Summary of Study ST001826
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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
| Study ID | ST001826 |
| Study Title | Metabolomic and lipidomic profiles of CKD in obese patients in serum and urine (part 3 of 3) |
| Study Type | Human nephropathy in CKD obese patients |
| 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 |
| borja.lanzon@urjc.es | |
| Phone | 663692554 |
| Submit Date | 2021-04-02 |
| Num Groups | 2 |
| Total Subjects | 16 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | GC-MS |
| Release Date | 2021-06-14 |
| Release Version | 1 |
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: | SU001903 |
| 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 |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA169349 | OD8 | OD |
| SA169350 | OD1 | OD |
| SA169351 | OD7 | OD |
| SA169352 | OD6 | OD |
| SA169353 | OD2 | OD |
| SA169354 | OD4 | OD |
| SA169355 | OD3 | OD |
| SA169356 | OD5 | OD |
| SA169357 | ODBS7 | ODBS |
| SA169358 | ODBS8 | ODBS |
| SA169359 | ODBS6 | ODBS |
| SA169360 | ODBS4 | ODBS |
| SA169361 | ODBS5 | ODBS |
| SA169362 | ODBS1 | ODBS |
| SA169363 | ODBS2 | ODBS |
| SA169364 | ODBS3 | ODBS |
| SA169365 | QC6 | QC |
| SA169366 | QC5 | QC |
| SA169367 | QC2 | QC |
| SA169368 | QC1 | QC |
| SA169369 | QC3 | QC |
| SA169370 | QC4 | QC |
| Showing results 1 to 22 of 22 |
Collection:
| Collection ID: | CO001896 |
| Collection Summary: | Urine, first void in the morning, were collected, aliquoted and stored at -80 °C until extraction. |
| Sample Type: | Urine |
| Collection Frequency: | First void |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001916 |
| Treatment Summary: | 150 µl of urine 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. |
Sample Preparation:
| Sampleprep ID: | SP001909 |
| 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. |
Combined analysis:
| Analysis ID | AN002962 |
|---|---|
| Analysis type | MS |
| Chromatography type | Normal phase |
| Chromatography system | Q Exactive GC orbitrap |
| Column | Agilent Technologies (30 m x 0.25mm, 0.25um) |
| MS Type | EI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE |
| Units | Area |
Chromatography:
| Chromatography ID: | CH002195 |
| Chromatography Summary: | GC-HRAM analysis were performed in a Q Exative 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. |
| Instrument Name: | Q Exactive GC orbitrap |
| Column Name: | Agilent Technologies (30 m x 0.25mm, 0.25um) |
| Chromatography Type: | Normal phase |
MS:
| MS ID: | MS002752 |
| Analysis ID: | AN002962 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | EI |
| 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. |
| Ion Mode: | POSITIVE |
