Our NMR methodological developments for the analysis of complex mixtures address the needs of a broad community of users in metabolomics and fluxomics. We are particularly keen of applying non-conventional approaches which have the potential to surpass the 1D NMR that were typically used until today, both for untargeted profiling or for targeted quantitative analysis of complex biological mixtures. These methods include ultrafast 2D NMR at medium and high magnetic field, hyperpolarized NMR or an original “metabisotopomics” approach that combines metabolomics and isotopic information. As methodology development experts, we do not focus on a specific applicative question but we rather like to explore a broad variety of research questions with our collaborators in food science, food chemical safety, forensics, health or plant sciences. Our team is integrated in the MetaboHUB infrastructure that gathers French expertise centers in metabolomics and fluxomics, as well as in the Corsaire metabolomics platform (Biogenouest).
Current team members: Jérémy Marchand, Marie Delage, Julien Gauvreau, Serigne Seck, Pia Mayer (visiting student), Estelle Martineau, Virginie Silvestre, Jonathan Farjon, Marine Letertre*, Patrick Giraudeau*
Past members: Adrien le Guennec, Sumit Mishra, Marine Piou, Serge Akoka, Aurore Michaud
Collaborations (past and present): Catherine Deborde and Annick Moing (INRAe Bordeaux), Gaud Dervilly-Pinel and Yann Guitton (LABERCA Nantes), Olivier Grovel and Samuel Bertrand (Isomer Nantes), Jean-Charles Portais (INSA Toulouse), Pascal de Tullio (Univ. Liège), Cécile Canlet, Marie Tremblay-Franco (Axiom Toulouse), Julien Boccard (Université de Genève), Soren Engelsen (Univ. Copenhagen)
While NMR-based metabolomics studies are mostly performed with 1H 1D NMR, the latter suffers from severe and numerous peak overlaps characterizing complex biological samples. In this context, we are evaluating the potential of various fast 2D NMR approaches for a variety of targeted and untargeted metabolomics applications. Fast and repeatable 2D NMR methods are indispensable in this field, not only for the sake of high-throughput analysis, but also to reduce the impact of hardware instabilities and consequently improve the precision.
Multi-dimensional methods based on ultrafast 2D NMR or non-uniform sampling have already been applied in different fields through past and current collaborations. These applications include the targeted quantification of metabolites in extracts, or the untargeted metabolomics or lipidomics analysis of various samples, to address research questions in chemical food safety, chemical ecology, or health. This strategy is explored both at high field and at medium field (benchtop spectrometers). The complementarity and the redundance of our continuum of fast 2D NMR methods for metabolomics and lipidomics studies are also being explored in terms of metabolic coverage (by annotating all the signals detected by each method) and statistical performances (by putting these methods in competition through multiblock integration). The results prove that fast 2D NMR methods increase the confidence of metabolite annotation and increase statistical analyse performances thanks to reduced signal overlap.
References:
- B. Gouilleux, J. Marchand, B. Charrier, G. S. Remaud, P. Giraudeau, High-throughput authentication of edible oils with benchtop Ultrafast 2D NMR, Food Chemistry, 244, 153 (2018)
- A. Marchand, E. Martineau, Y. Guitton, B. Le Bizec, G. Dervilly-Pinel, P. Giraudeau, A multidimensional 1H NMR lipidomics workflow to address chemical food safety issues, Metabolomics 14, 60, (2018)
- P. Giraudeau, NMR-based metabolomics and fluxomics: developments and future prospects, Analyst, 145, 2457, (2020).
- B. Féraud, E. Martineau, J. Leenders, B. Govaerts, P. de Tullio, P. Giraudeau, Metabolomics, Combining rapid 2D NMR experiments with novel pre-processing workflows and MIC quality measures for metabolomics, Metabolomics, 16, 42 (2020)
- E. Martineau, J.-N. Dumez, P. Giraudeau, Fast quantitative 2D NMR for metabolomics and lipidomics: A tutorial, Magn. Reson. Chem.58, 390 (2020).
