{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001825","ANALYSIS_ID":"AN002961","VERSION":"1","CREATED_ON":"May 11, 2021, 11:53 am"},

"PROJECT":{"PROJECT_TYPE":"Human nephropathy in CKD obese patients","PROJECT_SUMMARY":"Obesity is a global pandemic with an increase prevalence over the years. This condition elevates the risk of developing cardiovascular diseases, hypertension and renal pathologies, like chronic kidney disease (CKD). In the present study, the metabolomic and the lipidomic profiles of CKD obese patients were analyzed comparing with obese subjects without CKD. Subsequently, CKD obese patients underwent bariatric surgery and the effect of surgery in the CKD progression of these subjects was evaluated. Serum and urine were measured by LC-MS and GC-HRAM equipment.","INSTITUTE":"University Rey Juan Carlos","FIRST_NAME":"Borja","ADDRESS":"Avenida de Atenas S/N, Alcorcón, Madrid, 28922, Spain","EMAIL":"borja.lanzon@urjc.es","PHONE":"663692554","PROJECT_TITLE":"Metabolomic and lipidomic profiles of CKD in obese patients in serum and urine (part 2 of 3)","LAST_NAME":"Lanzon"},

"STUDY":{"STUDY_TITLE":"Metabolomic and lipidomic profiles of CKD in obese patients in serum and urine (part 2 of 3)","STUDY_SUMMARY":"Obesity is a global pandemic with an increase prevalence over the years. This condition elevates the risk of developing cardiovascular diseases, hypertension and renal pathologies, like chronic kidney disease (CKD). In the present study, the metabolomic and the lipidomic profiles of CKD obese patients were analyzed comparing with obese subjects without CKD. Subsequently, CKD obese patients underwent bariatric surgery and the effect of surgery in the CKD progression of these subjects was evaluated. Serum and urine were measured by LC-MS and GC-HRAM equipment.","INSTITUTE":"University Rey Juan Carlos","DEPARTMENT":"Basics Science of Health","LAST_NAME":"Lanzon","FIRST_NAME":"Borja","ADDRESS":"Avenida de Atenas S/N, Alcorcón, Madrid, 28922, Spain","EMAIL":"borja.lanzon@urjc.es","NUM_GROUPS":"3","TOTAL_SUBJECTS":"35","STUDY_COMMENTS":"Serum GC-HRAM data: part 2 of 3.","STUDY_TYPE":"Human nephropathy in CKD obese patients","PHONE":"663692554"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","AGE_OR_AGE_RANGE":"53 ± 15","WEIGHT_OR_WEIGHT_RANGE":"116 ± 25","GENDER":"Male and female"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"O1",
"Factors":{"Genotype":"O"},
"Additional sample data":{"RAW_FILE_NAME":"O1"}
},
{
"Subject ID":"-",
"Sample ID":"O2",
"Factors":{"Genotype":"O"},
"Additional sample data":{"RAW_FILE_NAME":"O2"}
},
{
"Subject ID":"-",
"Sample ID":"O3",
"Factors":{"Genotype":"O"},
"Additional sample data":{"RAW_FILE_NAME":"O3"}
},
{
"Subject ID":"-",
"Sample ID":"O4",
"Factors":{"Genotype":"O"},
"Additional sample data":{"RAW_FILE_NAME":"O4"}
},
{
"Subject ID":"-",
"Sample ID":"O5",
"Factors":{"Genotype":"O"},
"Additional sample data":{"RAW_FILE_NAME":"O5"}
},
{
"Subject ID":"-",
"Sample ID":"O6",
"Factors":{"Genotype":"O"},
"Additional sample data":{"RAW_FILE_NAME":"O6"}
},
{
"Subject ID":"-",
"Sample ID":"O7",
"Factors":{"Genotype":"O"},
"Additional sample data":{"RAW_FILE_NAME":"O7"}
},
{
"Subject ID":"-",
"Sample ID":"O8",
"Factors":{"Genotype":"O"},
"Additional sample data":{"RAW_FILE_NAME":"O8"}
},
{
"Subject ID":"-",
"Sample ID":"O9",
"Factors":{"Genotype":"O"},
"Additional sample data":{"RAW_FILE_NAME":"O9"}
},
{
"Subject ID":"-",
"Sample ID":"O10",
"Factors":{"Genotype":"O"},
"Additional sample data":{"RAW_FILE_NAME":"O10"}
},
{
"Subject ID":"-",
"Sample ID":"O11",
"Factors":{"Genotype":"O"},
