Summary of Study ST001943

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 PR001153. The data can be accessed directly via it's Project DOI: 10.21228/M8P10F 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 IDST001943
Study TitleUrinary signature of chronic kidney disease in patients with severe obesity by CE-MS
Study TypeHuman nephropathy in CKD obese patients
Study SummaryUrine metabolomic characterization of severe obese patients with and without chronic kidney disease (CKD) by CE-MS. Analysis was performed in patients before and after bariatric surgery. In the present studio, samples obtained from CKD patients with severe obesity before bariatric surgery will be referred as OD (obese disease). Samples obtained from CKD patients with severe obesity after bariatric surgery will be referred as ODBS (Obese disease bariatric surgery). Patients with severe obesity without CKD will be referenced as O (obese) and after BS, OBS (obese bariatric surgery). In healthy group, when results refer to the first void urine samples, the acronym will be Healthy1V, and the acronym for urine samples collected at 24-hour will be Healthy24h.
Institute
University Rey Juan Carlos
DepartmentBasics Science of Health
LaboratoryLAFEMEX
Last NameLanzon
First NameBorja
AddressAvenida de Atenas S/N
Emailborja.lanzon@urjc.es
Phone663692554
Submit Date2021-08-19
Num Groups6
Total Subjects27
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailCE-MS
Release Date2021-11-04
Release Version1
Borja Lanzon Borja Lanzon
https://dx.doi.org/10.21228/M8P10F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001153
Project DOI:doi: 10.21228/M8P10F
Project Title:Metabolomic and lipidomic profiles of CKD in obese patients in serum and urine (part 1 of 3)
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
Department:Basics Science of Health
Last Name:Lanzon
First Name:Borja
Address:Avenida de Atenas S/N
Email:borja.lanzon@urjc.es
Phone:663692554

Subject:

Subject ID:SU002035
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
Human Inclusion Criteria:(i) body mass index (BMI)>35kg/m2 plus GFR 30–60ml/min and proteinuria >1 g/24h or GFR>60ml/min and proteinuria >2.5 g/24h despite receiving maximally tolerated doses of renin-angiotensin-aldosterone system (RAAS) blocker and (ii) BMI>40kg/m2 with a GFR>30ml/min and proteinuria >0.5 g/24h despite receiving maximally tolerated doses of RAAS blocker. For the renal function criterion, eGFR was used. The follow-up time was 24 months.
Human Exclusion Criteria:1) Patients who had participated or were participating in another clinical trial or had taken an experimental drug in the last 28 days. 2) Patients with renal transplantation and/or chronic replacement therapy (hemodialysis and/or peritoneal dialysis). 3) Subjects with poorly controlled blood pressure (SBP > 170 mmHg or DBP > 110 mmHg). 4) Patients with a history of cardiovascular events in the past six months. 5) Patients treated with immunosuppressants. 6) Subjects with a history of renovascular disease, autoimmune diseases, cancer, drug use, or obstructive uropathy. 6) Patients who did not sign the informed consent. 7) Patients who were pregnant or lactating. eGFR was used to establish the renal function criteria. Patients were monitored for 24 months.

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA184270Healthy1V_5Healthy1V
SA184271Healthy1V_4Healthy1V
SA184272Healthy1V_1Healthy1V
SA184273Healthy1V_6Healthy1V
SA184274Healthy1V_2Healthy1V
SA184275Healthy1V_3Healthy1V
SA184276Healthy1V_7Healthy1V
SA184277Healthy1V_10Healthy1V
SA184278Healthy1V_9Healthy1V
SA184279Healthy1V_8Healthy1V
SA184280Healthy24h_4Healthy24h
SA184281Healthy24h_3Healthy24h
SA184282Healthy24h_2Healthy24h
SA184283Healthy24h_5Healthy24h
SA184284Healthy24h_8Healthy24h
SA184285Healthy24h_1Healthy24h
SA184286Healthy24h_9Healthy24h
SA184287Healthy24h_7Healthy24h
SA184288Healthy24h_6Healthy24h
SA184289Healthy24h_10Healthy24h
SA184290O_1O
SA184291OD_1O
SA184292O_2O
SA184293O_3O
SA184294O_4O
SA184295OD_8O
SA184296OD_7O
SA184297O_6O
SA184298OD_2O
SA184299OD_4O
SA184300OD_5O
SA184301OD_6O
SA184302O_5O
SA184303OD_3O
SA184304O_9O
SA184305O_7O
SA184306O_8O
SA184307OBS_3OBS
SA184308OBS_2OBS
SA184309OBS_1OBS
SA184310OBS_9OBS
SA184311OBS_5OBS
SA184312OBS_4OBS
SA184313OBS_8OBS
SA184314OBS_7OBS
SA184315OBS_6OBS
SA184316ODBS_4ODBS
SA184317ODBS_1ODBS
SA184318ODBS_3ODBS
SA184319ODBS_8ODBS
SA184320ODBS_2ODBS
SA184321ODBS_5ODBS
SA184322ODBS_6ODBS
SA184323ODBS_7ODBS
SA184324QC_CC_1QC_CC
SA184325QC_CC_2QC_CC
SA184326QC_CC_4QC_CC
SA184327QC_CC_3QC_CC
SA184328QC_CC_6QC_CC
SA184329QC_CC_8QC_CC
SA184330QC_CC_7QC_CC
SA184331QC_CC_5QC_CC
SA184332QC_CKD_7QC_CKD
SA184333QC_CKD_5QC_CKD
SA184334QC_CKD_6QC_CKD
SA184335QC_CKD_3QC_CKD
SA184336QC_CKD_2QC_CKD
SA184337QC_CKD_1QC_CKD
SA184338QC_CKD_8QC_CKD
SA184339QC_CKD_4QC_CKD
SA184340QC_Control_5QC_Control
SA184341QC_Control_1QC_Control
SA184342QC_Control_4QC_Control
SA184343QC_Control_3QC_Control
SA184344QC_Control_6QC_Control
SA184345QC_Control_2QC_Control
SA184346QC_Control_8QC_Control
SA184347QC_Control_7QC_Control
SA184348QC_Healthy_7QC_Healthy
SA184349QC_Healthy_8QC_Healthy
SA184350QC_Healthy_6QC_Healthy
SA184351QC_Healthy_1QC_Healthy
SA184352QC_Healthy_2QC_Healthy
SA184353QC_Healthy_3QC_Healthy
SA184354QC_Healthy_4QC_Healthy
SA184355QC_Healthy_5QC_Healthy
Showing results 1 to 86 of 86