- M. Letertre, P. Giraudeau, P. De Tullio, Nuclear magnetic resonance spectroscopy in clinical metabolomics and personalized medicine: current challenges and perspectives, Frontiers in Molecular Biosciences 8, 698337 (2021)
- C. Praud, M. Letertre, A. Dey, J.N. Dumez, P. Giraudeau, Fast 2D NMR for Metabolomics, Fast 2D Solution-state NMR: concepts and Applications, 377-414 (2023)
- A. Michaud, S. Bertrand, S. Akoka, J. Farjon, E. Martineau, N. Ruiz, T. Robiou du Pont, O. Grovel, P. Giraudeau, Exploring the complementarity of fast multipulse and multidimensional NMR methods for metabolomics: a chemical ecology case study. Anal. Methods. 16, 5166-5177 (2024)
- P. Mayer, J. Marchand, M.P.M Letertre, J.-N. Dumez, S.B. Engelsen, P. Giraudeau. Multi-solvent suppression ultrafast 2D COSY for high-throughput wine screening. Magn. Reson. Chem. 64, 416-426 (2026)
Supported by: ANR (MetaboHub and Unicorn), ERC (SUMMIT CoG grant), NExT (REFRAMED project), Région Pays de la Loire (RFI Food 4.2 Lipidotool and PULSAR), Biogenouest (CORSAIRE platform)
Current team members: Wiktor Adamski, Benoît Charrier, Yuliia Horbenko, Marine Letertre*, Patrick Giraudeau*
Past team members: Arnab Dey, Jean-Nicolas Dumez, Clément Praud, Bertrand Plainchont, Elodie Lesquin, Victor Ribay
Collaborations (past and present): Catherine Deborde and Annick Moing (INRAe Bordeaux), Sami Jannin (Univ. Lyon), Mikaël Croyal, Bertrand Cariou and Samy Hadjadj (M-SHARK Nantes), Lydie Nadal-Desbarats, Camille Dupuy and Jérémy Monteiro (MTH Tours).
Hyperpolarization methods can boost the sensitivity of NMR by several orders of magnitude. In particular, dissolution dynamic nuclear polarization (D-DNP) can yield sensitivity improvements by 4 to 5 orders of magnitude in liquid-state NMR. While D-DNP has been widely applied to in vivo situations, its application to analytical chemistry, and in particular to the analysis of complex mixtures, remains limited. We are exploring the potential of D-DNP in this context, with the aim to improve its applicability to metabolomics.
Thanks to the methodological developments in D-DNP through the ERC SUMMIT project, we were able to demonstrate that hyperpolarized 13C NMR at natural abundance could be efficiently incorporated into a full metabolomics workflow on clinical samples. In the case of urine samples from patients with Chronic Kidney Disease, D-DNP 13C NMR was able to highlight complementary biomarkers compared to those detected by conventional 1H NMR. We are currently exploring the potential of these methods for a broad range of applications in metabolomics, in particular through the MetaHyp ANR project.
Key References:
- A. Dey, B. Charrier, E. Martineau, C. Deborde, E. Gandriau, A. Moing, D. Jacob, D. Eschenko, M. Schnell, R. Melzi, D. Kurzbach, M. Ceillier, Q. Chappuis, S.F. Cousin, J.G. Kempf, S. Jannin, J.-N. Dumez, and P. Giraudeau, Hyperpolarized NMR Metabolomics at Natural 13C Abundance, Anal. Chem. 92, 14867 (2020)
- V. Ribay, A. Dey, B. Charrier, C. Praud, J. Mandral, J.-N. Dumez, M. P. M. Letertre, P. Giraudeau, Hyperpolarized 13C NMR Spectroscopy of Urine Samples at Natural Abundance by Quantitative Dissolution Dynamic Nuclear Polarization, 62, e202302110 (2023).
- A. Dey, B. Charrier, V. Ribay, J.-N. Dumez, P. Giraudeau, Hyperpolarized 1H and 13C NMR Spectroscopy in a Single Experiment for Metabolomics., Anal. Chem, 2023, 95, 16861 (2023)
- V. Ribay, B. Charrier, M. Croyal, B. Cariou, S. Hadjadj, J. Boccard, C. Cannet, J.-N. Dumez, M.P.M. Letertre, P. Giraudeau. Hyperpolarized 13C NMR metabolomics of urine samples at natural abundance applied to chronic kidney disease. J. Am. Chem. Soc. 147, 644-650 (2025)
Supported by: ERC (CoG SUMMIT 814747), ANR (T-ERC SUMMIT, MetaHyp), MetaboHub
Current team members: Iris Hallégouet, Benoît Charrier, Patrick Giraudeau, Jonathan Farjon*
Collaborations : Olivier Gonçalves, (GEPEA, Nantes Univ.), Andre Simpson (Toronto Univ.)
