Summary of Study ST001824

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.

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Study IDST001824
Study TitleMetabolomic and lipidomic profiles of CKD in obese patients in serum and urine (part 1 of 3)
Study TypeHuman nephropathy in CKD obese patients
Study SummaryObesity 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
DepartmentBasics Science of Health
Last NameLanzon
First NameBorja
AddressAvenida de Atenas S/N
Emailborja.lanzon@urjc.es
Phone663692554
Submit Date2021-04-02
Num Groups3
Total Subjects36
Study CommentsSerum LC-MS data: part 1 of 3. Samples were analyzed per duplicated.
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2021-06-14
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:SU001901
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
SA169233O11_1O
SA169234O11_2O
SA169235O10_1O
SA169236O9_2O
SA169237O9_1O
SA169238O12_1O
SA169239O13_1O
SA169240O14_2O
SA169241O1_1O
SA169242O14_1O
SA169243O13_2O
SA169244O8_2O
SA169245O12_2O
SA169246O10_2O
SA169247O3_2O
SA169248O4_1O
SA169249O8_1O
SA169250O2_2O
SA169251O1_2O
SA169252O2_1O
SA169253O4_2O
SA169254O3_1O
SA169255O7_1O
SA169256O5_1O
SA169257O7_2O
SA169258O6_2O
SA169259O5_2O
SA169260O6_1O
SA169261OD8_1OD
SA169262OD8_2OD
SA169263OD7_2OD
SA169264OD9_1OD
SA169265OD11_1OD
SA169266OD7_1OD
SA169267OD11_2OD
SA169268OD10_2OD
SA169269OD10_1OD
SA169270OD9_2OD
SA169271OD6_1OD
SA169272OD2_2OD
SA169273OD2_1OD
SA169274OD1_2OD
SA169275OD6_2OD
SA169276OD3_1OD
SA169277OD1_1OD
SA169278OD3_2OD
SA169279OD5_1OD
SA169280OD4_2OD
SA169281OD5_2OD
SA169282OD4_1OD
SA169283ODBS8_2ODBS
SA169284ODBS7_2ODBS
SA169285ODBS9_1ODBS
SA169286ODBS8_1ODBS
SA169287ODBS10_2ODBS
SA169288ODBS7_1ODBS
SA169289ODBS11_2ODBS
SA169290ODBS11_1ODBS
SA169291ODBS10_1ODBS
SA169292ODBS9_2ODBS
SA169293ODBS5_1ODBS
SA169294ODBS6_2ODBS
SA169295ODBS2_1ODBS
SA169296ODBS1_2ODBS
SA169297ODBS1_1ODBS
SA169298ODBS3_1ODBS
SA169299ODBS2_2ODBS
SA169300ODBS3_2ODBS
SA169301ODBS6_1ODBS
SA169302ODBS5_2ODBS
SA169303ODBS4_2ODBS
SA169304ODBS4_1ODBS
SA169305QC2_extQC
SA169306QC1QC
SA169307QC1_extQC
SA169308QC2QC
Showing results 1 to 76 of 76

Collection:

Collection ID:CO001894
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 ID:TR001914
Treatment Summary:10 µl of each serum sample were added to 10 µl of 0.9% NaCl and 120 µl of CHCl3: MeOH (2:1, v/v) containing a 2.5 ppm solution of different lipids standards. Lipids were extracted with CHCl3: MeOH (2:1, v/v).

Sample Preparation:

Sampleprep ID:SP001907
Sampleprep Summary:10 µl of each serum sample were added to 10 µl of 0.9% NaCl and 120 µl of CHCl3: MeOH (2:1, v/v) containing a 2.5 ppm solution of different lipids standards. Samples were randomized, vortex-mixed and put on ice for 30 min. After that, samples were centrifuged (9400 g, 3 min, 4 °C). Then, 60 µl of the lower layer of each sample was transferred to a glass vial with an insert and 60 µl of CHCl3: MeOH (2:1, v/v) was added. Samples were stored at -80 °C until LC-MS analysis.
Processing Storage Conditions:On ice
Extract Storage:-80℃

Combined analysis:

Analysis ID AN002960
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent Infinity 1290
Column Waters ACQUITY UPLC BEH C18
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6545 Q-TOF
Ion Mode POSITIVE
Units Area

Chromatography:

Chromatography ID:CH002193
Chromatography Summary:An ultra-high-performance liquid chromatography electrospray ionization quadrupole time-of-flight (UHPLC-ESI-Q-TOF-MS) were used to analyze the samples on positive ionization mode. Samples were analyzed by duplicate. UHPLC system was an Agilent Infinity 1290 provided by Agilent Technologies (Santa Clara, CA, USA) equipped with a multisampler (kept at -10 °C). Needle wash solutions were performed with 10% DCM in MeOH and ACN:MeOH:IPA:H2O (1:1:1:1, v/v/v/v), and 0.1% of HCOOH after each injection for 7.5 s. System were equipped with a column thermostat (maintained at 50 °C) and a quaternary solvent manager. An ACQUITY UPLC BEH C18 column was used for separations (2.1 mm x 100 mm, particle size 1.7 μm) purchased at Waters (Milford, CT, USA). Injection volume was 1 μl and flow rate was established at 0.4 ml/min. Mobile phases were composed of (A) H2O + NH4AC 10 mM + 0.1 % HCOOH and (B) ACN: IPA (1:1, v/v) + NH4AC 10 mM + 0.1 % HCOOH. Gradient was from 0 to 2 min 35-80 % B, 2 min to 7 min 80-100 % B and 7 to 14 min 100 % B. A re-equilibration of 7 min was performed after each run to bring system to initial conditions (35 % B).
Instrument Name:Agilent Infinity 1290
Column Name:Waters ACQUITY UPLC BEH C18
Column Temperature:50
Flow Gradient:0 to 2 min 35-80 % B, 2 min to 7 min 80-100 % B and 7 to 14 min 100 % B
Flow Rate:0.4 ml/min
Solvent A:100% water; 0.1% formic acid; 10 mM ammonium acetate
Solvent B:50% acetonitrile/50% isopropanol; 0.1% formic acid; 10 mM ammonium acetate
Chromatography Type:Reversed phase

MS:

MS ID:MS002750
Analysis ID:AN002960
Instrument Name:Agilent 6545 Q-TOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Mass Spectrometer was an Agilent 6545 quadrupole time-of-flight (Q-TOF) mounted with a dual jet stream electrospray (dual ESI) ion source interface. Nitrogen was obtained from a nitrogen generator (PEAK Scientific, Renfrewshire, Scotland, UK) as a sheath gas at a flow rate of 11 l/min at 379 °C. As a Collision gas was used Pure Nitrogen (6.0) from Praxair (Fredericia, Denmark). Capillary voltage was maintained at 3600 V and nozzle voltage was kept at 1500 V. Reference mass solution was prepared in consonance with Agilent guidelines, including ions at m/z 121.0509 and 922.0098. The second nebulizer was used to introduce the solution in the dual ESI ion source through the isocratic pump at a constant flow rate of 4 ml/min (split to 1:100 before nebulization). Acquisition mass range was 100 to 3000 m/z. Instrument used the extended dynamic range with an estimated resolution of 30.000 FWHM measured at 1521.9715 m/z (included in tune mixture) when instrument calibration was performed.
Ion Mode:POSITIVE
Capillary Voltage:3600 V
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