#METABOLOMICS WORKBENCH borjalanzon_20210402_054551 DATATRACK_ID:2556 STUDY_ID:ST001824 ANALYSIS_ID:AN002960 PROJECT_ID:PR001153 VERSION 1 CREATED_ON May 11, 2021, 11:44 am #PROJECT PR:PROJECT_TITLE Metabolomic and lipidomic profiles of CKD in obese patients in serum and urine PR:PROJECT_TITLE (part 1 of 3) PR:PROJECT_TYPE Human nephropathy in CKD obese patients PR:PROJECT_SUMMARY Obesity is a global pandemic with an increase prevalence over the years. This PR:PROJECT_SUMMARY condition elevates the risk of developing cardiovascular diseases, hypertension PR:PROJECT_SUMMARY and renal pathologies, like chronic kidney disease (CKD). In the present study, PR:PROJECT_SUMMARY the metabolomic and the lipidomic profiles of CKD obese patients were analyzed PR:PROJECT_SUMMARY comparing with obese subjects without CKD. Subsequently, CKD obese patients PR:PROJECT_SUMMARY underwent bariatric surgery and the effect of surgery in the CKD progression of PR:PROJECT_SUMMARY these subjects was evaluated. Serum and urine were measured by LC-MS and GC-HRAM PR:PROJECT_SUMMARY equipment. PR:INSTITUTE University Rey Juan Carlos PR:DEPARTMENT Basics Science of Health PR:LAST_NAME Lanzon PR:FIRST_NAME Borja PR:ADDRESS Avenida de Atenas S/N PR:EMAIL borja.lanzon@urjc.es PR:PHONE 663692554 #STUDY ST:STUDY_TITLE Metabolomic and lipidomic profiles of CKD in obese patients in serum and urine ST:STUDY_TITLE (part 1 of 3) ST:STUDY_TYPE Human nephropathy in CKD obese patients ST:STUDY_SUMMARY Obesity is a global pandemic with an increase prevalence over the years. This ST:STUDY_SUMMARY condition elevates the risk of developing cardiovascular diseases, hypertension ST:STUDY_SUMMARY and renal pathologies, like chronic kidney disease (CKD). In the present study, ST:STUDY_SUMMARY the metabolomic and the lipidomic profiles of CKD obese patients were analyzed ST:STUDY_SUMMARY comparing with obese subjects without CKD. Subsequently, CKD obese patients ST:STUDY_SUMMARY underwent bariatric surgery and the effect of surgery in the CKD progression of ST:STUDY_SUMMARY these subjects was evaluated. Serum and urine were measured by LC-MS and GC-HRAM ST:STUDY_SUMMARY equipment. ST:INSTITUTE University Rey Juan Carlos ST:DEPARTMENT Basics Science of Health ST:LAST_NAME Lanzon ST:FIRST_NAME Borja ST:ADDRESS Avenida de Atenas S/N ST:EMAIL borja.lanzon@urjc.es ST:PHONE 663692554 ST:NUM_GROUPS 3 ST:TOTAL_SUBJECTS 36 ST:STUDY_COMMENTS Serum LC-MS data: part 1 of 