"Additional sample data":{"RAW_FILE_NAME":"O11"}
},
{
"Subject ID":"-",
"Sample ID":"O12",
"Factors":{"Genotype":"O"},
"Additional sample data":{"RAW_FILE_NAME":"O12"}
},
{
"Subject ID":"-",
"Sample ID":"O13",
"Factors":{"Genotype":"O"},
"Additional sample data":{"RAW_FILE_NAME":"O13"}
},
{
"Subject ID":"-",
"Sample ID":"OD1",
"Factors":{"Genotype":"OD"},
"Additional sample data":{"RAW_FILE_NAME":"OD1"}
},
{
"Subject ID":"-",
"Sample ID":"OD2",
"Factors":{"Genotype":"OD"},
"Additional sample data":{"RAW_FILE_NAME":"OD2"}
},
{
"Subject ID":"-",
"Sample ID":"OD3",
"Factors":{"Genotype":"OD"},
"Additional sample data":{"RAW_FILE_NAME":"OD3"}
},
{
"Subject ID":"-",
"Sample ID":"OD4",
"Factors":{"Genotype":"OD"},
"Additional sample data":{"RAW_FILE_NAME":"OD4"}
},
{
"Subject ID":"-",
"Sample ID":"OD5",
"Factors":{"Genotype":"OD"},
"Additional sample data":{"RAW_FILE_NAME":"OD5"}
},
{
"Subject ID":"-",
"Sample ID":"OD6",
"Factors":{"Genotype":"OD"},
"Additional sample data":{"RAW_FILE_NAME":"OD6"}
},
{
"Subject ID":"-",
"Sample ID":"OD7",
"Factors":{"Genotype":"OD"},
"Additional sample data":{"RAW_FILE_NAME":"OD7"}
},
{
"Subject ID":"-",
"Sample ID":"OD8",
"Factors":{"Genotype":"OD"},
"Additional sample data":{"RAW_FILE_NAME":"OD8"}
},
{
"Subject ID":"-",
"Sample ID":"OD9",
"Factors":{"Genotype":"OD"},
"Additional sample data":{"RAW_FILE_NAME":"OD9"}
},
{
"Subject ID":"-",
"Sample ID":"OD10",
"Factors":{"Genotype":"OD"},
"Additional sample data":{"RAW_FILE_NAME":"OD10"}
},
{
"Subject ID":"-",
"Sample ID":"OD11",
"Factors":{"Genotype":"OD"},
"Additional sample data":{"RAW_FILE_NAME":"OD11"}
},
{
"Subject ID":"-",
"Sample ID":"ODBS1",
"Factors":{"Genotype":"ODBS"},
"Additional sample data":{"RAW_FILE_NAME":"ODBS1"}
},
{
"Subject ID":"-",
"Sample ID":"ODBS2",
"Factors":{"Genotype":"ODBS"},
"Additional sample data":{"RAW_FILE_NAME":"ODBS2"}
},
{
"Subject ID":"-",
"Sample ID":"ODBS3",
"Factors":{"Genotype":"ODBS"},
"Additional sample data":{"RAW_FILE_NAME":"ODBS3"}
},
{
"Subject ID":"-",
"Sample ID":"ODBS4",
"Factors":{"Genotype":"ODBS"},
"Additional sample data":{"RAW_FILE_NAME":"ODBS4"}
},
{
"Subject ID":"-",
"Sample ID":"ODBS5",
"Factors":{"Genotype":"ODBS"},
"Additional sample data":{"RAW_FILE_NAME":"ODBS5"}
},
{
"Subject ID":"-",
"Sample ID":"ODBS6",
"Factors":{"Genotype":"ODBS"},
"Additional sample data":{"RAW_FILE_NAME":"ODBS6"}
},
{
"Subject ID":"-",
"Sample ID":"ODBS7",
"Factors":{"Genotype":"ODBS"},
"Additional sample data":{"RAW_FILE_NAME":"ODBS7"}
},
{
"Subject ID":"-",
"Sample ID":"ODBS8",
"Factors":{"Genotype":"ODBS"},
"Additional sample data":{"RAW_FILE_NAME":"ODBS8"}
},
{
"Subject ID":"-",
"Sample ID":"ODBS9",
"Factors":{"Genotype":"ODBS"},
"Additional sample data":{"RAW_FILE_NAME":"ODBS9"}
},
{
"Subject ID":"-",
"Sample ID":"ODBS10",
"Factors":{"Genotype":"ODBS"},
"Additional sample data":{"RAW_FILE_NAME":"ODBS10"}
},
{
"Subject ID":"-",
"Sample ID":"ODBS11",
"Factors":{"Genotype":"ODBS"},
"Additional sample data":{"RAW_FILE_NAME":"ODBS11"}
},
{
"Subject ID":"-",
"Sample ID":"QC1",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC1"}
},
{
"Subject ID":"-",
"Sample ID":"QC2",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC2"}
},
{
"Subject ID":"-",
"Sample ID":"QC3",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC3"}
},
{
"Subject ID":"-",
"Sample ID":"QC4",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC4"}
},
{
"Subject ID":"-",
