Summary of Study ST003549
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 PR002185. The data can be accessed directly via it's Project DOI: 10.21228/M86527 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 | ST003549 |
| Study Title | Metabolomics analysis of kidney, brain, liver, and plasma from Aldh7a1-/- and Aldh7a1+/+ mice. |
| Study Summary | Metabolite analysis of kidney, brain, liver, and plasma isolated from Aldh7a1+/+ and Aldh7a1-/- (n=3/each) fed diets consisting of 0.9% w/w lysine and 18 ppm pyridoxine. Tissues were cryo-homogenized using a liquid nitrogen cooled mortar and pestle into a fine powder and approximately 25-50 mg of each tissue was transferred to a pre-weighed homogenization tube to which ~20 2.3 mm zirconia beads and 1 mL of 80% ice cold methanol were added. Tissues were homogenized using a bead mill and cleared by centrifugation at 4C, where each of the 3-4 cycles consisted of a 60 second homogenization at 6 m/s followed by a 30 second pause. A volume equivalent to 25 mg of tissue extract was transferred to a new tube, and 250 µL of 80% methanol containing 1 µL of stable isotope-labeled internal amino acid standard mix was added. Metabolites were concentrated using a SpeedVac until dry. For plasma metabolite analysis, 10 µL of plasma was added to 250 µl of 80% methanol containing 1 µL of stable isotope-labeled internal amino acid standard mix, vortexed at 4C for 10 minutes, and centrifuged. 0.9 mL of supernatant was transferred to a new tube and concentrated using a SpeedVac until dry. Metabolites were reconstituted into 25-50 µL of water, vortexed, centrifuged, and transferred to vials for analysis by LCMS. LCMS was performed using a ZIC-pHILIC LC column coupled to a Vanquish LC and a flow gradient consisting of 10 mM ammonium carbonate in water and pure acetonitrile. The LC was coupled to an Exploris 240 mass spectrometer operated in a polarity switching data-dependent Top 5 mode. Full MS scan parameters for both positive and negative mode were set to 67-1000 m/z at a resolution of 120k and ddMS2 were collected at a resolution of 30k. Data files are labeled with brain, liver, kidney, and plasma followed by a number. The number represents a mouse. Samples 1-3 are from Aldh7a1-/- mice and samples 4-6 are from Aldh7a1+/+ mice. |
| Institute | University of British Columbia |
| Department | Biochemistry & Molecular Biology |
| Laboratory | Parker laboratory |
| Last Name | Parker |
| First Name | Seth |
| Address | 950 W 28th Ave, Vancouver, British Columbia, V6H 0B3, Canada |
| seth.parker@bcchr.ca | |
| Phone | 6048753121 |
| Submit Date | 2024-11-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-11-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002185 |
| Project DOI: | doi: 10.21228/M86527 |
| Project Title: | Metabolomics analysis of tissues isolated from Aldh7a1+/+ and Aldh7a1-/- (KO) mice. |
| Project Type: | Manuscript |
| Project Summary: | ALDH7A1 is an enzyme involved in the catabolism of lysine. Using Aldh7a1-knockout (-/-) and wild-type (+/+) mice and metabolomics, we aim to determine how Aldh7a1-deficiency leads to the accumulation of lysine catabolites upstream of ALDH7A1 and affects other metabolic pathways. Our results suggest that there is a tissue-specific accumulation of lysine and other metabolites, with the brain exhibiting the largest number of significantly different metabolites. |
| Institute: | University of British Columbia |
| Department: | Biochemistry & Molecular Biology |
| Laboratory: | Parker laboratory |
| Last Name: | Parker |
| First Name: | Seth |
| Address: | 950 W 28th Ave, Vancouver, British Columbia, V6H 0B3, Canada |
| Email: | seth.parker@bcchr.ca |
| Phone: | 6048753121 |
Subject:
| Subject ID: | SU003678 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Age Or Age Range: | 15-17 week old mice. |
| Gender: | Male and female |
| Animal Feed: | 0.9% w/w lysine, 18 ppm pyridoxine (standard diets) |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Sample source |