3. Samples were analyzed per duplicated. #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:AGE_OR_AGE_RANGE 53 ± 15 SU:WEIGHT_OR_WEIGHT_RANGE 116 ± 25 SU:GENDER Male and female #FACTORS #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - O1_1 Genotype:O RAW_FILE_NAME=O1_1 SUBJECT_SAMPLE_FACTORS - O1_2 Genotype:O RAW_FILE_NAME=O1_2 SUBJECT_SAMPLE_FACTORS - O2_1 Genotype:O RAW_FILE_NAME=O2_1 SUBJECT_SAMPLE_FACTORS - O2_2 Genotype:O RAW_FILE_NAME=O2_2 SUBJECT_SAMPLE_FACTORS - O3_1 Genotype:O RAW_FILE_NAME=O3_1 SUBJECT_SAMPLE_FACTORS - O3_2 Genotype:O RAW_FILE_NAME=O3_2 SUBJECT_SAMPLE_FACTORS - O4_1 Genotype:O RAW_FILE_NAME=O4_1 SUBJECT_SAMPLE_FACTORS - O4_2 Genotype:O RAW_FILE_NAME=O4_2 SUBJECT_SAMPLE_FACTORS - O5_1 Genotype:O RAW_FILE_NAME=O5_1 SUBJECT_SAMPLE_FACTORS - O5_2 Genotype:O RAW_FILE_NAME=O5_2 SUBJECT_SAMPLE_FACTORS - O6_1 Genotype:O RAW_FILE_NAME=O6_1 SUBJECT_SAMPLE_FACTORS - O6_2 Genotype:O RAW_FILE_NAME=O6_2 SUBJECT_SAMPLE_FACTORS - O7_1 Genotype:O RAW_FILE_NAME=O7_1 SUBJECT_SAMPLE_FACTORS - O7_2 Genotype:O RAW_FILE_NAME=O7_2 SUBJECT_SAMPLE_FACTORS - O8_1 Genotype:O RAW_FILE_NAME=O8_1 SUBJECT_SAMPLE_FACTORS - O8_2 Genotype:O RAW_FILE_NAME=O8_2 SUBJECT_SAMPLE_FACTORS - O9_1 Genotype:O RAW_FILE_NAME=O9_1 SUBJECT_SAMPLE_FACTORS - O9_2 Genotype:O RAW_FILE_NAME=O9_2 SUBJECT_SAMPLE_FACTORS - O10_1 Genotype:O RAW_FILE_NAME=O10_1 SUBJECT_SAMPLE_FACTORS - O10_2 Genotype:O RAW_FILE_NAME=O10_2 SUBJECT_SAMPLE_FACTORS - O11_1 Genotype:O RAW_FILE_NAME=O11_1 SUBJECT_SAMPLE_FACTORS - O11_2 Genotype:O RAW_FILE_NAME=O11_2 SUBJECT_SAMPLE_FACTORS - O12_1 Genotype:O RAW_FILE_NAME=O12_1 SUBJECT_SAMPLE_FACTORS - O12_2 Genotype:O RAW_FILE_NAME=O12_2 SUBJECT_SAMPLE_FACTORS - O13_1 Genotype:O RAW_FILE_NAME=O13_1 SUBJECT_SAMPLE_FACTORS - O13_2 Genotype:O RAW_FILE_NAME=O13_2 SUBJECT_SAMPLE_FACTORS - O14_1 Genotype:O RAW_FILE_NAME=O14_1 SUBJECT_SAMPLE_FACTORS - O14_2 Genotype:O RAW_FILE_NAME=O14_2 SUBJECT_SAMPLE_FACTORS - OD1_1 Genotype:OD RAW_FILE_NAME=OD1_1 SUBJECT_SAMPLE_FACTORS - OD1_2 Genotype:OD RAW_FILE_NAME=OD1_2 SUBJECT_SAMPLE_FACTORS - OD2_1 Genotype:OD RAW_FILE_NAME=OD2_1 SUBJECT_SAMPLE_FACTORS - OD2_2 Genotype:OD RAW_FILE_NAME=OD2_2 SUBJECT_SAMPLE_FACTORS - OD3_1 Genotype:OD RAW_FILE_NAME=OD3_1 SUBJECT_SAMPLE_FACTORS - OD3_2 Genotype:OD RAW_FILE_NAME=OD3_2 SUBJECT_SAMPLE_FACTORS - OD4_1 Genotype:OD RAW_FILE_NAME=OD4_1 SUBJECT_SAMPLE_FACTORS - OD4_2 Genotype:OD RAW_FILE_NAME=OD4_2 SUBJECT_SAMPLE_FACTORS - OD5_1 