The source code provided in this repository is available under the CC BY-SA 4.0 license.
It is part of the submitted paper in the Metabolomics Journal, entitled :
"Optimizing 1D 1H-NMR profiling of plant samples for high throughput analysis: extract preparation, standardization, automation and spectra processing"
Authors: Catherine Deborde 1,2%, Jean-Xavier Fontaine 3%, Daniel Jacob 1,2, Adolfo Botana 4, Valérie Nicaise 5, Florence Forget 5, Sylvain Lecomte 3, Cédric Decourtil 3, Amar Hamadeh 3, François Mesnard 3, Annick Moing 1,2, Roland Molinié 3
- 1 UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine Bordeaux, av Edouard Bourlaux, F-33140 Villenave d’Ornon, France
- 2 Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine Bordeaux, av Edouard Bourlaux, F-33140 Villenave d’Ornon, France
- 3 BIOPI - EA 3900, Univ. Picardie Jules Verne, 33 rue Saint Leu, F-80039 Amiens, France
- 4 JEOL UK, Silver Court, Watchmead Road, Welwyn Garden City, AL7 1LT, UK
- 5 UR MycSA,INRA, Centre INRA de Nouvelle Aquitaine Bordeaux, av Edouard Bourlaux, F-33140 Villenave d’Ornon, France
- % These two authors have contributed equally to this work
For each sample:
- 1 - MeOD signal (from the extraction solution) is used for the field/frequency lock
- 2 - Shims are optimized using the TopShim program for gradient shimming (Z1 to Z6) followed by trimming of (Z1, Z2, X, Y) shims.
- 3 - The 90°pulse length is determined with pulsecal module.
To use this AU program, the file “au_metabo” must be loaded in the folder /opt/topspin(version)/exp/stan/nmr/au/src/user/.
It’s also necessary to registered the matrix of shim after 3D shim with name : “bestMeOD”.
You must also load the “tunemetabo” file in the folder /opt/topspin(version)/exp/stan/nmr/lists/group/
The determination of the two selected spectra quality criteria full width at half maximum (FWHM) for TMSP and MeOD resonances are obtained with the au_TMSPMeOH program