{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001371","ANALYSIS_ID":"AN002289","VERSION":"1","CREATED_ON":"May 5, 2020, 12:52 pm"},

"PROJECT":{"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"},

"STUDY":{"STUDY_TITLE":"Untargeted metabolomics of Quercus ilex acorns","STUDY_TYPE":"LC-MSE analysis","STUDY_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 the 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"},

"SUBJECT":{"SUBJECT_TYPE":"Plant","SUBJECT_SPECIES":"Quercus ilex","TAXONOMY_ID":"58334"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"B F_POS C",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"B F_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"B_POS C1",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"B_POS C1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"B_POS C2",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"B_POS C2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"B_POS C3",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"B_POS C3.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"B_POS C4",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"B_POS C4.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"B_POS C5",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"B_POS C5.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"BOL1_POS C",
"Factors":{"Mixture":"BOL"},
"Additional sample data":{"RAW_FILE_NAME":"BOL1_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"BOL2_POS C",
"Factors":{"Mixture":"BOL"},
"Additional sample data":{"RAW_FILE_NAME":"BOL2_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"BOL3_POS C",
"Factors":{"Mixture":"BOL"},
"Additional sample data":{"RAW_FILE_NAME":"BOL3_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"BR_POS C",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"BR_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"BR_POS C_1",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"BR_POS C_1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MAD1_POS C",
"Factors":{"Mixture":"MAD"},
"Additional sample data":{"RAW_FILE_NAME":"MAD1_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MAD2_POS C",
"Factors":{"Mixture":"MAD"},
"Additional sample data":{"RAW_FILE_NAME":"MAD2_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MAD3_POS C",
"Factors":{"Mixture":"MAD"},
"Additional sample data":{"RAW_FILE_NAME":"MAD3_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MIX FEN F_POS C",
"Factors":{"Mixture":"Phenolics mixture"},
"Additional sample data":{"RAW_FILE_NAME":"MIX FEN F_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MIX FEN_POS C",
"Factors":{"Mixture":"Phenolics mixture"},
"Additional sample data":{"RAW_FILE_NAME":"MIX FEN_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"NTC1_POS C",
"Factors":{"Mixture":"NTC"},
"Additional sample data":{"RAW_FILE_NAME":"NTC1_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"NTC2_POS C",
"Factors":{"Mixture":"NTC"},
"Additional sample data":{"RAW_FILE_NAME":"NTC2_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"NTC3_POS C",
"Factors":{"Mixture":"NTC"},
"Additional sample data":{"RAW_FILE_NAME":"NTC3_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"POL1_POS C",
"Factors":{"Mixture":"POL"},
"Additional sample data":{"RAW_FILE_NAME":"POL1_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"POL2_POS C",
"Factors":{"Mixture":"POL"},
"Additional sample data":{"RAW_FILE_NAME":"POL2_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"POL3_POS C",
"Factors":{"Mixture":"POL"},
"Additional sample data":{"RAW_FILE_NAME":"POL3_POS C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"QC MIX2_POS C01",
"Factors":{"Mixture":"Quality Control mixture"},
"Additional sample data":{"RAW_FILE_NAME":"QC MIX2_POS C01.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"QC MIX2_POS C02",
"Factors":{"Mixture":"Quality Control mixture"},
"Additional sample data":{"RAW_FILE_NAME":"QC MIX2_POS C02.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"QC MIX2_POS C03",
"Factors":{"Mixture":"Quality Control mixture"},
"Additional sample data":{"RAW_FILE_NAME":"QC MIX2_POS C03.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"QC MIX2_POS C04",
"Factors":{"Mixture":"Quality Control mixture"},
