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.
| Study ID | ST001328 |
| Study Title | Multiplatform, non-targeted analysis of lung extracts of uninfected and Mtb-infected C57BL/6 mice at 4 and 9 weeks p.i. |
| Study Summary | The 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 |
| Department | Departamento de Quimica y Bioquimica |
| Laboratory | Centro de Metabolomica y Bioanalisis (CEMBIO) |
| Last Name | Fernandez Garcia |
| First Name | Miguel |
| Address | Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain |
| miguel.fernandezgarcia@ceu.es | |
| Phone | +34690090778 |
| Submit Date | 2020-03-12 |
| Num Groups | 3 |
| Total Subjects | 13 |
| Num Males | 6 |
| Num Females | 7 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | GC-MS/LC-MS |
| Release Date | 2021-03-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000906 |
| Project DOI: | doi: 10.21228/M8KD7Z |
| Project Title: | Pulmonary Tuberculosis Mice Project |
| Project Type: | Natural disease progression assessment |
| Project Summary: | The 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. The potential benefit for the general research community arising from the combination of these analyses is to generate mass spectrometry data which has not been previously described for this model of the disease. This data may serve as a foundation for the validation of observations, data modeling, and biochemical interpretation of MS-based metabolic changes found in the comparisons between the different sample groups |
| Institute: | Universidad CEU San Pablo |
| Department: | Departamento de Quimica y Bioquimica |
| Laboratory: | Centro de Metabolomica y Bioanalisis (CEMBIO) |
| Last Name: | Fernandez Garcia |
| First Name: | Miguel |
| Address: | Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Spain |
| Email: | miguel.fernandezgarcia@ceu.es |
| Phone: | +34690090778 |
Subject:
| Subject ID: | SU001402 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6 |
| Age Or Age Range: | 8-10 weeks old |
| Gender: | Male and female |
| Animal Feed: | ad libitum |
| Animal Water: | ad libitum |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Pulmonary TB status |
|---|---|---|
| SA096365 | LCMSneg_4W3 | 4 weeks post-infection |
| SA096366 | GCMS_4W4 | 4 weeks post-infection |
| SA096367 | GCMS_4W1 | 4 weeks post-infection |
| SA096368 | LCMSneg_4W2 | 4 weeks post-infection |
| SA096369 | GCMS_4W2 | 4 weeks post-infection |
| SA096370 | LCMSpos_4W1 | 4 weeks post-infection |
| SA096371 | LCMSpos_4W4 | 4 weeks post-infection |
| SA096372 | LCMSpos_4W3 | 4 weeks post-infection |
| SA096373 | LCMSpos_4W2 | 4 weeks post-infection |
| SA096374 | LCMSneg_4W4 | 4 weeks post-infection |
| SA096375 | LCMSneg_4W1 | 4 weeks post-infection |
| SA096376 | GCMS_4W3 | 4 weeks post-infection |
| SA096377 | CEMS_4W1 | 4 weeks post-infection |
| SA096378 | CEMS_4W2 | 4 weeks post-infection |
| SA096379 | CEMS_4W3 | 4 weeks post-infection |
| SA096380 | CEMS_4W4 | 4 weeks post-infection |
| SA096381 | LCMSneg_9W4 | 9 weeks post-infection |
| SA096382 | LCMSneg_9W5 | 9 weeks post-infection |
| SA096383 | LCMSpos_9W1 | 9 weeks post-infection |
| SA096384 | LCMSpos_9W5 | 9 weeks post-infection |
| SA096385 | LCMSpos_9W4 | 9 weeks post-infection |
| SA096386 | LCMSpos_9W3 | 9 weeks post-infection |
| SA096387 | LCMSpos_9W2 | 9 weeks post-infection |
| SA096388 | LCMSneg_9W3 | 9 weeks post-infection |
| SA096389 | CEMS_9W1 | 9 weeks post-infection |
| SA096390 | CEMS_9W4 | 9 weeks post-infection |
| SA096391 | CEMS_9W3 | 9 weeks post-infection |
| SA096392 | CEMS_9W5 | 9 weeks post-infection |
| SA096393 | LCMSneg_9W1 | 9 weeks post-infection |
| SA096394 | LCMSneg_9W2 | 9 weeks post-infection |
| SA096395 | GCMS_9W5 | 9 weeks post-infection |
| SA096396 | CEMS_9W2 | 9 weeks post-infection |
| SA096397 | GCMS_9W3 | 9 weeks post-infection |
| SA096398 | GCMS_9W4 | 9 weeks post-infection |
| SA096399 | GCMS_9W2 | 9 weeks post-infection |
| SA096400 | GCMS_9W1 | 9 weeks post-infection |
| SA096401 | LCMSneg_UW3 | Control - uninfected |
| SA096402 | LCMSneg_UW4 | Control - uninfected |
| SA096403 | LCMSneg_UW2 | Control - uninfected |