|---|---|---|---|
| SA387804 | Brain_4 | Aldh7a1+/+ | Brain |
| SA387805 | Brain_5 | Aldh7a1+/+ | Brain |
| SA387806 | Brain_6 | Aldh7a1+/+ | Brain |
| SA387816 | Brain_1 | Aldh7a1-/- | Brain |
| SA387817 | Brain_2 | Aldh7a1-/- | Brain |
| SA387818 | Brain_3 | Aldh7a1-/- | Brain |
| SA387807 | Kidney_4 | Aldh7a1+/+ | Kidney |
| SA387808 | Kidney_5 | Aldh7a1+/+ | Kidney |
| SA387809 | Kidney_6 | Aldh7a1+/+ | Kidney |
| SA387819 | Kidney_3 | Aldh7a1-/- | Kidney |
| SA387820 | Kidney_2 | Aldh7a1-/- | Kidney |
| SA387821 | Kidney_1 | Aldh7a1-/- | Kidney |
| SA387810 | Liver_4 | Aldh7a1+/+ | Liver |
| SA387811 | Liver_6 | Aldh7a1+/+ | Liver |
| SA387812 | Liver_5 | Aldh7a1+/+ | Liver |
| SA387822 | Liver_3 | Aldh7a1-/- | Liver |
| SA387823 | Liver_2 | Aldh7a1-/- | Liver |
| SA387824 | Liver_1 | Aldh7a1-/- | Liver |
| SA387813 | Plasma_6 | Aldh7a1+/+ | Plasma |
| SA387814 | Plasma_5 | Aldh7a1+/+ | Plasma |
| SA387815 | Plasma_4 | Aldh7a1+/+ | Plasma |
| SA387825 | Plasma_1 | Aldh7a1-/- | Plasma |
| SA387826 | Plasma_2 | Aldh7a1-/- | Plasma |
| SA387827 | Plasma_3 | Aldh7a1-/- | Plasma |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO003671 |
| Collection Summary: | Liver, brain, or plasma samples collected from mice were snap frozen in liquid nitrogen and ground to a fine powder using a liquid nitrogen cooled mortar and pestle. Metabolites from 25 mg of tissues were extracted using a bead mill and 1 mL of 80% methanol containing internal isotopic standards. 10 µL of plasma was added to 250 µL of 80% methanol containing internal isotopic standards. All samples were analyzed using LCMS. |
| Sample Type: | Tissue or Plasma |
Treatment:
| Treatment ID: | TR003687 |
| Treatment Summary: | No treatment. |
Sample Preparation:
| Sampleprep ID: | SP003685 |
| Sampleprep Summary: | Dried samples were reconstituted in 50 µL of HPLC-grade water. Samples were vortexed for ~10 minutes, then centrifuged at 21,000 x g for 15 min at 4°C. 40 microliters were transferred to LC vials containing glass inserts for analysis. |
Combined analysis:
| Analysis ID | AN005833 | AN005834 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Merck SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | Merck SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Exploris 240 | Thermo Exploris 240 |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Ion counts | Ion counts |
Chromatography:
| Chromatography ID: | CH004432 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Merck SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
| Column Temperature: | 25°C |
| Flow Gradient: | 80-20%B (0-30 min), 20-20%B (30-40 minute), and 20-80%B (40-40.5 minute); the LC column was re-equilibrated using 80-80%B from 40.5-52 minute before subsequent injections |
| Flow Rate: | 100 uL/min |
| Solvent A: | 100% Water; 10 mM Ammonium Carbonate, pH 9.0 |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS005553 |
| Analysis ID: | AN005833 |
| Instrument Name: | Thermo Exploris 240 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The LC was coupled to a Thermo Scientific Exploris 240 mass spectrometer operating in heated electrospray ionization mode (HESI) for analysis. The following parameters were set for HESI: spray voltage 3.4 kV (positive) and 2 kV (negative), static spray voltage, sheath gas 25, aux gas 5, sweep gas 0.5, ion transfer tube temperature 320°C, and vaporizer temperature 75°C. The global parameters included an expected peak width of 20 seconds, mild trapping, and a default charge state of 1. A 40-min polarity switching data-dependent Top 5 method was used for positive mode and a data-dependent Top 3 method was used for negative mode. Full MS scan parameters for both positive and negative modes were set as follows: scan range 67-1000 m/z collected in profile mode, Orbitrap resolution 120,000, RF lens 70%, AGC target of 300%, and maximum injection time set to automatic. ddMS2 for positive mode were collected in centroid mode at an Orbitrap resolution of 