MTBLS56: Quantitative metabolic profiles of tomato flesh and seeds during fruit development: complementary analysis with ANN and PCA (NMR data).

Abstract

Global approach to characterize changes in metabolic profiles in two interdependent tissues Seed and Flesh from the same tomato fruits during tomato fruit development. Tomato, an essential crop in terms of economic importance and nutritional quality, is also used as a model species for all fleshy fruits and for genomics of Solanaceae. Tomato fruit quality at harvest is a direct function of its metabolite content, which in turn is a result of many physiological changes during fruit development. The aim of the work reported here was to develop a global approach to characterize changes in metabolic profiles in two interdependent tissues from the same tomato fruits. Absolute quantification data of compounds in flesh and seeds from 8 days to 45 days post anthesis (DPA) were obtained through untargeted (proton nuclear magnetic resonance, 1H-NMR).

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 Authors: Annick Moing, Daniel Jacob

  Release date: 24-Sep-2013

 Status: Public

Organism(s)

Solanum lycopersicum

  Study Design

untargeted metabolites

PO:whole plant development stage

EFO:portion of plant tissue

CHMO:nuclear magnetic resonance spectroscopy

EFO:metabolomic profiling

  Experimental Factors

Tissue

Development stage

Protocol Description
Sample collection Tomato (Solanum lycopersicum L., cv Ailsa Craig) plants were grown in a growth chamber with a 15-h-day (25 °C)/9-h-night (20 °C) cycle with an irradiance of 400 µmol/m2/s and 75–80% humidity. Individual flowers were tagged at anthesis (flower opening). The fruit number per truss was limited to six. Changes in fruit diameter were measured every 5 days on 12–36 fruits. The fruits were further selected according to size, color, and position on the truss (elimination of the first and last fruit of the truss), and collected at six times expressed in days post anthesis (DPA):
- division phase (8 DPA), [Plant ontology FF.01]
- transition between division and expansion phases (12 DPA), [Plant ontology FF.02]
- expansion phase (20 DPA), [Plant ontology FF.03]
- mature green stage (35 DPA) [Plant ontology FF.04]
- and red ripe fruit (45 DPA). [Plant ontology FR.04]

For each stage, three pools of fruit were harvested from 15 plants:
- 12 fruit pools for 8 and 12 DPA
- and 6 fruit pools for 20–45 DPA

Each fruit pool was collected from at least six plants. For each pool, the locular content was rapidly separated into seeds and locular tissue. Flesh samples were constituted of all the fruit tissues, including the locular tissue, without the seeds. All samples were rapidly frozen and ground in liquid nitrogen and stored at 80 °C until use for metabolite profiling.
Extraction Polar metabolites were extracted according to Moing et al.[1]. Briefly, for each sample, two subsamples (50 mg DW each) were extracted successively with 80% ethanol–water, 50% ethanol–water (v/v) and water at 80 °C for 15 min. The supernatants were combined, dried under vacuum and lyophilized.

Ref:
[1] Moing A., Maucourt M., Renaud C., Gaudillère M., Brouquisse R., Lebouteiller B., Gousset-Dupont A., Vidal J., Granot D., Denoyes-Rothan B., Lerceteau-Kohler E., Rolin D. (2004). Quantitative metabolic profiling by 1-dimensional 1H-NMR analyses: application to plant genetics and functional genomics. Funct. Plant Biol. 31, 889–902. doi:10.1071/FP04066
NMR sample The dried extracts were titrated with KOD to pH 6 in 400 mM potassium phosphate buffer in D2O, and lyophilized again. The dried titrated extracts were stored in darkness under vacuum at room temperature before 1H-NMR analysis within one week. Each dried titrated extract was solubilised in 0.5 ml D2O containing the sodium salt of (trimethylsilyl)propionic-2,2,3,3-d4 acid (TSP) at a final concentration of 0.01% for chemical shift calibration. Ethylene diamine tetraacetic acid disodium salt was added at a final concentration of 20 mM to chelate paramagnetic cations and improve spectrum resolution, especially in the citrate region.
NMR spectroscopy 1H-NMR spectra were recorded at 500.162 MHz on a Bruker Avance spectrometer using a 5 mm inverse probe and the ERETIC method [1] for quantification as described previously [2]. Ethylene diamine tetraacetic acid disodium salt was added at a final concentration of 20 mM to chelate paramagnetic cations and improve spectrum resolution, especially in the citrate region.

