Affiliation(s)
- C Testa
- General Chemistry Institute, Urbino University, Italy
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9
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Testa C, Desideri D, Meli M, Roselli C, Bassignani A, Finazzi P. Determination of uranium, thorium and radium in waters, soils and muds around a uranium mine in decommissioning. Appl Radiat Isot 1994. [DOI: 10.1016/0969-8043(94)90079-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Testa C, Desideri D, Meli MA, Roselli C, Bassignani A, Finazzi PB. Radium, uranium and thorium concentrations in low specific activity scales and in waters of some oil and gas production plants. J Radioanal Nucl Chem 1993. [DOI: 10.1007/bf02134582] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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