Past team members : Dylan Bouillaud, Anastasiia Shvetsova
Understanding biological processes at an atomic level is essential, and observing living organisms in real time can provide valuable insights. Nuclear magnetic resonance (NMR) spectroscopy is a non-destructive and non-invasive technique capable of characterising the chemistry of living organisms during biochemical processes or after environmental stresses.
Investigating small living organisms in water presents different challenges (see Figure). Firstly, it is essential to maintain physiological conditions and flow NMR is a solution. Thus, the NMR spectrometer is connected to the physiological medium via capillaries and a pump, allowing the water containing the organisms to be circulated for study. Additionally, metabolites can be better detected by eliminating the major water signal and using fast repetition NMR, to enhance sensitivities. Furthermore, due to the complexity of multicellular organisms, NMR methods must be developed to overcome signal overlaps in 1D 1H spectra. Fast 2D NMR is particularly suitable for spreading the signals over two dimensions, making the analysis easier and is compatible with a shorter temporal scale for monitoring faster events.
The first microorganisms we investigate were microalgae as photosynthetic organisms with a very high biochemical diversity and a great ability to produce valuable biomass. Only a minor part of the millions of species living on earth are currently known, therefore microalgae form a subject with a strong investigation potential. Some microalgae such as Parachlorella Kessleri and Nannochloropsis Gaditana are known to accumulate lipids under nitrogen starving stress conditions. This behavior is interesting because it forms the basis of the third-generation biofuel production, a promising alternative energy.
In this context, we explored the potential of multiscale NMR for the analysis of microalgae cells and their lipidic extracts. The main challenge was to identify and quantify lipids in microalgae aqueous cultures. With this aim, high field NMR provides the best sensitivity and resolution to reveal lipids from extracts. Moreover, compact flow NMR was a suitable apparatus for real time online monitoring of bioprocesses such as the accumulation of lipids in microalgae during a nitrogen starvation in photobioreactor. We are starting a new project on the control of Phaeodactylum Tricornutum metabolism able to exudate lipids droplets in the cultivation medium for making energy. Moreover, in the field of space missions in limited room area, another project with the European Space Agency will be dedicated to show performances of compact flow NMR to control Limnospira Indica (Spirulina) to produce highly nutritive metabolites as food for astronauts.
The second application of this in vivo approach was using a high-field flow NMR instrument in combination with a fast and more sensitive 2D 1H-13C method. With this strategy, the goal was to monitor at natural abundance the metabolism of small crustaceans called Daphnia Magna. As a proof of concept they were investigated during anoxia and recovery to simulate how they could adapt and become more resilient to environmental changes.
References:
- D. Bouillaud, J. Farjon, O. Gonçalves, P. Giraudeau, Magnetic Resonance in Chemistry 2019, 57, 794–804.
- D. Bouillaud, V. Heredia, T. Castaing-Cordier, D. Drouin, B. Charrier, O. Gonçalves, J. Farjon, P. Giraudeau, Algal Research 2019, 43, 101624.
- D. Bouillaud, D. Drouin, B. Charrier, C. Jacquemmoz, J. Farjon, P. Giraudeau, O. Gonçalves, Process Biochemistry 2020, 93, 63–68.
- J. Farjon, K. Downey, K. Ronda, W. Wolff, K. Steiner, A. Simpson, Improved 2D 1H–13C NMR permits in vivo analysis of Daphnia magna metabolism without isotopic enrichment, Talanta 292 (2025) 127857.
Supported by Région Pays de la Loire (Pari scientifique AMER-METAL 2017-2020), CNRS (Projets interdisciplinarité RMN-(ME)2-TAL 2017-2020 et International Emerging Actions MUFINES 2021-2022), European Space Agency (SPACE_ALG 2024-2027), PEPR B-BEST (ALGADVANCE 2023 - 2028)
Current team members: Jonathan Farjon*
Collaboration : Denis Courtier-Murias, (LEE, Univ. G. Eiffel)
Emerging pollutants represent a special threat due to the broad and efficient application within modern technologies. The soil matrix is extremely complex and difficult to be studied in situ but also in the laboratory as soil constituents (minerals, organic matter and microbes) can interact with contaminants. The complexity of soils and the lack of powerful techniques capable to obtain detailed information of the phenomena occurring inside the soil hinder the complete understanding of processes controlling contaminant fate in soils. Under such a context, NMR is a valuable technique to identify, quantify and track molecular interactions.