Ref:
[1] Akoka S, Barantin L, Trierweiler M. Concentration Measurement by Proton NMR Using the ERETIC Method. Anal Chem. 1999 Jul 1;71(13):2554-7. doi:10.1021/ac981422i. PMID:21662801
[2] Moing A., Maucourt M., Renaud C., Gaudillère M., Brouquisse R., Lebouteiller B., Gousset-Dupont A., Vidal J., Granot D., Denoyes-Rothan B., Lerceteau-Kohler E., Rolin D. (2004). Quantitative metabolic profiling by 1-dimensional 1H-NMR analyses: application to plant genetics and functional genomics. Funct. Plant Biol. 31, 889–902. doi:10.1071/FP04066
NMR assay 64 scans of 32K data points were acquired with a spectral width of 6000 Hz, acquisition time of 2.73 s, 90° pulse angle and recycle delays of 25 s. An automation procedure (automatic shimming and automatic sample loading) requiring about 40 min per sample was used for data acquisition.
Data transformation Preliminary data processing was carried out with XWINNMR software (Bruker Biospin, Karlsruhe, Germany). FIDs were Fourier transformed (0.3 Hz line broadening), manually phased and baseline corrected. The resulting spectra were aligned by shifting TSP signal to zero.
Metabolite identification Metabolite concentrations in the NMR tube were calculated using the metabolite mode of AMIX software (version 3.5.6, Bruker) for calculation of resonance areas, followed by data export to Excel software. Quantification was carried out using a glucose calibration curve and the proton amount corresponding to each resonance for all compounds except fructose, glutamine and glutamate. These metabolites were quantified using specific calibration curves of the corresponding compound. Metabolite concentrations in each sample were then calculated based on concentrations in the NMR tube and sample dry weight. The concentration of each organic or amino acid was expressed as g of the acid form per weight unit.

1H-1H COSY (2D-Homonuclear Correlation Spectroscopy) experiments were carried out to verify the identity of known compounds and to determine if signals from unknown compounds truly corresponded to signals from different compounds. Each COSY spectrum was obtained using the cosyqf45 pulse program (COSY using a 45° read pulse), relaxation delay of 1 s, 90° pulse of 9.75 μs, spectral width 6000 and 5000 Hz for f1 and f2 dimensions respectively, 4 K datapoints in f2, 256 in f1. The concentration of NMR unknown compounds was calculated on the assumption that the measured resonance corresponded to one proton and using an arbitrary molecular weight of 100 Da.
Source Name Organism Variant Organism part Protocol REF Sample Name Tissue Development stage Unit
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig fruit Sample collection S8.1.1 Seed 8 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S8.2.1 Seed 8 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S8.3.1 Seed 8 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S8.123.2 Seed 8 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S12.1.1 Seed 12 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S12.1.2 Seed 12 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S12.2.1 Seed 12 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S12.2.2 Seed 12 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S12.3.1 Seed 12 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S12.3.2 Seed 12 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S20.1.1 Seed 20 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S20.1.2 Seed 20 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S20.2.1 Seed 20 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S20.2.2 Seed 20 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S20.3.1 Seed 20 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S20.3.2 Seed 20 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S35.1.1 Seed 35 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S35.1.2 Seed 35 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S35.2.1 Seed 35 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S35.2.2 Seed 35 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S35.3.1 Seed 35 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S35.3.2 Seed 35 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S45.1.2 Seed 45 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S45.2.2 Seed 45 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig seed Sample collection S45.3.2 Seed 45 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F8.1.1 Pericarp 8 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F8.1.2 Pericarp 8 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F8.2.1 Pericarp 8 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F8.2.2 Pericarp 8 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F8.3.1 Pericarp 8 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F12.1.1 Pericarp 12 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F12.1.2 Pericarp 12 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F12.2.1 Pericarp 12 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F12.2.2 Pericarp 12 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F12.3.1 Pericarp 12 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F12.3.2 Pericarp 12 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F20.1.1 Pericarp 20 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F20.1.2 Pericarp 20 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F20.2.1 Pericarp 20 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F20.2.2 Pericarp 20 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F20.3.1 Pericarp 20 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F20.3.2 Pericarp 20 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F35.1.1 Pericarp 35 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F35.1.2 Pericarp 35 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F35.2.1 Pericarp 35 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F35.2.2 Pericarp 35 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F35.3.1 Pericarp 35 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F35.3.2 Pericarp 35 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F45.1.1 Pericarp 45 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F45.1.2 Pericarp 45 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F45.2.2 Pericarp 45 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F45.2.1 Pericarp 45 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F45.3.1 Pericarp 45 day
Tomato2006 Solanum lycopersicum Solanum lycopersicum cv. Ailsa Craig pericarp Sample collection F45.3.2 Pericarp 45 day

