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Paulhe N, Canlet C, Damont A, Peyriga L, Durand S, Deborde C, Alves S, Bernillon S, Berton T, Bir R, Bouville A, Cahoreau E, Centeno D, Costantino R, Debrauwer L, Delabrière A, Duperier C, Emery S, Flandin A, Hohenester U, Jacob D, Joly C, Jousse C, Lagree M, Lamari N, Lefebvre M, Lopez-Piffet C, Lyan B, Maucourt M, Migne C, Olivier MF, Rathahao-Paris E, Petriacq P, Pinelli J, Roch L, Roger P, Roques S, Tabet JC, Tremblay-Franco M, Traïkia M, Warnet A, Zhendre V, Rolin D, Jourdan F, Thévenot E, Moing A, Jamin E, Fenaille F, Junot C, Pujos-Guillot E, Giacomoni F. PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management. Metabolomics 2022; 18:40. [PMID: 35699774 PMCID: PMC9197906 DOI: 10.1007/s11306-022-01899-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/22/2022] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Accuracy of feature annotation and metabolite identification in biological samples is a key element in metabolomics research. However, the annotation process is often hampered by the lack of spectral reference data in experimental conditions, as well as logistical difficulties in the spectral data management and exchange of annotations between laboratories. OBJECTIVES To design an open-source infrastructure allowing hosting both nuclear magnetic resonance (NMR) and mass spectra (MS), with an ergonomic Web interface and Web services to support metabolite annotation and laboratory data management. METHODS We developed the PeakForest infrastructure, an open-source Java tool with automatic programming interfaces that can be deployed locally to organize spectral data for metabolome annotation in laboratories. Standardized operating procedures and formats were included to ensure data quality and interoperability, in line with international recommendations and FAIR principles. RESULTS PeakForest is able to capture and store experimental spectral MS and NMR metadata as well as collect and display signal annotations. This modular system provides a structured database with inbuilt tools to curate information, browse and reuse spectral information in data treatment. PeakForest offers data formalization and centralization at the laboratory level, facilitating shared spectral data across laboratories and integration into public databases. CONCLUSION PeakForest is a comprehensive resource which addresses a technical bottleneck, namely large-scale spectral data annotation and metabolite identification for metabolomics laboratories with multiple instruments. PeakForest databases can be used in conjunction with bespoke data analysis pipelines in the Galaxy environment, offering the opportunity to meet the evolving needs of metabolomics research. Developed and tested by the French metabolomics community, PeakForest is freely-available at https://github.com/peakforest .
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Affiliation(s)
- Nils Paulhe
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Cécile Canlet
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, 31300, Toulouse, France
| | - Annelaure Damont
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, 91191, Gif sur Yvette, France
| | - Lindsay Peyriga
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics & Fluxomics (ANR-11-INBS-0010), 31077, Toulouse, France
| | - Stéphanie Durand
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Catherine Deborde
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Sandra Alves
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, 91191, Gif sur Yvette, France
| | - Stephane Bernillon
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Thierry Berton
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Raphael Bir
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Alyssa Bouville
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, 31300, Toulouse, France
| | - Edern Cahoreau
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics & Fluxomics (ANR-11-INBS-0010), 31077, Toulouse, France
| | - Delphine Centeno
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Robin Costantino
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, 31300, Toulouse, France
| | - Laurent Debrauwer
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, 31300, Toulouse, France
| | - Alexis Delabrière
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, 91191, Gif sur Yvette, France
| | - Christophe Duperier
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Sylvain Emery
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Amelie Flandin
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Ulli Hohenester
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, 91191, Gif sur Yvette, France
| | - Daniel Jacob
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Charlotte Joly
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Cyril Jousse
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Marie Lagree
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Nadia Lamari
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Marie Lefebvre
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Claire Lopez-Piffet
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Bernard Lyan
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Mickael Maucourt
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Carole Migne
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Marie-Francoise Olivier
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, 91191, Gif sur Yvette, France
| | - Estelle Rathahao-Paris
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, 91191, Gif sur Yvette, France
| | - Pierre Petriacq
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Julie Pinelli
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Léa Roch
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Pierrick Roger
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, 91191, Gif sur Yvette, France
| | - Simon Roques
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Jean-Claude Tabet
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, 91191, Gif sur Yvette, France
| | - Marie Tremblay-Franco
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, 31300, Toulouse, France
| | - Mounir Traïkia
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Anna Warnet
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, 91191, Gif sur Yvette, France
| | - Vanessa Zhendre
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Dominique Rolin
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Fabien Jourdan
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, 31300, Toulouse, France
| | - Etienne Thévenot
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, 91191, Gif sur Yvette, France
| | - Annick Moing
- Université de Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 71 av E. Bourlaux, 33140, Villenave d'Ornon, France
| | - Emilien Jamin
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, 31300, Toulouse, France
| | - François Fenaille
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, 91191, Gif sur Yvette, France
| | - Christophe Junot
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, 91191, Gif sur Yvette, France
| | - Estelle Pujos-Guillot
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Franck Giacomoni
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France.