Collection:

Collection ID:CO002028
Collection Summary:First morning void and 24-hour urine samples, were collected, aliquoted and stored at -80°C until extraction. 24-h urine samples were prepared collecting all the urine after the first morning void until the first urine in the next day.
Sample Type:Urine
Collection Frequency:First void and 24h urines
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002047
Treatment Summary:CKD patients with severe obesity and non-CKD patients with severe obesity underwent bariatric surgery.

Sample Preparation:

Sampleprep ID:SP002041
Sampleprep Summary:100 µL of each urine sample were mixed in a 100 µL IS (internal standard) mixture with 0.4 mM of methionine sulfone and 2 mM of paracetamol containing 5% of acetonitrile, then, samples were vortexed. Some CKD patients showed an elevated proteinuria and in order to avoid capillary collapse, a Merck Milipore filters (Ultrafiltration Device with Ultracel YM-T membrane, product 4104) were used. Samples mixed with IS mixture were added to filters and centrifuged (2000 g, 60 min, 4 °C). Then, 90 µl of each sample was transferred to a glass vial. Samples were stored at -20°C until analysis. Stability and reproducibility of the system were checked with quality control (QC) samples. Four types of QC samples were prepared combining 60 µl of each sample after filtration: 1. QC from OD and OD BS samples (QC CKD). 2. QC from O and O BS samples (QC Control). 3. QC from OD, OD BS and O and OD BS samples (QC CC). 4. QC from Healthy 1H and Healthy 24H samples (QC Healthy). QC samples were vortex-mixed, transferred to a vial and stored at -20°C until analysis.
Processing Storage Conditions:-80℃
Extract Storage:On ice

Combined analysis:

Analysis ID AN003187
Analysis type MS
Chromatography type None (Direct infusion)
Chromatography system none
Column none
MS Type ESI
MS instrument type CE-TOF
MS instrument name Agilent 6224 TOF
Ion Mode POSITIVE
Units Area

Chromatography:

Chromatography ID:CH002355
Chromatography Summary:Analysis were performed in a capillary electrophoresis (CE) system coupled to a TOF-MS analyser (TOF: time-of-flight) purchased from Agilent Technologies (CE: 7100, MS: 6224). In coupling process, steath liquid was supplied by an ISO pump (Agilent 1200) to increase the volatility and compensate the volume for MS through an electrospray source. A fused silica capillary was used to perform metabolite separation (100 cm total length x 50 μm i.d. x 360 μm o.d., provided by Agilent Technologies). Capillary was conditioned with water, BGE and NaOH. Before analysis, capillary was rinsed for 5 min at 950 mbar with BGE and was applied a voltage of 30kV for 10 s to displace BGE ions. After conditioning, sample was loaded applying 50 mbar for 50 s, then, BGE was applied at 100 mbar for 10 s. In the capillary was applied a pressure of 25 mbar and a voltage of 30 kV to achieve metabolite separation. A positively charged spray is formed by a flow of 0.6 mL min−1 (1:100 split) when separated compounds leave the capillary from the auxiliary liquid system with a nebulization pressure of 10 psig with nitrogen and a capillary voltage of 3500 V. A hot nitrogen flow of 10 mL min−1 at 200 °C was applied to dry the spray.
Instrument Name:none
Column Name:none
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS002965
Analysis ID:AN003187
Instrument Name:Agilent 6224 TOF
Instrument Type:CE-TOF
MS Type:ESI
MS Comments:Ions in gaseous state were directed to the TOF using two different voltages for the fragmentor (125 V and 200 V) and voltages of 65 V and 750 V for the skimmer and the octopole, respectively. Mass range was set from 70 to 1050 Da at a scanning rate of 1.02 scans per second. Data was collected in ESI positive ion mode. MassHunter Workstation version B.06.01 (Agilent Technologies) was used to monitor CE-MS analysis. Voltage of 125 V in the fragmentor was applied to ordinary samples and QC control samples. Data acquired at 125 V, equivalent to MS1, provided information about adducts, isotopes, multimers and fragments ions with low intensity. Voltage of 200 V in the fragmentor was applied to four QC (covering the four types of QC prepared). Data acquired at 200 V is similar to data obtained in 10 eV MS/MS, although has been previously reported that some fragment ions could differ. An equilibration QC was prepared to adapt and prepare the equipment for the conditions of the samples to be analysed. Equilibration QC was prepared as a pool of the four types of QC used to cover completely the biological diversity of the samples. Equilibration QC was analysed before samples. QC samples were disposed throughout the instrumental analysis.
Ion Mode:POSITIVE
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