The interaction between humic acid (HA) and coated nanoparticles (NPs) is critical in environmental sciences, especially for understanding the behaviour of NPs in natural waters. To reveal NPs interactions with HA, 1H 2D Multi-Exponential Transverse Relaxation spectroscopy. Analysis showed the biggest effect on two chemical shift regions, corresponding to lipids and carbohydrates from Pahokee Peat HA, revealing that smaller molecules within these regions exhibit the most significant changes in T2 values upon the addition of coated NPs.
Poly- and perfluoroalkyl substances (PFAS) are used in a wide range of industrial, agricultural and domestic applications, being most of them toxic in cocktail, persistent in the environment and bioaccumulative. The very recent investigation of different PFAS alone and in mixture was started in soil of increasing complexity by combining NMR spectroscopy, relaxometry and imaging.
References:
Dia, M., Farjon, J., Raveleau, C., Simpson, A., Peyneau, P.-E., Béchet, B. and Courtier-Murias, D. (2025). Magn Reson Chem, 63: 63-48.
Supported by CNRS (Projets PFAS CHEMIST 2023-2025), ANR (COMMON 2025 - 2029)
Current team members: Marie Delage, Julien Gauvreau, Jérémy Marchand, Benoît Charrier, Virginie Silvestre, Estelle Martineau, Patrick Giraudeau, Marine Letertre*
Past members: Clément Rosique, Victor Ribay
Collaborations (past and present): Gaud Dervilly, Yann Guitton and Anne-Lise Royer (PF MELISA, LABERCA, Nantes), Daniel Jacob (INRAE Bordeaux), Cécile Canlet et Marie Tremblay-Franco (Axiom Toulouse), Mikaël Croyal and Chloé Cloteau (M-SHARK Nantes), Bertrand Cariou et Samy Hadjadj (Equipe IV Institut du Thorax), Antoine Roquilly and Ana Motos Galera (CR2TI UMR1064), Julien Boccard (Geneva University), Claire Cannet (Bruker Biospin)
We are currently exploring the applicability of the non-conventional NMR methods developed in the team (fast 2D, hyperpolarised and benchtop NMR) to clinical and pre-clinical metabolomics to overcome the current limitations of commonly used 1D 1H NMR-based metabolomics. These methods that are aimed to be more sensitive, resolved and/or accessible, taken in combination with the advantages of Mass Spectrometry (MS), have the potential to strengthen personalized medicine. Fast 2D NMR methods allow to spread signals over two dimensions, which have proven to facilitate metabolite annotation and statistical performances (see section 8) and has been successfully applied to various biofluids and animal tissues. Hyperpolarized NMR provides a major sensitivity enhancement and dissolution-dynamic nuclear polarization (d-DNP) coupled to NMR was successfully applied for the first time to a metabolomic study on urine samples from CKD patients.
Furthermore, we are gaining in competences in the targeted profiling of pre-clinical biomarkers for specifics pathologies. For instance, 1D 1H lipoprotein NMR profiles were recorded on plasma from patients with type 2 diabetes administrated with either placebo or alirocumab, provided key results showing that NMR (1) gives absolute concentrations which highly correlate with the ones obtained by other clinical analysis (Fig. a) and (2) gives access to biomarkers, such as LDL-triglycerides and -ApoB100 (among many others lipoproteins-related biomarkers), which are very complicated to obtain by MS or clinical tests without numerous and tedious sample manipulations (Fig. b). Several projects are currently ongoing following the combined targeted analysis of these pre-clinical biomarkers and untargeted analysis of plasma samples issued from large clinical studies (N between 100 to 1700 samples).
Key References:
- M. Letertre, P. Giraudeau, P. De Tullio, Nuclear magnetic resonance spectroscopy in clinical metabolomics and personalized medicine: current challenges and perspectives, Front. Mol. Biosc. 8, 698337 (2021).