Genotype:OD RAW_FILE_NAME=OD5_1 SUBJECT_SAMPLE_FACTORS - OD5_2 Genotype:OD RAW_FILE_NAME=OD5_2 SUBJECT_SAMPLE_FACTORS - OD6_1 Genotype:OD RAW_FILE_NAME=OD6_1 SUBJECT_SAMPLE_FACTORS - OD6_2 Genotype:OD RAW_FILE_NAME=OD6_2 SUBJECT_SAMPLE_FACTORS - OD7_1 Genotype:OD RAW_FILE_NAME=OD7_1 SUBJECT_SAMPLE_FACTORS - OD7_2 Genotype:OD RAW_FILE_NAME=OD7_2 SUBJECT_SAMPLE_FACTORS - OD8_1 Genotype:OD RAW_FILE_NAME=OD8_1 SUBJECT_SAMPLE_FACTORS - OD8_2 Genotype:OD RAW_FILE_NAME=OD8_2 SUBJECT_SAMPLE_FACTORS - OD9_1 Genotype:OD RAW_FILE_NAME=OD9_1 SUBJECT_SAMPLE_FACTORS - OD9_2 Genotype:OD RAW_FILE_NAME=OD9_2 SUBJECT_SAMPLE_FACTORS - OD10_1 Genotype:OD RAW_FILE_NAME=OD10_1 SUBJECT_SAMPLE_FACTORS - OD10_2 Genotype:OD RAW_FILE_NAME=OD10_2 SUBJECT_SAMPLE_FACTORS - OD11_1 Genotype:OD RAW_FILE_NAME=OD11_1 SUBJECT_SAMPLE_FACTORS - OD11_2 Genotype:OD RAW_FILE_NAME=OD11_2 SUBJECT_SAMPLE_FACTORS - ODBS1_1 Genotype:ODBS RAW_FILE_NAME=ODBS1_1 SUBJECT_SAMPLE_FACTORS - ODBS1_2 Genotype:ODBS RAW_FILE_NAME=ODBS1_2 SUBJECT_SAMPLE_FACTORS - ODBS2_1 Genotype:ODBS RAW_FILE_NAME=ODBS2_1 SUBJECT_SAMPLE_FACTORS - ODBS2_2 Genotype:ODBS RAW_FILE_NAME=ODBS2_2 SUBJECT_SAMPLE_FACTORS - ODBS3_1 Genotype:ODBS RAW_FILE_NAME=ODBS3_1 SUBJECT_SAMPLE_FACTORS - ODBS3_2 Genotype:ODBS RAW_FILE_NAME=ODBS3_2 SUBJECT_SAMPLE_FACTORS - ODBS4_1 Genotype:ODBS RAW_FILE_NAME=ODBS4_1 SUBJECT_SAMPLE_FACTORS - ODBS4_2 Genotype:ODBS RAW_FILE_NAME=ODBS4_2 SUBJECT_SAMPLE_FACTORS - ODBS5_1 Genotype:ODBS RAW_FILE_NAME=ODBS5_1 SUBJECT_SAMPLE_FACTORS - ODBS5_2 Genotype:ODBS RAW_FILE_NAME=ODBS5_2 SUBJECT_SAMPLE_FACTORS - ODBS6_1 Genotype:ODBS RAW_FILE_NAME=ODBS6_1 SUBJECT_SAMPLE_FACTORS - ODBS6_2 Genotype:ODBS RAW_FILE_NAME=ODBS6_2 SUBJECT_SAMPLE_FACTORS - ODBS7_1 Genotype:ODBS RAW_FILE_NAME=ODBS7_1 SUBJECT_SAMPLE_FACTORS - ODBS7_2 Genotype:ODBS RAW_FILE_NAME=ODBS7_2 SUBJECT_SAMPLE_FACTORS - ODBS8_1 Genotype:ODBS RAW_FILE_NAME=ODBS8_1 SUBJECT_SAMPLE_FACTORS - ODBS8_2 Genotype:ODBS RAW_FILE_NAME=ODBS8_2 SUBJECT_SAMPLE_FACTORS - ODBS9_1 Genotype:ODBS RAW_FILE_NAME=ODBS9_1 SUBJECT_SAMPLE_FACTORS - ODBS9_2 Genotype:ODBS RAW_FILE_NAME=ODBS9_2 SUBJECT_SAMPLE_FACTORS - ODBS10_1 Genotype:ODBS RAW_FILE_NAME=ODBS10_1 SUBJECT_SAMPLE_FACTORS - ODBS10_2 Genotype:ODBS RAW_FILE_NAME=ODBS10_2 SUBJECT_SAMPLE_FACTORS - ODBS11_1 Genotype:ODBS RAW_FILE_NAME=ODBS11_1 SUBJECT_SAMPLE_FACTORS - ODBS11_2 Genotype:ODBS RAW_FILE_NAME=ODBS11_2 SUBJECT_SAMPLE_FACTORS - QC1 Genotype:QC RAW_FILE_NAME=QC1 SUBJECT_SAMPLE_FACTORS - QC1_ext Genotype:QC RAW_FILE_NAME=QC1_ext SUBJECT_SAMPLE_FACTORS - QC2 Genotype:QC RAW_FILE_NAME=QC2 SUBJECT_SAMPLE_FACTORS - QC2_ext Genotype:QC RAW_FILE_NAME=QC2_ext #COLLECTION CO:COLLECTION_SUMMARY Serum samples were collected for CKD obese patients (OD), obese patients without CO:COLLECTION_SUMMARY CKD (O) and CKD obese patients who underwent bariatric surgery (OD BS). Samples CO:COLLECTION_SUMMARY were centrifuged (3500 rpm, 15 min at 4 °C), aliquoted and stored at -80 °C CO:COLLECTION_SUMMARY until extraction. CO:SAMPLE_TYPE Blood (serum) CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY 10 µl of each serum sample were added to 10 µl of 0.9% NaCl and 120 µl of TR:TREATMENT_SUMMARY CHCl3: MeOH (2:1, v/v) containing a 2.5 ppm solution of different lipids TR:TREATMENT_SUMMARY standards. Lipids were extracted with CHCl3: MeOH (2:1, v/v). #SAMPLEPREP SP:SAMPLEPREP_SUMMARY 10 µl of each serum sample were added to 10 µl of 0.9% NaCl and 120 µl of SP:SAMPLEPREP_SUMMARY CHCl3: MeOH (2:1, v/v) containing a 2.5 ppm solution of different lipids SP:SAMPLEPREP_SUMMARY standards. Samples were randomized, vortex-mixed and put on ice for 30 min. SP:SAMPLEPREP_SUMMARY After that, samples were centrifuged (9400 g, 3 min, 4 °C). Then, 60 µl of the SP:SAMPLEPREP_SUMMARY lower layer of each sample was transferred to a glass vial with an insert and 60 SP:SAMPLEPREP_SUMMARY µl of CHCl3: MeOH (2:1, v/v) was added. Samples were stored at -80 °C until SP:SAMPLEPREP_SUMMARY LC-MS analysis. SP:PROCESSING_STORAGE_CONDITIONS On ice SP:EXTRACT_STORAGE -80℃ #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY An ultra-high-performance liquid chromatography electrospray ionization CH:CHROMATOGRAPHY_SUMMARY quadrupole time-of-flight (UHPLC-ESI-Q-TOF-MS) were used to analyze the samples CH:CHROMATOGRAPHY_SUMMARY on positive ionization mode. Samples were analyzed by duplicate. UHPLC system CH:CHROMATOGRAPHY_SUMMARY was an Agilent Infinity 1290 provided by Agilent Technologies (Santa Clara, CA, CH:CHROMATOGRAPHY_SUMMARY USA) equipped with a multisampler (kept at -10 °C). Needle wash solutions were CH:CHROMATOGRAPHY_SUMMARY performed with 10% DCM in MeOH and ACN:MeOH:IPA:H2O (1:1:1:1, v/v/v/v), and 0.1% CH:CHROMATOGRAPHY_SUMMARY of HCOOH after each injection for 7.5 s. System were equipped with a column CH:CHROMATOGRAPHY_SUMMARY thermostat (maintained at 50 °C) and a quaternary solvent manager. An ACQUITY CH:CHROMATOGRAPHY_SUMMARY