Summary of Study ST004096
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 PR002573. The data can be accessed directly via it's Project DOI: 10.21228/M82C09 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004096 |
| Study Title | The loss of Peroxiredoxin 2 in mice leads to a disrupted biochemical aging phenotype in erythrocytes |
| Study Summary | Biochemical aging is a complex, multi-factorial process involving declines in energy metabolism and the ability to maintain redox states over time. The peroxiredoxin family of enzymes is critical for maintenance of cellular redox states. In mice, enucleate mature red blood cells (RBC) have a lifespan of about 50 days and thus provide an ideal cell to track cellular aging in vivo. In order to characterize the consequence of compromised redox function, we assessed the RBC metabolome at different time points using biotin labeling to isolate specific RBC populations. 183 distinct metabolites were profiled and quantified using mass spectrometry from cell populations of defined ages at approximately 1, 2, and 3 weeks. Interestingly, the general patterns between RBC derived from wildtype and Prdx2 knockout mice RBC were concordant with one another, with significant alterations in ATP producing reactions, as well as redox maintenance and membrane structure maintenance related metabolic reactions. However, most of the age-related metabolite shifts seen in both wildtype and Prdx2 knockout RBC over time were noted to be significantly more pronounced in the Prdx2 knockouts, suggesting an ‘older’ biochemical age phenotype. |
| Institute | Scripps Research Institute |
| Laboratory | Jeffrey Friedman |
| Last Name | Friedman |
| First Name | Jeffrey |
| Address | 10550 North Torrey Pines Road La Jolla, CA 92037 |
| njamshidi@mednet.ucla.edu | |
| Phone | 310.794.1411 |
| Submit Date | 2025-07-09 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | GC-MS/LC-MS |
| Release Date | 2025-12-24 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002573 |
| Project DOI: | doi: 10.21228/M82C09 |
| Project Title: | The loss of Peroxiredoxin 2 in mice disrupts the biochemical aging phenotype in erythrocytes |
| Project Type: | Targeted time course metabolomic profiles of red blood cells in vivo |
| Project Summary: | Biochemical aging is a complex, multi-factorial process involving declines in energy metabolism and the ability to maintain redox states over time. The peroxiredoxin family of enzymes is critical for maintenance of cellular redox states. In mice, enucleate mature red blood cells (RBC) have a lifespan of about 50 days and thus provide an ideal cell to track cellular aging in vivo. In order to characterize the consequence of compromised redox function, we assessed the RBC metabolome at different time points using biotin labeling to isolate specific RBC populations. 183 distinct metabolites were profiled and quantified using mass spectrometry from cell populations of defined ages at approximately 1, 2, and 3 weeks. Interestingly, the general patterns between RBC derived from wildtype and Prdx2 knockout mice RBC were concordant with one another, with significant alterations in ATP producing reactions, as well as redox maintenance and membrane structure maintenance related metabolic reactions. However, most of the age-related metabolite shifts seen in both wildtype and Prdx2 knockout RBC over time were noted to be significantly more pronounced in the Prdx2 knockouts, suggesting an ‘older’ biochemical age phenotype. |
| Institute: | Scripps Research Institute |
| Laboratory: | Jeffrey Friedman |
| Last Name: | Friedman |
| First Name: | Jeffrey |
| Address: | 10550 North Torrey Pines Road La Jolla, CA 92037 |
| Email: | njamshidi@mednet.ucla.edu |
| Phone: | 310.794.1411 |
| Funding Source: | from NIH RO1 DK080232, R21 DK075763 and W8IXWH-10-2-0059 |
| Publications: | submitted |
| Contributors: | Edward D. Karoly, Robert Mohney |
Subject:
| Subject ID: | SU004242 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57/BL6 or Prdx2 knockout male mice from The Jackson Laboratory |
| Gender: | Male |
| Animal Animal Supplier: | The Jackson Laboratory |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | GENOTYPE | GROUP_DESC | DAY |
|---|---|---|---|---|---|
| SA474227 | TSRI-00060 | RBC | PRDX2 | Biotin + | 15 |
| SA474228 | TSRI-00059 | RBC | PRDX2 | Biotin + | 15 |
| SA474229 | TSRI-00058 | RBC | PRDX2 | Biotin + | 15 |
| SA474230 | TSRI-00057 | RBC | PRDX2 | Biotin + | 15 |
| SA474239 | TSRI-00068 | RBC | PRDX2 | Biotin - | 15 |
| SA474240 | TSRI-00067 | RBC | PRDX2 | Biotin - | 15 |
