Summary of Study ST001303

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 PR000884. The data can be accessed directly via it's Project DOI: 10.21228/M8DX2P 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 IDST001303
Study TitleTGF-Beta 3 heterozygous mice
Study TypeMice nephropathy in lipotoxic model
Study SummaryTransforming growth factor β (TGFβ) family comprises the main player in the development of fibrosis including three isoforms: TGFβ1, TGFβ2 and TGFβ3. TGFβ3 may play an antifibrotic role at the renal level, counteracting the role of TGFβ1, using a mouse model heterozygous for the TGFβ3 gene (TGFβ3+/-). Partial deletion of TGFβ3 causes in the mice albuminuria, loss of glomerular filtration rate, accelerated fibrosis, epithelial-to-mesenchymal transition and increment of glomerular basement membrane thickening.
Institute
University Rey Juan Carlos
DepartmentBasics Science of Health
Last NameLanzon
First NameBorja
AddressAvenida de Atenas S/N
Emailborja.lanzon@urjc.es
Phone663692554
Submit Date2019-12-19
Num Groups2
Total Subjects14
Num Males14
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailGC-MS/LC-MS
Release Date2020-03-03
Release Version1
Borja Lanzon Borja Lanzon
https://dx.doi.org/10.21228/M8DX2P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Combined analysis:

Analysis ID AN002169 AN002170 AN002171
Analysis type MS MS MS
Chromatography type Reversed phase Reversed phase GC
Chromatography system Agilent 1290 Infinity II Agilent 1290 Infinity II Agilent 7890B
Column Poroshell 120 EC-C8 (100 x 2.1mm,2.5um) Poroshell 120 EC-C8 (100 x 2.1mm,2.5um) Agilent DB5-MS (30m x 0.25mm, 0.25um)
MS Type ESI ESI EI
MS instrument type QTOF QTOF GC QTOF
MS instrument name Agilent 6545 Agilent 6545 Agilent 7890A
Ion Mode POSITIVE NEGATIVE POSITIVE
Units Area Area Area

MS:

MS ID:MS002018
Analysis ID:AN002169
Instrument Name:Agilent 6545
Instrument Type:QTOF
MS Type:ESI
MS Comments:A UHPLC system (1290 Infinity UHPLC system, Agilent Technologies, Waldbronn, Germany), consisting of two degassers, two binary pumps, and a thermostated autosampler (maintained at 4°C) coupled with 6545 QTOF MS detector, was used in positive and negative ESI modes. In brief, 1 μL of each sample was injected into a reverse-phase Zorbax Eclipse Plus C8 column, 2.1 × 150 mm; 1.8 μm (Agilent Technologies) thermostated at 60°C. The gradient used for the analysis consisted of a mobile phase A (10 mM ammonium formate in Milli-Q water) and mobile phase B (10 mM ammonium formate in methanol:isopropanol, 85:15) pumped at 0.5 mL/min. The chromatography gradient started at 82% phase B, increasing to 90% B in 17 min. The gradient then increased to 100% B by minute 18 and was maintained for 2 minutes until 20 min. The starting condition was returned to by 21.5 min, followed by an 8.5 min reequilibration time, taking the total run time to 30 min. Data were collected in full scan mode from 100 to 1200 m/z, with a scan rate of 1.02 scans/s. The capillary voltage was set to 3500 V; the drying gas flow rate was 12 L/min at 290°C and gas nebulizer 45 psi, fragmentor voltage 175 V, and octopole radio frequency voltage (OCT RF Vpp) 750 V. Two reference masses were used over the course of the whole analysis: m/z 121.0509 (protonated purine) and m/z 922.0098 (protonated hexakis, (1H,1H,3H-tetrafluoropropoxy)phosphazine (HP-921)). These masses were continuously infused into the system to provide constant mass correction. Samples were randomly analyzed throughout the run.
Ion Mode:POSITIVE
  
MS ID:MS002019
Analysis ID:AN002170
Instrument Name:Agilent 6545
Instrument Type:QTOF
MS Type:ESI
MS Comments:A UHPLC system (1290 Infinity UHPLC system, Agilent Technologies, Waldbronn, Germany), consisting of two degassers, two binary pumps, and a thermostated autosampler (maintained at 4°C) coupled with 6545 QTOF MS detector, was used in positive and negative ESI modes. In brief, 1 μL of each sample was injected into a reverse-phase Zorbax Eclipse Plus C8 column, 2.1 × 150 mm; 1.8 μm (Agilent Technologies) thermostated at 60°C. The gradient used for the analysis consisted of a mobile phase A (0.1% formic acid in Milli-Q water) and mobile phase B (0.1% formic acid in methanol:isopropanol, 85:15) pumped at 0.5 mL/min. The chromatography gradient started at 82% phase B, increasing to 90% B in 17 min. The gradient then increased to 100% B by minute 18 and was maintained for 2 minutes until 20 min. The starting condition was returned to by 21.5 min, followed by an 8.5 min reequilibration time, taking the total run time to 30 min. Data were collected in full scan mode from 100 to 1000 m/z for the negative modes, with a scan rate of 1.02 scans/s. The capillary voltage was set to 3000 V; the drying gas flow rate was 12 L/min at 290°C and gas nebulizer 45 psi, fragmentor voltage 175 V, and octopole radio frequency voltage (OCT RF Vpp) 750 V. Two reference masses were used over the course of the whole analysis: m/z 112.9856 (proton-abstracted TFA anion) and m/z 966.0007 (formate adduct of HP921) for the negative mode. These masses were continuously infused into the system to provide constant mass correction. Samples were randomly analyzed throughout the run.
Ion Mode:NEGATIVE
  
MS ID:MS002020
Analysis ID:AN002171
Instrument Name:Agilent 7890A
Instrument Type:GC QTOF
MS Type:EI
MS Comments:An Agilent GC instrument (7890A) coupled to an inert mass spectrometer with triple-Axis detector (5975C, Agilent Technologies) was used for kidney tissue fingerprinting. Briefly, 1 μL of derivatized samples were injected by an Agilent autosampler (7693). Samples were automatically injected in split mode (split ratio 1:12), into an Agilent ultra-inert deactivated glass wool split liner. Compound separation was achieved using a pre-column (10 m J&W integrated with Agilent 122-5532G) combined with a GC column DB5-MS (length, 30m; inner diameter, 0.25 mm; and 0.25 μm film of 95% dimethyl/5% diphenylpolysiloxane). The flow rate of helium carrier gas was constant at : 0.938 mL/min through the column. The lock of the retention time (RTL) relative to the internal standard (methyl stearate) peak at 19.66 minutes was performed. The column oven temperature was initially set at 60°C (maintained for 1 minute), then raised by 10°C/min until it reached 325°C, and then was held at this temperature for 10 minutes before cooling down. The injector and the transfer line temperatures were established at 250°C and 280°C, respectively. MS system: the electron impact ionization operating parameters were set as follows: filament source temperature, 230°C; electron ionization energy, 70 eV. Mass spectra were collected over a mass range of 50-600 m/z at a scan rate of 10 spectra/s. Data were acquired using the Agilent MSD ChemStation Software (Agilent Technologies). For retention index determination, a mixture of n-alkanes (C8-C28) dissolved in nhexane was run prior to the samples. Data were acquired using Agilent MSD ChemStation Software (Agilent Technologies).
Ion Mode:POSITIVE
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