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Schwendner P, Bohmeier M, Rettberg P, Beblo-Vranesevic K, Gaboyer F, Moissl-Eichinger C, Perras AK, Vannier P, Marteinsson VT, Garcia-Descalzo L, Gómez F, Malki M, Amils R, Westall F, Riedo A, Monaghan EP, Ehrenfreund P, Cabezas P, Walter N, Cockell C. Beyond Chloride Brines: Variable Metabolomic Responses in the Anaerobic Organism Yersinia intermedia MASE-LG-1 to NaCl and MgSO 4 at Identical Water Activity. Front Microbiol 2018; 9:335. [PMID: 29535699 PMCID: PMC5835128 DOI: 10.3389/fmicb.2018.00335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/12/2018] [Indexed: 11/18/2022] Open
Abstract
Growth in sodium chloride (NaCl) is known to induce stress in non-halophilic microorganisms leading to effects on the microbial metabolism and cell structure. Microorganisms have evolved a number of adaptations, both structural and metabolic, to counteract osmotic stress. These strategies are well-understood for organisms in NaCl-rich brines such as the accumulation of certain organic solutes (known as either compatible solutes or osmolytes). Less well studied are responses to ionic environments such as sulfate-rich brines which are prevalent on Earth but can also be found on Mars. In this paper, we investigated the global metabolic response of the anaerobic bacterium Yersinia intermedia MASE-LG-1 to osmotic salt stress induced by either magnesium sulfate (MgSO4) or NaCl at the same water activity (0.975). Using a non-targeted mass spectrometry approach, the intensity of hundreds of metabolites was measured. The compatible solutes L-asparagine and sucrose were found to be increased in both MgSO4 and NaCl compared to the control sample, suggesting a similar osmotic response to different ionic environments. We were able to demonstrate that Yersinia intermedia MASE-LG-1 accumulated a range of other compatible solutes. However, we also found the global metabolic responses, especially with regard to amino acid metabolism and carbohydrate metabolism, to be salt-specific, thus, suggesting ion-specific regulation of specific metabolic pathways.
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Affiliation(s)
- Petra Schwendner
- School of Physics and Astronomy, UK Center for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Maria Bohmeier
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Petra Rettberg
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Kristina Beblo-Vranesevic
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Frédéric Gaboyer
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, Orléans, France
| | - Christine Moissl-Eichinger
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Alexandra K. Perras
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Department of Microbiology and Archaea, University of Regensburg, Regensburg, Germany
| | | | - Viggó T. Marteinsson
- MATIS - Prokaria, Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Reykjavik, Iceland
| | | | - Felipe Gómez
- Instituto Nacional de Técnica Aeroespacial - Centro de Astrobiología, Madrid, Spain
| | - Moustafa Malki
- Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Frances Westall
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, Orléans, France
| | - Andreas Riedo
- Leiden Observatory, Universiteit Leiden, Leiden, Netherlands
| | | | - Pascale Ehrenfreund
- Leiden Observatory, Universiteit Leiden, Leiden, Netherlands
- Space Policy Institute, George Washington University, Washington, DC, United States
| | - Patricia Cabezas
- Space Policy Institute, George Washington University, Washington, DC, United States
- European Science Foundation, Strasbourg, France
| | - Nicolas Walter
- Space Policy Institute, George Washington University, Washington, DC, United States
- European Science Foundation, Strasbourg, France
| | - Charles Cockell
- School of Physics and Astronomy, UK Center for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
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4
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van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, Klapa MI, Kohlbacher O, Koort K, Kultima K, Le Corguillé G, Moreno P, Moschonas NK, Neumann S, O'Donovan C, Reczko M, Rocca-Serra P, Rosato A, Salek RM, Sansone SA, Satagopam V, Schober D, Shimmo R, Spicer RA, Spjuth O, Thévenot EA, Viant MR, Weber RJM, Willighagen EL, Zanetti G, Steinbeck C. The future of metabolomics in ELIXIR. F1000Res 2017; 6. [PMID: 29043062 PMCID: PMC5627583 DOI: 10.12688/f1000research.12342.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/31/2017] [Indexed: 01/11/2023] Open
Abstract
Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the "Future of metabolomics in ELIXIR" was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases.