| SA474241 | TSRI-00066 | RBC | PRDX2 | Biotin - | 15 |
| SA474242 | TSRI-00065 | RBC | PRDX2 | Biotin - | 15 |
| SA474231 | TSRI-00076 | RBC | PRDX2 | Biotin + | 20 |
| SA474232 | TSRI-00073 | RBC | PRDX2 | Biotin + | 20 |
| SA474233 | TSRI-00075 | RBC | PRDX2 | Biotin + | 20 |
| SA474234 | TSRI-00074 | RBC | PRDX2 | Biotin + | 20 |
| SA474243 | TSRI-00081 | RBC | PRDX2 | Biotin - | 20 |
| SA474244 | TSRI-00082 | RBC | PRDX2 | Biotin - | 20 |
| SA474245 | TSRI-00083 | RBC | PRDX2 | Biotin - | 20 |
| SA474246 | TSRI-00084 | RBC | PRDX2 | Biotin - | 20 |
| SA474235 | TSRI-00044 | RBC | PRDX2 | Biotin + | 8 |
| SA474236 | TSRI-00043 | RBC | PRDX2 | Biotin + | 8 |
| SA474237 | TSRI-00042 | RBC | PRDX2 | Biotin + | 8 |
| SA474238 | TSRI-00041 | RBC | PRDX2 | Biotin + | 8 |
| SA474247 | TSRI-00050 | RBC | PRDX2 | Biotin - | 8 |
| SA474248 | TSRI-00051 | RBC | PRDX2 | Biotin - | 8 |
| SA474249 | TSRI-00052 | RBC | PRDX2 | Biotin - | 8 |
| SA474250 | TSRI-00049 | RBC | PRDX2 | Biotin - | 8 |
| SA474251 | TSRI-00053 | RBC | WT | Biotin + | 15 |
| SA474252 | TSRI-00056 | RBC | WT | Biotin + | 15 |
| SA474253 | TSRI-00055 | RBC | WT | Biotin + | 15 |
| SA474254 | TSRI-00054 | RBC | WT | Biotin + | 15 |
| SA474263 | TSRI-00064 | RBC | WT | Biotin - | 15 |
| SA474264 | TSRI-00063 | RBC | WT | Biotin - | 15 |
| SA474265 | TSRI-00062 | RBC | WT | Biotin - | 15 |
| SA474266 | TSRI-00061 | RBC | WT | Biotin - | 15 |
| SA474255 | TSRI-00072 | RBC | WT | Biotin + | 20 |
| SA474256 | TSRI-00071 | RBC | WT | Biotin + | 20 |
| SA474257 | TSRI-00070 | RBC | WT | Biotin + | 20 |
| SA474258 | TSRI-00069 | RBC | WT | Biotin + | 20 |
| SA474267 | TSRI-00077 | RBC | WT | Biotin - | 20 |
| SA474268 | TSRI-00078 | RBC | WT | Biotin - | 20 |
| SA474269 | TSRI-00079 | RBC | WT | Biotin - | 20 |
| SA474270 | TSRI-00080 | RBC | WT | Biotin - | 20 |
| SA474259 | TSRI-00037 | RBC | WT | Biotin + | 8 |
| SA474260 | TSRI-00040 | RBC | WT | Biotin + | 8 |
| SA474261 | TSRI-00038 | RBC | WT | Biotin + | 8 |
| SA474262 | TSRI-00039 | RBC | WT | Biotin + | 8 |
| SA474271 | TSRI-00048 | RBC | WT | Biotin - | 8 |
| SA474272 | TSRI-00047 | RBC | WT | Biotin - | 8 |
| SA474273 | TSRI-00046 | RBC | WT | Biotin - | 8 |
| SA474274 | TSRI-00045 | RBC | WT | Biotin - | 8 |
| Showing results 1 to 48 of 48 |
Collection:
| Collection ID: | CO004235 |
| Collection Summary: | RBC of defined age were isolated using streptavidin-magnetic beads and LD columns (Miltenyi, Auburn, CA) to pull down biotin labeled cells for comparative biochemical studies. 100 μl of streptavidin beads were added to a variable volume of saline washed, packed red cells. The volume of packed cells used ranged between 150— 600 μl, depending upon the percentage of biotinylated cells in the sample. In order to increase the fraction of biotin - cells available at day 8, animals for this point were phlebotomized 1 day after biotin labeling to stimulate production of new cells prior to harvest at day 8. In each separation, a total of 100 μl of biotin labeled cells was targeted for purification. Cells were distributed to those analyses requiring viable cells, with the remaining cells stored at -80°C until used for metabolomics. Mean purity of all Biotin+ samples was 96.4% and 87% in all Biotin- samples. Purity was determined by FACS analysis following staining with a streptavidin:PE conjugate (Southern Biotech). |
| Sample Type: | Erythrocytes |
| Collection Method: | venipuncture |
| Collection Location: | Described in summary |
| Collection Frequency: | Described in summary |
| Volumeoramount Collected: | Described in summary |
| Storage Conditions: | Described in summary |
Treatment:
| Treatment ID: | TR004251 |
| Treatment Summary: | Biotin labeling was done using a single intravenous injection (100 μl) of sulfo-NHS-ester biotin suspended in sterile saline at a concentration of 4mg/ml 28,29. Once labeled, RBC survival was followed at intervals by staining a small (1-5 μl) blood sample with an avidin-conjugated fluorophore and determining the fraction of labeled cells remaining by flow cytometry (FACS). |
Sample Preparation:
| Sampleprep ID: | SP004248 |
