Summary of Study ST001825

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 ID	ST001825
Study Title	Metabolomic and lipidomic profiles of CKD in obese patients in serum and urine (part 2 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
Email	borja.lanzon@urjc.es
Phone	663692554
Submit Date	2021-04-02
Num Groups	3
Total Subjects	35
Study Comments	Serum GC-HRAM data: part 2 of 3.
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:	SU001902
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
SA169309	O11	O
SA169310	O10	O
SA169311	O12	O
SA169312	O13	O
SA169313	O1	O
SA169314	O8	O
SA169315	O9	O
SA169316	O3	O
SA169317	O2	O
SA169318	O5	O
SA169319	O4	O
SA169320	O7	O
SA169321	O6	O
SA169322	OD9	OD
SA169323	OD11	OD
SA169324	OD7	OD
SA169325	OD10	OD
SA169326	OD8	OD
SA169327	OD2	OD
SA169328	OD6	OD
SA169329	OD3	OD
SA169330	OD1	OD
SA169331	OD4	OD
SA169332	OD5	OD
SA169333	ODBS9	ODBS
SA169334	ODBS8	ODBS
SA169335	ODBS10	ODBS
SA169336	ODBS7	ODBS
SA169337	ODBS11	ODBS
SA169338	ODBS6	ODBS
SA169339	ODBS1	ODBS
SA169340	ODBS5	ODBS
SA169341	ODBS2	ODBS
SA169342	ODBS4	ODBS
SA169343	ODBS3	ODBS
SA169344	QC5	QC
SA169345	QC4	QC
SA169346	QC1	QC
SA169347	QC2	QC
SA169348	QC3	QC

Showing results 1 to 40 of 40

Showing results 1 to 40 of 40

Collection:

Collection ID:	CO001895
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:	TR001915
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.

Sample Preparation:

Sampleprep ID:	SP001908
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.

Sampleprep ID:

SP001908

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	AN002961
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:	CH002194
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.
Instrument Name:	Q Exactive GC orbitrap
Column Name:	Agilent Technologies (30 m x 0.25mm, 0.25um)
Chromatography Type:	Normal phase

MS:

MS ID:	MS002751
Analysis ID:	AN002961
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