Assay 

Assay file name: a_tomato_2006_metabolite profiling_NMR spectroscopy.txt
Measurement: metabolite profiling
Technology: NMR spectroscopy
Platform: Bruker

Instrumentation

Sample Name Protocol REF Extraction Method Extract Name Protocol REF NMR tube type Solvent Sample pH Temperature Unit Labeled Extract Name Label Protocol REF Instrument NMR Probe Number of transients Pulse sequence name Magnetic field strength Unit Acquisition Parameter Data File Protocol REF NMR Assay Name Free Induction Decay Data File Protocol REF Normalization Name Derived Spectral Data File Protocol REF Data Transformation Name Metabolite Assignment File
S8.1.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S8.1.1 Data transformation S8.1.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S8.2.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S8.2.1 Data transformation S8.2.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S8.3.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S8.3.1 Data transformation S8.3.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S8.123.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S8.123.2 Data transformation S8.123.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S12.1.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S12.1.1 Data transformation S12.1.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S12.1.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S12.1.2 Data transformation S12.1.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S12.2.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S12.2.1 Data transformation S12.2.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S12.2.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S12.2.2 Data transformation S12.2.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S12.3.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S12.3.1 Data transformation S12.3.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S12.3.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S12.3.2 Data transformation S12.3.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S20.1.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S20.1.1 Data transformation S20.1.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S20.1.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S20.1.2 Data transformation S20.1.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S20.2.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S20.2.1 Data transformation S20.2.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S20.2.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S20.2.2 Data transformation S20.2.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S20.3.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S20.3.1 Data transformation S20.3.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S20.3.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S20.3.2 Data transformation S20.3.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S35.1.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S35.1.1 Data transformation S35.1.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S35.1.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S35.1.2 Data transformation S35.1.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S35.2.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S35.2.1 Data transformation S35.2.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S35.2.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S35.2.2 Data transformation S35.2.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S35.3.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S35.3.1 Data transformation S35.3.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S35.3.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S35.3.2 Data transformation S35.3.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S45.1.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S45.1.2 Data transformation S45.1.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S45.2.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S45.2.2 Data transformation S45.2.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
S45.3.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay S45.3.2 Data transformation S45.3.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F8.1.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F8.1.1 Data transformation F8.1.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F8.1.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F8.1.2 Data transformation F8.1.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F8.2.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F8.2.1 Data transformation F8.2.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F8.2.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F8.2.2 Data transformation F8.2.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F8.3.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F8.3.1 Data transformation F8.3.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F12.1.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F12.1.1 Data transformation F12.1.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F12.1.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F12.1.2 Data transformation F12.1.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F12.2.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F12.2.1 Data transformation F12.2.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F12.2.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F12.2.2 Data transformation F12.2.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F12.3.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F12.3.1 Data transformation F12.3.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F12.3.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F12.3.2 Data transformation F12.3.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F20.1.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F20.1.1 Data transformation F20.1.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F20.1.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F20.1.2 Data transformation F20.1.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F20.2.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F20.2.1 Data transformation F20.2.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F20.2.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F20.2.2 Data transformation F20.2.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F20.3.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F20.3.1 Data transformation F20.3.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F20.3.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F20.3.2 Data transformation F20.3.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F35.1.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F35.1.1 Data transformation F35.1.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F35.1.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F35.1.2 Data transformation F35.1.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F35.2.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F35.2.1 Data transformation F35.2.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F35.2.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F35.2.2 Data transformation F35.2.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F35.3.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F35.3.1 Data transformation F35.3.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F35.3.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F35.3.2 Data transformation F35.3.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F45.1.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F45.1.1 Data transformation F45.1.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F45.1.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F45.1.2 Data transformation F45.1.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F45.2.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F45.2.2 Data transformation F45.2.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F45.2.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F45.2.1 Data transformation F45.2.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F45.3.1 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F45.3.1 Data transformation F45.3.1.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
F45.3.2 Extraction NMR sample 5 mm standard D2O 6 25 degree Celsius hydrogen molecular entity NMR spectroscopy Bruker AVANCE 500 MHz spectrometer 5 mm inverse 64 11.7 UO:tesla NMR assay F45.3.2 Data transformation F45.3.2.dx Metabolite identification m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
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File
metexplore_mapping.json
F12.1.1.dx
F12.1.2.dx
F12.2.1.dx
F12.2.2.dx
F12.3.1.dx
F12.3.2.dx
F20.1.1.dx
F20.1.2.dx
F20.2.1.dx
F20.2.2.dx
F20.3.1.dx
F20.3.2.dx
F35.1.1.dx
F35.1.2.dx
F45.3.2.dx
F8.1.1.dx
F8.1.2.dx
F45.3.1.dx
F45.2.2.dx
F45.2.1.dx
F45.1.2.dx
F8.2.1.dx
F8.2.2.dx
F8.3.1.dx
S12.1.1.dx
S12.1.2.dx
S12.2.1.dx
S12.2.2.dx
S12.3.1.dx
S12.3.2.dx
S20.1.1.dx
S20.1.2.dx
S20.2.1.dx
S20.2.2.dx
S20.3.1.dx
S20.3.2.dx
F45.1.1.dx
F35.3.2.dx
F35.3.1.dx
S35.1.1.dx
S35.1.2.dx
S35.2.1.dx
S35.2.2.dx
S35.3.1.dx
S35.3.2.dx
S45.1.2.dx
S45.2.2.dx
S45.3.2.dx
F35.2.2.dx
F35.2.1.dx
S8.1.1.dx
S8.123.2.dx
S8.2.1.dx
S8.3.1.dx
i_Investigation.txt
XXm_tomato_2006_metabolite profiling_NMR spectroscopy.tsv
a_tomato_2006_metabolite profiling_NMR spectroscopy.txt
m_tomato_2006_metabolite profiling_NMR spectroscopy_v2_maf.tsv
m_tomato_2006_metabolite profiling_NMR spectroscopy.tsv
audit
s_Tomato_2006.txt