| SA096404 | LCMSpos_UW1 | Control - uninfected |
| SA096405 | GCMS_UW1 | Control - uninfected |
| SA096406 | GCMS_UW2 | Control - uninfected |
| SA096407 | CEMS_UW4 | Control - uninfected |
| SA096408 | CEMS_UW3 | Control - uninfected |
| SA096409 | CEMS_UW2 | Control - uninfected |
| SA096410 | GCMS_UW3 | Control - uninfected |
| SA096411 | GCMS_UW4 | Control - uninfected |
| SA096412 | LCMSpos_UW4 | Control - uninfected |
| SA096413 | LCMSpos_UW3 | Control - uninfected |
| SA096414 | LCMSpos_UW2 | Control - uninfected |
| SA096415 | CEMS_UW1 | Control - uninfected |
| SA096416 | LCMSneg_UW1 | Control - uninfected |
| Showing results 1 to 52 of 52 |
Collection:
| Collection ID: | CO001397 |
| Collection Summary: | Both male and female age-matched C57BL/6 mice (8-10 weeks old) were infected with Mtb H37Rv in animal BSL-3 laboratory and monitored with food and water ad libitum. Mice were sacrificed by anesthesia with isoflurane followed by gentle cervical dislocation as approved by institutional Animal Protocol Number (APN): 08591. Mice experimental procedures were approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Alabama at Birmingham, USA. For mice studies, we adhered as per national/international regulation of “Public Health Service Policy on Humane Care and Use of Laboratory Animals” (NIH), and “Animal Welfare Act and Animal Welfare Regulations” (USDA). Mouse genotype was confirmed by PCR and Western blotting. Mtb H37Rv was grown at 37 °C with shaking in BD Difco Middlebrook 7H9 media supplemented with 0.2 % glycerol, ADS (Albumin, Dextrose, NaCl) with 0.02 % tyloxapol. Mice were infected with 5 x 104 Mtb H37Rv via the intratracheal route. Lungs were collected from uninfected (n = 4), and Mtb-infected mice at 4- and 9-weeks post-infection (n = 4 and n = 5, respectively), and stored immediately at -80 °C for further processing and metabolite extraction. |
| Sample Type: | Lung |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001417 |
| Treatment Summary: | Mice were infected with 5 x 104 Mtb H37Rv via the intratracheal route and zero timepoint and monitored for disease progression until lung collection at 4 or 9 weeks post-infection |
| Treatment: | Infection |
| Treatment Route: | Intratracheal |
| Treatment Dose: | 5 x 10^4 Mtb H37Rv |
Sample Preparation:
| Sampleprep ID: | SP001410 |
| Sampleprep Summary: | After lung collection, 1 mL of 50 % methanol was added to 100 mg of Mtb-infected or uninfected lung tissue and homogenized in a dounce homogenizer to prepare a uniform suspension. For CE-TOF/MS, 200 uL of homogenate were mixed with 200 L of 0.2 M formic acid and vortexed for 2 min. The samples were cleared by centrifugation at 16000 x g for 10 min at 4 °C and the supernatant was filter-sterilized using 0.22 um spin-X columns (Sigma). For GC-QTOF/MS and LC-QTOF/MS, 200 uL of each sample homogenate were mixed with 800 L of 80:20 methanol:MTBE (Methyl tert-butyl ether) and vortexed for 2 min. Metabolites were then extracted for 1 h with shaking at room temperature and then centrifuged at 4000 x g at 20 °C for 20 min. Supernatants were sterile filtered using 0.22 um Spin-X columns. All samples were passed through a Millipore filter (30-kDa cutoff) to remove large proteins. Samples were dried under high vacuum and stored at -80 °C until further platform-specific processing and analysis. For CE-ESI(+)-TOF/MS analysis, The dried samples were resuspended in Milli-Q water containing 0.1 mM formic acid and 0.2 mM methionine sulfone (internal standard) (Sigma-Aldrich, Germany) by vortexing for 1 min. After subsequent centrifugation (12600 x g, 15 min), the resulting clear solution was analyzed. For GC-QTOF/MS analysis, The above described dried samples were re-suspended in 450 µL of MeOH:H2O:MTBE (74:10:16) and after centrifugation at 12600 x g, 15 min at 4 °C, the supernatant was transferred to a vial with insert and evaporated to dryness under high vacuum. The obtained dried extracts were derivatized by a MPS autosampler for GC/MS analysis as previously described (Fiehn O., 2006). For LC-QTOF/MS analysis, The above described dried samples were resuspended in 200 µL of methanol:water:MTBE (7.4:1:1.6), vortexed for 1.5 h and centrifuged (4000 x g, 10 min, 4 °C). Clear solutions were analyzed. |
