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Services description

The Facility supports studies of plant functional genomics, genetics, pathology, ecophysiology and systems biology for regional, national and international research programs. It is also used for the study of plant-derived products and for pharmacological approaches.



The samples are sent to the Facility under the form specified in the Detailed Analysis List or in the Service Form.

lcms  webfig

Biochemical phenotyping of plant samples

  • Automated analyses on microplates: total proteins, starch, sucrose, glucose, fructose, malate, fumarate (under proviso), citrate, total free amino acids, glutamate, proline, chlorophylls a and b (from one extraction)
  • Quantification of amino acids by UHPLC-fluorimetry
  • Analysis of phenolics (HPLC-UV/Visible, LC-MS ion trap, LC-NMR)

Metabolomic profiling-Metabolome of plant samples 

  • Quantification of major polar metabolites by 1H-NMR of polar extracts
  • Acquisition and analysis of metabolomic fingerprints by 1H-NMR of polar extracts
  • Acquisition and analysis of metabolomic fingerprints by LC-Orbitrap-MS of semi-polar extracts
  • Lipid profiling-Lipidome of plant samples 

Lipid analysis (phospholipids, neutral lipids, sphingolipids…)

  • Analysis and quantification of fatty acids by GC-FID or GC-MS
  • Analysis and quantification of lipids by GC-FID, GC-MS or TLC
  • Analysis of waxes and lipid polymers by GC-MS and GC-FID
  • Relative quantification of plant sphingolipid by LC-MS
  • Acquisition and analysis of lipidomic profiles by MS/MS and LC-Qtrap-MS

Compound identification 

  • Structural analysis of polyphenols (using MS and NMR)


  • Automated measurement of central-metabolism enzymes (glycolysis, TCA cycle, Calvin-pentose phosphates, sucrose metabolism, nitrogen assimilation)
  • Acquisition of spectra for the measurement of 13C isotopic enrichments on fractions, for metabolic flux measurement


Technological developments - R&D

  • Robotisation of sample grinding and weighing,
  • Obtention of rapid metabolic signatures by high-throughput 1H-NMR,
  • Ultra-fast 2D NMR and 13C NMR developments, in collaboration,
  • Quantitative MS-based analysis of intermediary compounds of central metabolism, 
  • Lipidomics of plant samples,
  • Transfer of high-throughput metabolic phenotyping to diverse models,
  • Identification of compounds using LC-SPE-NMR and multidimensional NMR,
  • Constitution of a library/database of reference compounds and corresponding spectra,
  • Bioinformatic tools for NMR spectra processing, handling and sharing,
  • Tools for data handling, sharing and mining.


Open use of analytical equipment 

  • Training and technical support
  • Use of :


 Equipment designation

 High-density Metabolomics-Metabolic profiling
  • LCMS MicrOTOf-Q (Bruker)
  • UHPLC-LTQ/Orbitrap (Thermo)
  • UHPLC-Fluo-DAD (Dionex)
  • 500 MHz NMR spectrometer AVANCE III
  • pH meter for NMR metabolomic/metabolic profiling extracts (Mettler Toledo)
  • Robot Titration BTpH
 High-throughput metabolic phenotyping
  • Robots de pipetage Starlet (Hamilton)
  • Microplate readers (Safas)
  • Microplate reader Fluo Xenius (Safas)
  • Tissue Lyser II grinding system (Retsch)
  • Capper-decapper for screw cap tubes (Hamilton)
  • Broyeur Geno-grinder (2 equipments)
  • ADC2 (Camag)
  • UV lamp for visualization of TLC spots (Camag)
  • GC-FID system (Agilent)
  • GC-MS system (Agilent)
  • UPLC-Qtrap 6500 (Agilent/Sciex)
  • UHPLC-LTQ/Orbitrap (Thermo)
 Polyphenols- Structural identification
  • 600 MHz NMR spectrometer (Avance III, Bruker) equipped with an LC and SPE interface
  • LC-MSn ion-trap system (Bruker)
  • UV-Vis Spectrometer CARY 300 (Varian)

Related services 

Expertise and analysis of results


Examplary open data produced by the Facility

Open data title Data type Database Identifier Corresponding publication or dataset authors

Impaired cell growth under ammonium stress explained by modeling the energy cost of vacuole expansion in tomato leaves

Targeted metabolomics, enzymatic and ion data Recherche Data Gouv
DOI: 10.15454/BL3GYM
Poucet et al. The Plant Journal (2022)

Metabolomic responses of maize leaf to progressive controlled chilling 

NMR and LC-MS datasets and metadata Data INRAE
Urrutia et al. Plant, Cell & Environment (2021) 
Metabolome of tomato fruit pericarp of gbp1-c CRISPR mutant NMR and LC-MS datasets and metadata Data INRAE
Musseau et al. Plant Cell (2020) 32:3188
1H-NMR profiling of wheat spikelet samples 1H-NMR spectra INRA Dataverse
Deborde et al. Metabolomics (2019) 15:28
Maize grains and maize grain-based diets dataset LC-MS and NMR datasets Zenodo
Bernillon et al. (2018) Metabolomics 14:36
Representative 1H NMR spectra of extract of trout feed 1H NMR spectra Zenodo
Roques et al. Metabolomics (2018) 14:155
Plasma NMR metabolomic of rainbow trout fed diets with marine and plant ingredients 1H NMR spectra & biochemical datasets Zenodo
Gatesoupe et al. Aquaculture Nutrition (2018) 24:1563
Maize leaf, field conditions, AMAIZING project 1H-NMR spectra & Quantitative data MERY-B
Lamari et al. Metabolomics (2018) 14:132
Quantitative metabolic profiles of tomato flesh and seeds during fruit development 1H-NMR spectra & Quantitative data Metabolights
Mounet et al. Metabolomics (2007) 3: 273

Bordeaux Metabolome Facility promotes spectra and data deposition into reference repositories such as MetaboLights, zenodo or Data INRAE. It can provide advice or help for data uploading.


Results and confidentiality

The results are communicated to the user in printed or electronic format. Without any user’s answer within ten days from receipt, the results are considered as accepted and the service as closed. However, the Facility members remain at the disposal of users for any question, and help in result valorisation or data diffusion.

The Facility makes every effort to ensure:  

  • a high  level of equipment performance through maintenance schedule and regular monitoring,
  • accompanying users (feasibility study, training for hands-on use, interaction during the service provision, expertise),
  • raw data backup during the provision of service.

The Facility has an obligation of means and not an obligation of results. Therefore the Facility should not be held responsible for any mistake done by users or unexpected equipment failure.

Confidentiality: The facility undertakes not to disclose any information concerning the project except the user’s name, its unit of origin and the project title. Upon request the project title can be kept confidential.