UPLC BEH C18 column was used for separations (2.1 mm x 100 mm, particle size 1.7 CH:CHROMATOGRAPHY_SUMMARY μm) purchased at Waters (Milford, CT, USA). Injection volume was 1 μl and flow CH:CHROMATOGRAPHY_SUMMARY rate was established at 0.4 ml/min. Mobile phases were composed of (A) H2O + CH:CHROMATOGRAPHY_SUMMARY NH4AC 10 mM + 0.1 % HCOOH and (B) ACN: IPA (1:1, v/v) + NH4AC 10 mM + 0.1 % CH:CHROMATOGRAPHY_SUMMARY HCOOH. Gradient was from 0 to 2 min 35-80 % B, 2 min to 7 min 80-100 % B and 7 CH:CHROMATOGRAPHY_SUMMARY to 14 min 100 % B. A re-equilibration of 7 min was performed after each run to CH:CHROMATOGRAPHY_SUMMARY bring system to initial conditions (35 % B). CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent Infinity 1290 CH:COLUMN_NAME ACQUITY UPLC BEH C18 CH:FLOW_GRADIENT 0 to 2 min 35-80 % B, 2 min to 7 min 80-100 % B and 7 to 14 min 100 % B CH:FLOW_RATE 0.4 ml/min CH:COLUMN_TEMPERATURE 50 CH:SOLVENT_A H2O + NH4AC 10 mM + 0.1 % HCOOH CH:SOLVENT_B ACN: IPA (1:1, v/v) + NH4AC 10 mM + 0.1 % HCOOH #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6545 Q-TOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Mass Spectrometer was an Agilent 6545 quadrupole time-of-flight (Q-TOF) mounted MS:MS_COMMENTS with a dual jet stream electrospray (dual ESI) ion source interface. Nitrogen MS:MS_COMMENTS was obtained from a nitrogen generator (PEAK Scientific, Renfrewshire, Scotland, MS:MS_COMMENTS UK) as a sheath gas at a flow rate of 11 l/min at 379 °C. As a Collision gas MS:MS_COMMENTS was used Pure Nitrogen (6.0) from Praxair (Fredericia, Denmark). Capillary MS:MS_COMMENTS voltage was maintained at 3600 V and nozzle voltage was kept at 1500 V. MS:MS_COMMENTS Reference mass solution was prepared in consonance with Agilent guidelines, MS:MS_COMMENTS including ions at m/z 121.0509 and 922.0098. The second nebulizer was used to MS:MS_COMMENTS introduce the solution in the dual ESI ion source through the isocratic pump at MS:MS_COMMENTS a constant flow rate of 4 ml/min (split to 1:100 before nebulization). MS:MS_COMMENTS Acquisition mass range was 100 to 3000 m/z. Instrument used the extended dynamic MS:MS_COMMENTS range with an estimated resolution of 30.000 FWHM measured at 1521.9715 m/z MS:MS_COMMENTS (included in tune mixture) when instrument calibration was performed. MS:CAPILLARY_VOLTAGE 3600 V MS:MS_RESULTS_FILE ST001824_AN002960_Results.txt UNITS:Area Has m/z:Yes Has RT:Yes RT units:Minutes #END