Summary of Study ST001371

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000937. The data can be accessed directly via it's Project DOI: 10.21228/M8K97X This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001371
Study TitleUntargeted metabolomics of Quercus ilex acorns
Study TypeLC-MSE analysis
Study SummaryUPLC-MSE analysis of samples from Quercus ilex acorns flour. The objective of the study is to obtain a metabolomic profile of several acorns from different trees. This phytochemical analysis and characterization will be a base for the identification of bioactive, antinutritional, or toxic compounds and traceability analysis.
Institute
Universidad de Córdoba
DepartmentDepartment Biochemistry and Molecular Biology
LaboratoryAgroforestry and Plant Biochemistry, Proteomics and Systems Biology
Last NameLópez-Hidalgo
First NameCristina
AddressCampus de Rabanales; Edificio C6, Planta Baja
Emailn12lohic@uco.es
Phone626894948
Submit Date2020-04-25
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2020-06-01
Release Version1
Cristina López-Hidalgo Cristina López-Hidalgo
https://dx.doi.org/10.21228/M8K97X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000937
Project DOI:doi: 10.21228/M8K97X
Project Title:Untargeted metabolomics of Quercus ilex acorns
Project Type:LC-MSE analysis
Project Summary:UPLC-MSE analysis of samples from Quercus ilex acorns flour. The objective of the study is to obtain a metabolomic profile of several acorns from different trees. This phytochemical analysis and characterization will be a base for identification of bioactive, antinutritional, or toxic compounds and traceability analysis.
Institute:Universidad de Córdoba
Department:Department Biochemistry and Molecular Biology
Laboratory:Agroforestry and Plant Biochemistry, Proteomics and Systems Biology
Last Name:López-Hidalgo
First Name:Cristina
Address:Campus de Rabanales; Edificio C6, Planta Baja
Email:n12lohic@uco.es
Phone:626894948
Funding Source:This work was supported by the University of Cordoba and financial support from the Spanish Ministry of Economy and Competitiveness (Project BIO2015-64737-R2).
Publications:Phytochemical composition and variability among Quercus ilex acorns determined by NIRS and MS-based approaches

Subject:

Subject ID:SU001445
Subject Type:Plant
Subject Species:Quercus ilex
Taxonomy ID:58334

Factors:

Subject type: Plant; Subject species: Quercus ilex (Factor headings shown in green)

mb_sample_id local_sample_id Mixture
SA099809B_NEG C3Blank
SA099810B_NEG C2Blank
SA099811B_NEG C1Blank
SA099812B_NEG C4Blank
SA099813B_NEG C5Blank
SA099814B F_POS CBlank
SA099815BR_NEG CBlank
SA099816BR_NEG C_1Blank
SA099817B F_NEG CBlank
SA099818B_POS C5Blank
SA099819BR_POS CBlank
SA099820B_POS C3Blank
SA099821B_POS C2Blank
SA099822B_POS C1Blank
SA099823BR_POS C_1Blank
SA099824B_POS C4Blank
SA099803BOL1_POS CBOL
SA099804BOL3_POS CBOL
SA099805BOL1_NEG CBOL
SA099806BOL2_NEG CBOL
SA099807BOL2_POS CBOL
SA099808BOL3_NEG CBOL
SA099825MAD2_POS CMAD
SA099826MAD1_POS CMAD
SA099827MAD2_NEG CMAD
SA099828MAD3_NEG CMAD
SA099829MAD3_POS CMAD
SA099830MAD1_NEG CMAD
SA099831NTC3_POS CNTC
SA099832NTC3_NEG CNTC
SA099833NTC2_NEG CNTC
SA099834NTC1_NEG CNTC
SA099835NTC1_POS CNTC
SA099836NTC2_POS CNTC
SA099843MIX FEN F_NEG CPhenolics mixture
SA099844MIX FEN_NEG CPhenolics mixture
SA099845MIX FEN_POS CPhenolics mixture
SA099846MIX FEN F_POS CPhenolics mixture
SA099837POL3_NEG CPOL
SA099838POL1_NEG CPOL
SA099839POL2_NEG CPOL
SA099840POL1_POS CPOL
SA099841POL3_POS CPOL
SA099842POL2_POS CPOL
SA099847QC MIX2_NEG C03Quality Control mixture
SA099848QC MIX2_NEG C04Quality Control mixture
SA099849QC MIX2_NEG C02Quality Control mixture
SA099850QC MIX2_POS C01Quality Control mixture
SA099851QC MIX2_POS C03Quality Control mixture
SA099852QC MIX2_POS C04Quality Control mixture
SA099853QC MIX2_POS C02Quality Control mixture
SA099854QC MIX2_NEG C01Quality Control mixture
Showing results 1 to 52 of 52