30,000, isolation window of 1.5 m/z, an AGC target set to standard, a maximum injection time set to automatic, and a normalized collision energy set to 10%, 30%, and 80%. ddMS2 for negative mode were collected in centroid mode at an Orbitrap resolution of 30,000, isolation window of 2 m/z, an AGC target set to standard, a maximum injection time set to automatic, and a normalized collision energy set to 30%. For both positive and negative ddMS2, we applied an intensity threshold of 5e4 and a dynamic exclusion of 5 ppm for 10 seconds, excluding isotopes. A targeted selected ion monitoring (tSIM) scan was also included for pipecolate and P6C/P2C, and the retention time ranges were based on elution of authentic standards (pipecolate) or from positive samples (Aldh7a1-deficient tissues). The tSIM scan for pipecolate was collected from 8-12 minutes in negative mode at an isolation window of 4 m/z (for metabolomics) or 18 m/z (for isotope-tracing experiments, to include m/z shifts), an Orbitrap resolution of 120,000, a RF lens at 70%, an automatic maximum injection time, and collected in profile mode. The tSIM scan for P6C/P2C was collected from 6-10 minutes in positive mode at an isolation window of 4 m/z (for metabolomics) or 18 m/z (for isotope-tracing experiments, to include m/z shifts), an Orbitrap resolution of 120,000, a RF lens at 70%, an automatic maximum injection time, and collected in profile mode. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005554 |
| Analysis ID: | AN005834 |
| Instrument Name: | Thermo Exploris 240 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The LC was coupled to a Thermo Scientific Exploris 240 mass spectrometer operating in heated electrospray ionization mode (HESI) for analysis. The following parameters were set for HESI: spray voltage 3.4 kV (positive) and 2 kV (negative), static spray voltage, sheath gas 25, aux gas 5, sweep gas 0.5, ion transfer tube temperature 320°C, and vaporizer temperature 75°C. The global parameters included an expected peak width of 20 seconds, mild trapping, and a default charge state of 1. A 40-min polarity switching data-dependent Top 5 method was used for positive mode and a data-dependent Top 3 method was used for negative mode. Full MS scan parameters for both positive and negative modes were set as follows: scan range 67-1000 m/z collected in profile mode, Orbitrap resolution 120,000, RF lens 70%, AGC target of 300%, and maximum injection time set to automatic. ddMS2 for positive mode were collected in centroid mode at an Orbitrap resolution of 30,000, isolation window of 1.5 m/z, an AGC target set to standard, a maximum injection time set to automatic, and a normalized collision energy set to 10%, 30%, and 80%. ddMS2 for negative mode were collected in centroid mode at an Orbitrap resolution of 30,000, isolation window of 2 m/z, an AGC target set to standard, a maximum injection time set to automatic, and a normalized collision energy set to 30%. For both positive and negative ddMS2, we applied an intensity threshold of 5e4 and a dynamic exclusion of 5 ppm for 10 seconds, excluding isotopes. A targeted selected ion monitoring (tSIM) scan was also included for pipecolate and P6C/P2C, and the retention time ranges were based on elution of authentic standards (pipecolate) or from positive samples (Aldh7a1-deficient tissues). The tSIM scan for pipecolate was collected from 8-12 minutes in negative mode at an isolation window of 4 m/z (for metabolomics) or 18 m/z (for isotope-tracing experiments, to include m/z shifts), an Orbitrap resolution of 120,000, a RF lens at 70%, an automatic maximum injection time, and collected in profile mode. The tSIM scan for P6C/P2C was collected from 6-10 minutes in positive mode at an isolation window of 4 m/z (for metabolomics) or 18 m/z (for isotope-tracing experiments, to include m/z shifts), an Orbitrap resolution of 120,000, a RF lens at 70%, an automatic maximum injection time, and collected in profile mode. |
| Ion Mode: | NEGATIVE |