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Affiliation(s)
- Merlijn van Rijswijk
- ELIXIR-NL, Dutch Techcentre for Life Sciences, Utrecht, 3503 RM, Netherlands.,Netherlands Metabolomics Center, Leiden, 2333 CC, Netherlands
| | - Charlie Beirnaert
- ADReM, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, 2020, Belgium
| | - Christophe Caron
- ELIXIR-FR, French Institute of Bioinformatics, Gif-sur-Yvette, F-91198, France
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain
| | - Victoria Dominguez
- ELIXIR-FR, French Institute of Bioinformatics, Gif-sur-Yvette, F-91198, France
| | - Warwick B Dunn
- School of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UK
| | - Timothy M D Ebbels
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Franck Giacomoni
- INRA, UNH, Human Nutrition Unit, PFEM, Metabolism Exploration Platform, MetaboHUB-Clermont, Clermont Auvergne University, Clermont-Ferrand, F-63000, France
| | | | - Thomas Hankemeier
- Netherlands Metabolomics Center, Leiden, 2333 CC, Netherlands.,Leiden Academic Centre for Drug Research, Leiden University, Leiden, 2300 RA, Netherlands
| | - Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Jose L Izquierdo-Garcia
- Centro Nacional Investigaciones Cardiovasculares, Madrid, 28029, Spain.,CIBER de Enfermedades Respiratorias, Madrid, 28029 , Spain
| | | | - Fabien Jourdan
- Toxalim, UMR 1331, Université de Toulouse, Toulouse, F-31300, France
| | - Namrata Kale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Maria I Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, GR-26504, Greece
| | - Oliver Kohlbacher
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.,Department of Computer Science, University of Tübingen, Tübingen, 72076, Germany.,Center for Bioinformatics, University of Tübingen, Tübingen, 72076, Germany
| | - Kairi Koort
- The Centre of Excellence in Neural and Behavioural Sciences, Tallinn, Tallinn, 10120, Estonia.,School of Natural Sciences and Health, Tallinn University, 10120, 10120, Estonia
| | - Kim Kultima
- Department of Medical Sciences, Uppsala University, Uppsala, 752 36, Sweden
| | - Gildas Le Corguillé
- ELIXIR-FR, French Institute of Bioinformatics, Gif-sur-Yvette, F-91198, France.,UPMC, CNRS, FR2424, ABiMS, Station Biologique, Roscoff, F-29680, France
| | - Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Nicholas K Moschonas
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, GR-26504, Greece.,Department of General Biology, School of Medicine, University of Patras, Patras, GR-26504, Greece
| | - Steffen Neumann
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, 06120, Germany
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | | | - Philippe Rocca-Serra
- Oxford e-Research Centre, Engineering Science Department, University of Oxford, Oxford, OX1 3QG, UK
| | - Antonio Rosato
- Magnetic Resonance Center, Interuniversity Consortium for Magnetic Resonance on MetalloProteins, University of Florence, Florence, 50121, Italy
| | - Reza M Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Engineering Science Department, University of Oxford, Oxford, OX1 3QG, UK
| | - Venkata Satagopam
- Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Daniel Schober
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, 06120, Germany
| | - Ruth Shimmo
- The Centre of Excellence in Neural and Behavioural Sciences, Tallinn, Tallinn, 10120, Estonia.,School of Natural Sciences and Health, Tallinn University, 10120, 10120, Estonia
| | - Rachel A Spicer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, 752 36, Sweden
| | - Etienne A Thévenot
- CEA, LIST, Laboratory for Data Analysis and Systems' Intelligence, MetaboHUB, Gif-sur-Yvette, F-91191, France
| | - Mark R Viant
- School of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ralf J M Weber
- School of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UK
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, NL-6200, Netherlands
| | - Gianluigi Zanetti
- CRS4, Data Intensive Computing Group, Ed.1 POLARIS, Pula, 09010, Italy
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