Collection:

Collection ID:CO001440
Collection Summary:Sample collection: Mature acorns from holm oak (Quercus ilex L. subsp.ballota [Desf.] Samp.) were collected from four different trees located in Aldea de Cuenca (province of Cordoba, Andalusia, Spain). All acorns were picked at the optimal harvest maturity window on the same day. Sorting, disinfection, and storage of healthy acorns were conducted according to Bonner & Vozzo, (1987). Acorn flour preparation: Healthy acorns (20 units per tree) were scarified with a knife by making transversal and longitudinal cuts, thus permitting the pericarp to be rapidly removed. Flour was prepared by seed (without seed coat) grinding with liquid nitrogen in a blade mill (IKA Dry Mill Basic A10) until a powder was obtained (Valero Galván, Jorrín Novo, Cabrera, et al., 2012). Flour was lyophilized and then macerated in a mortar until a fine powder was obtained. Samples were stored at 4 ºC in within a desiccator, in darkness, until NIRS analysis or metabolite extraction.
Sample Type:Acorns
Storage Conditions:Room temperature

Treatment:

Treatment ID:TR001460
Treatment Summary:Mature acorns from holm oak (Quercus ilex L. subsp.ballota [Desf.] Samp.) were collected from nine different trees. From these, four were selected for metabolomic analysis (POL, BOL, NTC, and MAD).
Plant Growth Location:Aldea de Cuenca (province of Cordoba, Andalusia, Spain)

Sample Preparation:

Sampleprep ID:SP001453
Sampleprep Summary:Metabolites were extracted from acorn flour as described by Valledor et al., (2014), with minor modifications. 600 µL of ice-cold methanol: chloroform: water (5:2:2) was added to 50 mg of acorn flour, mixed by vortexing, and the mixture sonicated (ultrasonic bath, 40 kHZ for 10 min). After centrifugation (4 oC, 4 min, 20,000 × g), the pellet was once more extracted with 200 µL of cold methanol: chloroform: water (5:2:2). The two supernatants were combined and vacuum dried at 30 oC (Speedvac, Eppendorf Vacuum Concentrator Plus/5301). Dried extracts were reconstituted in methanol, centrifuged at 20,000 × g for 10 min, filtered through 0.22 µm PTPE membranes (Thermo Scientific, MA, USA) and filtrate collected in 1.5 mL LC/MS certified sample vials.
Processing Storage Conditions:Room temperature
Extract Storage:On ice
Sample Resuspension:Methanol

Combined analysis:

Analysis ID AN002288 AN002289
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity H-Class Waters Acquity H-Class
Column Waters C18 (100 x 2.1mm,1.7um) Waters C18 (100 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Waters Synapt G2 XS Waters Synapt G2 XS
Ion Mode POSITIVE NEGATIVE
Units abundance abundance

Chromatography:

Chromatography ID:CH001681
Chromatography Summary:MS analysis was conducted in an ultra-performance liquid chromatography (UPLC Acquity H-Class, Waters, Milford, USA) coupled to a quadrupole time of flight (QTof) G2-XS mass spectrometer (Waters, Milford, USA). The chromatographic separation was carried out in a C18 column (2.1×100 mm, 1.7 µm, Waters, Milford, USA), kept at 45 °C. The injection volume was 5 µL, and the flow rate set at 0.450 mL min−1. Mobile phases consisted of 0.1 % formic acid in Milli-Q water (A) and methanol (B). The gradient elution profile was as follow (time, % B): 0 min, 2% B; 0.25 min, 2 % B; 12.25 min, 99 % B; 13.0 min, 99 % B; 13.01 min; 2 % B; 17.00 min; 2 % B and then the column was equilibrated for 5 min prior to each analysis.
Instrument Name:Waters Acquity H-Class
Column Name:Waters C18 (100 x 2.1mm,1.7um)
Column Temperature:45
Flow Rate:0.450 mL min−1
Sample Injection:5
Solvent A:100% water; 0.1% formic acid
Solvent B:100% methanol; 0.1% formic acid
Analytical Time:17 min
Time Program:17 min
Chromatography Type:Reversed phase

MS:

MS ID:MS002132
Analysis ID:AN002288
Instrument Name:Waters Synapt G2 XS
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS analysis was conducted in an ultra-performance liquid chromatography (UPLC Acquity H-Class, Waters, Milford, USA) coupled to a quadrupole time of flight (QTof) G2-XS mass spectrometer (Waters, Milford, USA). The chromatographic separation was carried out in a C18 column (2.1×100 mm, 1.7 µm, Waters, Milford, USA), kept at 45 °C. The injection volume was 5 µL, and the flow rate set at 0.450 mL min−1. Mobile phases consisted of 0.1 % formic acid in Milli-Q water (A) and methanol (B). The gradient elution profile was as follow (time, % B): 0 min, 2% B; 0.25 min, 2 % B; 12.25 min, 99 % B; 13.0 min, 99 % B; 13.01 min; 2 % B; 17.00 min; 2 % B and then the column was equilibrated for 5 min prior to each analysis. The MS acquisition was performed in negative and positive ionization modes in a scan range from m/z 100 to 1200 and time acquisition of 0 to 17 min. The analysis type performed was accurate mass screening on MSE data with a low collision energy of 4.00 eV and a high-energy ramp of 10.00 to 45.00 eV. The capillary and cone voltage were set at 2.50 kV and 40 V, respectively. The desolvation gas was set to 600 L h−1, the cone gas set to 50 L h−1 and the source and desolvation temperature was set to 100 °C and 250 °C, respectively. For automated accurate mass measurement, a solution of leucine-enkephalin (200 ng mL−1) in methanol: water (50:50) with 0.1% formic acid was used as lock mass and pumped at a flow rate of 5 µL min−1. The molecule of leucine-enkephalin (m/z 556.2766 in ESI+ and m/z 554.262 in ESI−) was used for recalibrating the mass axis and ensuring a robust accurate mass measurement at any time. For continuous quality assurance and to provide confidence in the data, quality control (QC), a mix prepared from equal volumes of all the samples was injected between every three samples in the batch along with methanol as a blank run to correct a drift of the raw signal intensity during the analysis. All the data acquired were exported by Waters UNIFI software in order to analyze by the software Progenesis QI (Nonlinear Dynamics, Newcastle, United Kingdom).
Ion Mode:POSITIVE
Collision Energy:4.00 eV
Fragment Voltage:High-ernergy ramp of 10.00 to 45.00 eV
Fragmentation Method:MSE
  
MS ID:MS002133
Analysis ID:AN002289
Instrument Name:Waters Synapt G2 XS
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS analysis was conducted in an ultra-performance liquid chromatography (UPLC Acquity H-Class, Waters, Milford, USA) coupled to a quadrupole time of flight (QTof) G2-XS mass spectrometer (Waters, Milford, USA). The chromatographic separation was carried out in a C18 column (2.1×100 mm, 1.7 µm, Waters, Milford, USA), kept at 45 °C. The injection volume was 5 µL, and the flow rate set at 0.450 mL min−1. Mobile phases consisted of 0.1 % formic acid in Milli-Q water (A) and methanol (B). The gradient elution profile was as follow (time, % B): 0 min, 2% B; 0.25 min, 2 % B; 12.25 min, 99 % B; 13.0 min, 99 % B; 13.01 min; 2 % B; 17.00 min; 2 % B and then the column was equilibrated for 5 min prior to each analysis. The MS acquisition was performed in negative and positive ionization modes in a scan range from m/z 100 to 1200 and time acquisition of 0 to 17 min. The analysis type performed was accurate mass screening on MSE data with a low collision energy of 4.00 eV and a high-energy ramp of 10.00 to 45.00 eV. The capillary and cone voltage were set at 2.50 kV and 40 V, respectively. The desolvation gas was set to 600 L h−1, the cone gas set to 50 L h−1 and the source and desolvation temperature was set to 100 °C and 250 °C, respectively. For automated accurate mass measurement, a solution of leucine-enkephalin (200 ng mL−1) in methanol: water (50:50) with 0.1% formic acid was used as lock mass and pumped at a flow rate of 5 µL min−1. The molecule of leucine-enkephalin (m/z 556.2766 in ESI+ and m/z 554.262 in ESI−) was used for recalibrating the mass axis and ensuring a robust accurate mass measurement at any time. For continuous quality assurance and to provide confidence in the data, quality control (QC), a mix prepared from equal volumes of all the samples was injected between every three samples in the batch along with methanol as a blank run to correct a drift of the raw signal intensity during the analysis. All the data acquired were exported by Waters UNIFI software in order to analyze by the software Progenesis QI (Nonlinear Dynamics, Newcastle, United Kingdom).
Ion Mode:NEGATIVE
Collision Energy:4.00 eV
Fragment Voltage:High-ernergy ramp of 10.00 to 45.00 eV
Fragmentation Method:MSE
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