"Sample ID":"QC5",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC5"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Serum samples were collected for CKD obese patients (OD), obese patients without CKD (O) and CKD obese patients who underwent bariatric surgery (OD BS). Samples were centrifuged (3500 rpm, 15 min at 4 °C), aliquoted and stored at -80 °C until extraction.","SAMPLE_TYPE":"Blood (serum)","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"30 µl of serum of each sample were randomized and vortex-mixed with 400 µl of MeOH at -20 °C containing 1 ppm of a mix of internal standards. Samples were oximated and silylated. Samples were analyzed in a Orbitrap system."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"30 µl of serum of each sample were randomized and vortex-mixed with 400 µl of MeOH at -20 °C containing 1 ppm of the following internal standards: heptadecanoic acid, valine-d8, succinic acid-d4 and glutamic acid-d5 (Sigma-Aldrich). Samples were incubated on ice for 30 min and centrifuged (9600 rpm, 3 min). After that, 350 µl (400 µl for urine) of the supernatant of each serum sample were transferred to a V-shaped GC-vial. Stability and reproducibility of the system were checked with pooled samples prepared colleting from all the extracts the same quantity of the remained supernatant. Afterwards, pooled samples were vortex-mixed, centrifuged and 350 µl (400 µl for urine) of the supernatant of each aliquot were transferred to a V-shaped GC-vial. Derivatization. Supernatants were evaporate to dryness in a nitrogen flow. Then, samples were converted to trimethylsilyl (TMS) and methoxime (MEOX) derivate(s). Consequently, 25 µl of MOX reagent in pyridine (20 mg/ml) were added, samples were vortex-mixed and incubated for 60 min at 45 °C. After oximation, silylation was performed adding 25 µl of MSTFA, samples were vortex-mixed and incubated for 60 min at 45 °C."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"GC-HRAM analysis were performed in a Q Exactive GC Orbitrap system (Thermo Scientific), mounted with a Rxi Guard column purchased at Restek (10 m X 0.37 mm, 0.25 µm i.d.) and a capillary column provided by Agilent Technologies (30 m, 0.25 mm, 0.25 µm i.d.). Injection (1µ) was done in splitless mode with a TriPlus RSH autosampler system provided by Thermo. Oven temperature was keep at 70 °C for the first 5 minutes. Then, temperature was increased to 260 °C (10 °C/min) to reach in the final step 300 °C (40 °C/min) for 5 min. The carrier gas used was Helium with a flow of 2.0 ml/min. Scan range and resolution were adjusted to 50 – 500 m/z and 60,000 respectively. MS Detector was operated in EI positive mode.","CHROMATOGRAPHY_TYPE":"Normal phase","INSTRUMENT_NAME":"Q Exactive GC orbitrap","COLUMN_NAME":"Agilent Technologies 30 m, 0.25 mm, 0.25 µm"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"GC-HRAM analysis were performed in a Q Exactive GC Orbitrap system (Thermo Scientific), mounted with a Rxi Guard column purchased at Restek (10 m X 0.37 mm, 0.25 µm i.d.) and a capillary column provided by Agilent Technologies (30 m, 0.25 mm, 0.25 µm i.d.). Injection (1µ) was done in splitless mode with a TriPlus RSH autosampler system provided by Thermo. Oven temperature was keep at 70 °C for the first 5 minutes. Then, temperature was increased to 260 °C (10 °C/min) to reach in the final step 300 °C (40 °C/min) for 5 min. The carrier gas used was Helium with a flow of 2.0 ml/min. Scan range and resolution were adjusted to 50 – 500 m/z and 60,000 respectively. MS Detector was operated in EI positive mode. The ion source and the transfer line were kept at 280 °C.","MS_RESULTS_FILE":"ST001825_AN002961_Results.txt UNITS:Area Has m/z:Yes Has RT:Yes RT units:Minutes"}

}