| Sample Derivatization: | In GC-EI-QTOF/MS analyses, Briefly, aldehyde and keto groups were first converted to O-methyloximes by reaction with 10 µL pyridine containing 15 mg/mL O-methoxyamine (Sigma-Aldrich, Germany) for 60 min at 70 °C. In a second step, acid hydrogen-containing metabolites were trimethylsilylated by reaction with 10 µL N,O-Bis(trimethylsilyl)trifluoroacetamide (BSTFA) (Sigma-Aldrich, Germany) to enhance the GC/MS metabolite coverage |
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 |
MS:
| MS ID: | MS002057 |
| Analysis ID: | AN002211 |
| Instrument Name: | Agilent 6520 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Mass spectrometry detection was performed in positive ESI mode in a full scan from 100 to 1000 m/z. Samples were analyzed in separate runs (positive and negative ionization modes), in a randomized order. Capillary voltage was set to 4.5 kV; the drying gas flow rate was 10 L·min-1 at 350 °C and gas nebulizer at 40 psi; fragmentor voltage, skimmer voltage and octopole radio frequency voltage were set to 175, 65 and 750 V, respectively. Data were collected at a scan rate of 1.05 spectra·s-1. The resulting LC-QTOF/MS data files were cleaned of background noise and unrelated ions by the Batch Recursive Feature Extraction tool with Agilent MassHunter Profinder software version B.06.00. Data were extracted using data mining algorithms of the software. |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 4.5 kV |
| Dry Gas Flow: | 10 L·min-1 |
| Dry Gas Temp: | 350 °C |
| Gas Pressure: | 40 psi |
| Octpole Voltage: | 750 V |
| MS ID: | MS002058 |
| Analysis ID: | AN002212 |
| Instrument Name: | Agilent 6520 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Mass spectrometry detection was performed in negative ESI mode in a full scan from 100 to 1000 m/z. Samples were analyzed in separate runs (positive and negative ionization modes), in a randomized order. Capillary voltage was set to 4.5 kV; the drying gas flow rate was 10 L·min-1 at 350 °C and gas nebulizer at 40 psi; fragmentor voltage, skimmer voltage and octopole radio frequency voltage were set to 175, 65 and 750 V, respectively. Data were collected at a scan rate of 1.05 spectra·s-1. The resulting LC-QTOF/MS data files were cleaned of background noise and unrelated ions by the Batch Recursive Feature Extraction tool with Agilent MassHunter Profinder software version B.06.00. Data were extracted using data mining algorithms of the software. |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 4.5 kV |
| Dry Gas Flow: | 10 L·min-1 |
| Dry Gas Temp: | 350 °C |
| Gas Pressure: | 40 psi |
| Octpole Voltage: | 750 V |
| MS ID: | MS002059 |
| Analysis ID: | AN002213 |
| Instrument Name: | Agilent 7200 QTOF |
| Instrument Type: | QTOF |
| MS Type: | EI |
| MS Comments: | The analysis was performed on an Agilent Technologies 7200 accurate mass Q/TOF analyzer equipped with an electron ionization (EI) source.The MS scan mode was chosen as the acquisition mode, with the mass range of 50-650 m/z and an acquisition rate of 10 spectra·s-1. The individual analytical fingerprints obtained were deconvoluted using MassHunter Unknown Analysis version B.07.00. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002060 |
| Analysis ID: | AN002214 |
| Instrument Name: | Agilent 6224 TOF |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | The optimized MS parameters were: fragmentor 125 V, Skimmer 65 V, octopole 750 V, nebulizer pressure 10 psi, drying gas temperature at 200 °C and flow rate 10.0 L·min-1. The capillary voltage was 3500 V. Data were acquired in positive electrospray ionization (ESI) mode with a full scan from m/z 50 to 1000 at a rate of 1 spectra·s-1. The resulting CE-TOF/MS data files were cleaned of background noise and unrelated ions by the Batch Recursive Feature Extraction tool with Agilent MassHunter Profinder version B.06.00 software. Data were extracted using a data mining algorithm based on the software. |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3.5 kV |
| Dry Gas Flow: | 10 L·min-1 |
| Octpole Voltage: | 750 V |