| Sampleprep Summary: | In each separation, a total of 100 μl of biotin labeled cells was targeted for purification. Cells were distributed to those analyses requiring viable cells, with the remaining cells stored at -80°C until used for metabolomics. Mean purity of all Biotin+ samples was 96.4% and 87% in all Biotin- samples. The sample preparation process was carried out using the automated MicroLab STAR system from Hamilton Company. Recovery standards were added prior to the first step in the extraction process for QC purposes. Sample preparation was conducted using a proprietary series of organic and aqueous extractions to remove the protein fraction while allowing maximum recovery of small molecules. The resulting extract was divided into two fractions; one for analysis by LC and one for analysis by GC. Samples were placed briefly on a TurboVap to remove the organic solvent. Each sample was then frozen and dried under vacuum. Samples were then prepared for the appropriate instrument, either LC/MS or GC/MS. For QA/QC purposes, a number of additional samples are included with each day’s analysis. Furthermore, a selection of QC compounds is added to every sample, including those under test. These compounds are carefully chosen so as not to interfere with the measurement of the endogenous compounds. These QC samples includes: 1) large pool of human plasma samples maintained by Metabolon, 2) pool created from a small specific aliquot from this experiment, 3) aliquot of ultra-pure water, 4) aliquot of solvents used in the extractions. These QC samples are primarily used to evaluate the process control for each study as well as aiding in the data curation. |
| Sampleprep Protocol Filename: | TSRI-01-22VW_methods.pdf |
| Sampleprep Protocol Comments: | See protocol file |
| Processing Method: | See protocol file |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | See protocol file |
| Extract Enrichment: | See protocol file |
| Subcellular Location: | Cytosol |
Combined analysis:
| Analysis ID | AN006789 | AN006790 | AN006791 |
|---|---|---|---|
| Chromatography ID | CH005157 | CH005158 | CH005159 |
| MS ID | MS006488 | MS006489 | MS006490 |
| Analysis type | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | GC |
| Chromatography system | Waters Acquity | Waters Acquity | Thermo-Finnigan Trace DSQ |
| Column | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | PerkinElmer Velocity-5 (30m x 0.25mm x 0.25um) |
| MS Type | ESI | ESI | EI |
| MS instrument type | Triple quadrupole | Triple quadrupole | Single quadrupole |
| MS instrument name | Thermo-Finnigan LTQ | Thermo-Finnigan LTQ | Thermo-Finnigan Trace DSQ |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE |
| Units | counts | counts | counts |
Chromatography:
| Chromatography ID: | CH005157 |
| Chromatography Summary: | Acidic extracts |
| Methods Filename: | TSRI-01-22VW_methods.pdf |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | Linear gradient from 5% B to 80% B over 3.35 minutes. |
| Flow Rate: | 350 microL/min |
| Solvent A: | 100% water; 0.1% Formic acid |
| Solvent B: | 100% methanol; 0.1% Formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH005158 |
| Chromatography Summary: | Basic extracts |
| Methods Filename: | TSRI-01-22VW_methods.pdf |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99% B in 0.5 minutes. |
| Flow Rate: | 350 microL/min |
| Solvent A: | 100% water; 6.5mM Ammonium bicarbonate |
| Solvent B: | 95% methanol/5% water; 6.5mM Ammonium bicarbonate |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH005159 |
| Chromatography Summary: | The samples destined for analysis by GC-MS were dried under vacuum desiccation for a minimum of 18 h prior to being derivatized under dried nitrogen. Derivatized samples were separated on a 5% diphenyl / 95% dimethyl polysiloxane fused silica PerkinElmer Velocity-5 (30m x 0.25mm x 0.25µm) column with helium as carrier gas and a temperature ramp from 60° to 340°C in a 16 min period. |
| Methods Filename: | TSRI-01-22VW_methods.pdf |
| Instrument Name: | Thermo-Finnigan Trace DSQ |
| Column Name: | PerkinElmer Velocity-5 (30m x 0.25mm x 0.25um) |
| Column Temperature: | 60 to 340 over a 16 minute period |
| Flow Gradient: | - |
| Flow Rate: | - |
| Solvent A: | - |
| Solvent B: | - |
| Chromatography Type: | GC |
MS:
| MS ID: | MS006488 |
| Analysis ID: | AN006789 |
| Instrument Name: | Thermo-Finnigan LTQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Acidic |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | TSRI-01-22VW_methods.pdf |
| MS ID: | MS006489 |
| Analysis ID: | AN006790 |
| Instrument Name: | Thermo-Finnigan LTQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Basic |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | TSRI-01-22VW_methods.pdf |
| MS ID: | MS006490 |
| Analysis ID: | AN006791 |
| Instrument Name: | Thermo-Finnigan Trace DSQ |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| MS Comments: | The GC column was 5% phenyl and the temperature ramp is from 60° to 340° C in a 16 minute period. |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | TSRI-01-22VW_methods.pdf |