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Validations marked with (*) have been allowed by the MetaboLights Curators.
Click here for the detailed description of Validations.
Condition Status Description Requirement Group Message
PASSES Study Title MANDATORY STUDY OK
PASSES Study Description MANDATORY STUDY OK
PASSES Study text successfully parsed OPTIONAL STUDY OK
PASSES Study Contact(s) have listed email MANDATORY CONTACT OK
PASSES Sample(s) MANDATORY SAMPLES OK
PASSES Sample Name consistency check MANDATORY ASSAYS OK
PASSES Publication(s) associated with this Study MANDATORY PUBLICATION OK
PASSES Minimal Experimental protocol MANDATORY PROTOCOLS OK
PASSES Comprehensive Experimental protocol OPTIONAL PROTOCOLS OK
PASSES Extraction protocol description MANDATORY PROTOCOLS OK
PASSES Data transformation protocol description MANDATORY PROTOCOLS OK
PASSES Metabolite Identification protocol description MANDATORY PROTOCOLS OK
PASSES NMR sample protocol description MANDATORY PROTOCOLS OK
PASSES NMR spectroscopy protocol description MANDATORY PROTOCOLS OK
PASSES NMR assay protocol description MANDATORY PROTOCOLS OK
PASSES Sample Collection protocol description MANDATORY PROTOCOLS OK
PASSES Protocols text successfully parsed OPTIONAL PROTOCOLS OK
PASSES Organism name MANDATORY ORGANISM OK
PASSES Organism part MANDATORY ORGANISM OK
PASSES Study Factors MANDATORY FACTORS OK
PASSES Assay platform information OPTIONAL ASSAYS OK
FAILS Assay has raw files referenced MANDATORY FILES Assay 1 has raw files missing. Column(s): free induction decay data file, has no files referenced
FAILS Assay referenced raw files detection in filesystem MANDATORY FILES No Assay raw files are referenced
PASSES Assay(s) MANDATORY ASSAYS OK
PASSES All Assays have Metabolite Assignment File (MAF) referenced OPTIONAL FILES OK
PASSES Metabolite Assignment File (MAF) is present in Study folder MANDATORY FILES OK
PASSES Metabolite Assignment File (MAF) has correct format MANDATORY FILES OK
PASSES Metabolite Identification File (MAF) content MANDATORY FILES OK
PASSES ISA-Tab investigation file check MANDATORY ISATAB OK

Pathways - Assay 



MetExplore Pathways Mapping

Name DB Identifier Mapped Metabolite(s)