- V. Ribay, A. Dey, B. Charrier, C. Praud, J. Mandral, J.N. Dumez, M. Letertre, P. Giraudeau, Hyperpolarized 13C NMR Spectroscopy of Urine Samples at Natural Abundance by Quantitative Dissolution Dynamic Nuclear Polarization, Angew. Chem. Int. Ed. 62 (27), e202302110 (2023).
- V. Ribay, C. Praud, M. Letertre, J.N. Dumez, P. Giraudeau, Hyperpolarized NMR metabolomics, Curr. Opin. in Chem.l Biol. 74, 102307 (2023)
- Cariou, B., Thys, A., Oliveira, A.R., Letertre, M.P.M., Guyomarch, B., Carpentier, M., Cannet, C., Morcel, P., Ernould, A., Flet, L., et al. (2025). Effect of alirocumab on postprandial hyperlipidaemia in patients with type 2 diabetes: A randomized, double-blind, placebo-controlled, cross-over trial. Diabetes Obes. Metab. 27, 3006–3016.
- Ribay, V., Charrier, B., Croyal, M., Cariou, B., Hadjadj, S., Boccard, J., Cannet, C., Dumez, J.-N., Letertre, M.P.M.*, and Giraudeau, P.* (2025). Hyperpolarized 13C NMR Metabolomics of Urine Samples at Natural Abundance Applied to Chronic Kidney Disease. J. Am. Chem. Soc. 147, 644–650.
- Rodrigues Oliveira, A., Chevalier, C., Wargny, M., Pakulska, V., Caradeuc, C., Cloteau, C., Letertre, M.P.M., Giraud, N., Bertho, G., Bigot–Corbel, E., et al. (2025). Methylglyoxal-Induced Glycation of Plasma Albumin: From Biomarker Discovery to Clinical Use for Prediction of New-Onset Diabetes in Individuals with Prediabetes. Clin. Chem. 71, 688–699.
Supported by: PULSAR, AMI NExT Ingérierie-Santé (REFRAMED), ANR JCJC (UNICORN), ANR PRCE (ANR METAHYP), ANR (MetaboHub), Biogenouest (CORSAIRE platform), and European Research Council (CoG SUMMIT)
Current team members: Marie Delage, Julien Gauvreau, Sérigne Seck, Estelle Martineau, Patrick Giraudeau, Marine Letertre*
Collaborations (past and present): Gaud Dervilly, Yann Guitton and Anne-Lise Royer (LABERCA Nantes), Cécile Canlet et Marie Tremblay-Franco (Axiom Toulouse), Mikaël Croyal and Chloé Cloteau (M-SHARK Nantes), Bertrand Cariou et Samy Hadjadj (Equipe IV Institut du Thorax), Julien Boccard (Geneva University)
To benchmark the newly proposed methods described in the previous section, between each other’s but also with the other analytical foundation of metabolomics, namely mass spectrometry, multiblock integration is being applied. This approach aims at putting different datasets acquired on different methods in competition, to highlight which one is able to capture the largest part of variations between two classes of compounds and to improve biological interpretation.
Encouraging results were obtained for the use of fast 2D NMR methods in metabolomics by analysing plasma extracts from pigs exposed or not to bisphenol A (BPA) and analysed by 1D 1H NMR and three fast 2D NMR methods. The latter are those which capture the largest part of the inter-sample variability, probably thanks to less signal overlap compared to 1D 1H NMR, allowing cleaner signal integration and thus sample discrimination through statistical analyses(Fig.). This statistical comparison of several methods also allows to merge the discriminative performance of each method and thus obtain more discriminant models. This strategy is currently being applied through several of our projects with applications in chemical food safety and health.
Key References:
- M. Letertre, G. Dervilly, P. Giraudeau, Combined nuclear magnetic resonance spectroscopy and mass spectremtry approaches for metabolomics, Analytical Chemistry 93, 1, 500-518 (2020)
- Cloteau, C., Letertre, M.P.M., Boccard, J., Pezzolato, M., Bozzetta, E., Le Bizec, B., and Dervilly Pinel, G. (2026). A comprehensive metabolomics approach for enhanced detection of growth promoting practices in livestock. Food Addit. Contam. Part A 0, 1–14.
Supported by: PULSAR, AMI NExT Ingérierie-Santé (REFRAMED), ANR JCJC (UNICORN), ANR PRCE (ANR METAHYP), ANR (MetaboHub), Biogenouest (CORSAIRE platform), and European Research Council (CoG SUMMIT)