Summary of Study ST001328

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 PR000906. The data can be accessed directly via it's Project DOI: 10.21228/M8KD7Z 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 IDST001328
Study TitleMultiplatform, non-targeted analysis of lung extracts of uninfected and Mtb-infected C57BL/6 mice at 4 and 9 weeks p.i.
Study SummaryThe goal of this multiplatform, non-targeted metabolomics study was to explore the metabolic alterations occurring during the natural progression of pulmonary tuberculosis in a murine model of disease (C57BL/6 genotype). For this purpose, we used gas chromatography, capillary electrophoresis, and reversed-phase liquid chromatography coupled to high-resolution mass analyzers (GC-EI-QTOF/MS, CE-ESI(+)-QTOF/MS, LC-ESI(+)-QTOF/MS and LC-ESI(-)-QTOF/MS to analyze lung extracts of age and sex-matched uninfected mice (UW, n=4), Mycobacterium tuberculosis-infected mice at 4 weeks post-infection (4W, n=4) and Mycobacterium tuberculosis-infected mice at 9 weeks post-infection. All data were acquired in MS1 mode, following a canonical non-targeted workflow.
Institute
Universidad CEU San Pablo
DepartmentDepartamento de Quimica y Bioquimica
LaboratoryCentro de Metabolomica y Bioanalisis (CEMBIO)
Last NameFernandez Garcia
First NameMiguel
AddressFacultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain
Emailmiguel.fernandezgarcia@ceu.es
Phone+34690090778
Submit Date2020-03-12
Num Groups3
Total Subjects13
Num Males6
Num Females7
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailGC-MS/LC-MS
Release Date2021-03-15
Release Version1
Miguel Fernandez Garcia Miguel Fernandez Garcia
https://dx.doi.org/10.21228/M8KD7Z
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Combined analysis:

Analysis ID AN002211 AN002212 AN002213 AN002214
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase GC CE
Chromatography system Agilent 1200 Agilent 1200 Agilent 7890B Agilent 7100 CE
Column Agilent Poroshell 120 EC-C8 (150 x 2.1mm,2.7um) Agilent Poroshell 120 EC-C8 (150 x 2.1mm,2.7um) Agilent DB5-MS (30m x 0.25mm, 0.25um) Agilent bare-fused silica capillary (96 cm x 50 um i.d.)
MS Type ESI ESI EI ESI
MS instrument type QTOF QTOF QTOF TOF
MS instrument name Agilent 6520 QTOF Agilent 6520 QTOF Agilent 7200 QTOF Agilent 6224 TOF
Ion Mode POSITIVE NEGATIVE POSITIVE POSITIVE
Units Abundance Abundance Abundance Abundance

Chromatography:

Chromatography ID:CH001621
Chromatography Summary:5 μL of extracted lung samples were injected into a thermostated (60 °C) Agilent Poroshell 120 EC-C8 column (150 mm × 2.1 mm, 2.7 μm; Agilent Technologies, CA, USA) with a guard column Ascentis Express C8 (5 mm × 2.1 mm, 2.7 μm; Supelco, Bellefonte, PA, USA). The flow rate was 0.4 mL·min-1 with solvent A (10 mM ammonium formate in Milli-Q water) and solvent B (10 mM ammonium formate in methanol and 15 % of isopropanol) for analysis in positive ionization mode. Initial conditions at time 0 were 82 % B, increasing to 96 % B in 30 min. This was then held until 38 min. The gradient then increased to 100 % B by 38.5 min and held until 40.5 min. The conditions were then returned to the starting conditions by 42 min, followed by an 8 min re-equilibration time. The total run time of the method was 50 min.
Instrument Name:Agilent 1200
Column Name:Agilent Poroshell 120 EC-C8 (150 x 2.1mm,2.7um)
Column Temperature:60
Flow Gradient:Initial conditions at time 0 were 82 % B, increasing to 96 % B in 30 min. This was then held until 38 min. The gradient then increased to 100 % B by 38.5 min and held until 40.5 min. The conditions were then returned to the starting conditions by 42 min, followed by an 8 min re-equilibration time. The total run time of the method was 50 min.
Flow Rate:0.4mL·min-1
Solvent A:100% water; 0.1% formic acid
Solvent B:85% methanol/15% isopropanol; 0.1 % formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH001622
Chromatography Summary:5 μL of extracted lung samples were injected into a thermostated (60 °C) Agilent Poroshell 120 EC-C8 column (150 mm × 2.1 mm, 2.7 μm; Agilent Technologies, CA, USA) with a guard column Ascentis Express C8 (5 mm × 2.1 mm, 2.7 μm; Supelco, Bellefonte, PA, USA). The flow rate was 0.4 mL·min-1 with solvent A (MilliQ water with 0.1 % formic acid), and solvent B (methanol with 0.1 % formic acid and 15 % of isopropanol) for analysis in negative ionization mode. Initial conditions at time 0 were 82 % B, increasing to 96 % B in 30 min. This was then held until 38 min. The gradient then increased to 100 % B by 38.5 min and held until 40.5 min. The conditions were then returned to the starting conditions by 42 min, followed by an 8 min re-equilibration time. The total run time of the method was 50 min.
Instrument Name:Agilent 1200
Column Name:Agilent Poroshell 120 EC-C8 (150 x 2.1mm,2.7um)
Column Temperature:60
Flow Gradient:Initial conditions at time 0 were 82 % B, increasing to 96 % B in 30 min. This was then held until 38 min. The gradient then increased to 100 % B by 38.5 min and held until 40.5 min. The conditions were then returned to the starting conditions by 42 min, followed by an 8 min re-equilibration time. The total run time of the method was 50 min.
Flow Rate:0.4mL·min-1
Solvent A:100% water; 0.1% formic acid
Solvent B:85% methanol/15% isopropanol; 0.1 % formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH001623
Chromatography Summary:1 µL of sample was injected into a multimode inlet at 230 °C with a split ratio set at 1:12 with 9.354 mL·min-1 connected to a capillary column (30 m x 0.25 mm x 0.25 µm; Agilent, Germany). Helium was used as carrier gas, at a flow rate of 0.78 mL·min-1. Column temperature was 60 °C for 1 min and then programmed to increase at a rate of 10 °C·min-1 until 325 °C which was maintained for 10 min. Total runtime was 37.5 min.
Instrument Name:Agilent 7890B
Column Name:Agilent DB5-MS (30m x 0.25mm, 0.25um)
Flow Rate:9.354 mL·min-1
Chromatography Type:GC
  
Chromatography ID:CH001624
Chromatography Summary:The separation occurred in a fused-silica capillary (Agilent Technologies) (total length, 96 cm; i.d., 50 μm) under normal polarity with a background electrolyte containing 1.0 M formic acid in 10 % (v/v) methanol at 20 °C. Sheath liquid (6 µL·min-1) was methanol/water (1/1, v/v) containing 1.0 mM formic acid with two reference masses to allow correction and high mass resolution in the MS. Samples were hydrodynamically injected at 50 mbar for 35 s and stacked by injecting background electrolyte at 100 mbar for 10 s.
Instrument Name:Agilent 7100 CE
Column Name:Agilent bare-fused silica capillary (96 cm x 50 um i.d.)
Chromatography Type:CE
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