"Additional sample data":{"RAW_FILE_NAME":"QC MIX2_POS C04.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"B F_NEG C",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"B F_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"B_NEG C1",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"B_NEG C1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"B_NEG C2",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"B_NEG C2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"B_NEG C3",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"B_NEG C3.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"B_NEG C4",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"B_NEG C4.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"B_NEG C5",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"B_NEG C5.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"BOL1_NEG C",
"Factors":{"Mixture":"BOL"},
"Additional sample data":{"RAW_FILE_NAME":"BOL1_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"BOL2_NEG C",
"Factors":{"Mixture":"BOL"},
"Additional sample data":{"RAW_FILE_NAME":"BOL2_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"BOL3_NEG C",
"Factors":{"Mixture":"BOL"},
"Additional sample data":{"RAW_FILE_NAME":"BOL3_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"BR_NEG C",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"BR_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"BR_NEG C_1",
"Factors":{"Mixture":"Blank"},
"Additional sample data":{"RAW_FILE_NAME":"BR_NEG C_1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MAD1_NEG C",
"Factors":{"Mixture":"MAD"},
"Additional sample data":{"RAW_FILE_NAME":"MAD1_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MAD2_NEG C",
"Factors":{"Mixture":"MAD"},
"Additional sample data":{"RAW_FILE_NAME":"MAD2_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MAD3_NEG C",
"Factors":{"Mixture":"MAD"},
"Additional sample data":{"RAW_FILE_NAME":"MAD3_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MIX FEN F_NEG C",
"Factors":{"Mixture":"Phenolics mixture"},
"Additional sample data":{"RAW_FILE_NAME":"MIX FEN F_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MIX FEN_NEG C",
"Factors":{"Mixture":"Phenolics mixture"},
"Additional sample data":{"RAW_FILE_NAME":"MIX FEN_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"NTC1_NEG C",
"Factors":{"Mixture":"NTC"},
"Additional sample data":{"RAW_FILE_NAME":"NTC1_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"NTC2_NEG C",
"Factors":{"Mixture":"NTC"},
"Additional sample data":{"RAW_FILE_NAME":"NTC2_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"NTC3_NEG C",
"Factors":{"Mixture":"NTC"},
"Additional sample data":{"RAW_FILE_NAME":"NTC3_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"POL1_NEG C",
"Factors":{"Mixture":"POL"},
"Additional sample data":{"RAW_FILE_NAME":"POL1_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"POL2_NEG C",
"Factors":{"Mixture":"POL"},
"Additional sample data":{"RAW_FILE_NAME":"POL2_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"POL3_NEG C",
"Factors":{"Mixture":"POL"},
"Additional sample data":{"RAW_FILE_NAME":"POL3_NEG C.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"QC MIX2_NEG C01",
"Factors":{"Mixture":"Quality Control mixture"},
"Additional sample data":{"RAW_FILE_NAME":"QC MIX2_NEG C01.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"QC MIX2_NEG C02",
"Factors":{"Mixture":"Quality Control mixture"},
"Additional sample data":{"RAW_FILE_NAME":"QC MIX2_NEG C02.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"QC MIX2_NEG C03",
"Factors":{"Mixture":"Quality Control mixture"},
"Additional sample data":{"RAW_FILE_NAME":"QC MIX2_NEG C03.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"QC MIX2_NEG C04",
"Factors":{"Mixture":"Quality Control mixture"},
"Additional sample data":{"RAW_FILE_NAME":"QC MIX2_NEG C04.mzXML"}
}
],
"COLLECTION":{"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_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)"},

"SAMPLEPREP":{"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"},

"CHROMATOGRAPHY":{"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.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity H-Class","COLUMN_NAME":"C18 column (2.1×100 mm, 1.7 µm, Waters, Milford, USA)","FLOW_RATE":"0.450 mL min−1","COLUMN_TEMPERATURE":"45","SOLVENT_A":"0.1 % formic acid in Milli-Q water","SOLVENT_B":"0.1 % formic acid in methanol","SAMPLE_INJECTION":"5","ANALYTICAL_TIME":"17 min","TIME_PROGRAM":"17 min"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Agroforestry and Plant Biochemistry, Proteomics and Systems Biology","DETECTOR_TYPE":"QTOF","DATA_FORMAT":".raw and .mzXML"},

"MS":{"INSTRUMENT_NAME":"Waters Synapt G2 XS QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","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).","COLLISION_ENERGY":"4.00 eV","FRAGMENT_VOLTAGE":"High-ernergy ramp of 10.00 to 45.00 eV","FRAGMENTATION_METHOD":"MSE","MS_RESULTS_FILE":"ST001371_AN002289_Results.txt UNITS:abundance Has m/z:Yes Has RT:Yes RT units:Minutes"}

}