Summary of Study ST002372
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 PR001525. The data can be accessed directly via it's Project DOI: 10.21228/M8K71Z 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 | ST002372 |
| Study Title | Extracellular pyruvate secretion by activated CD8+ T cells revealed by [U-13C]glucose tracing |
| Study Summary | WT OT-I CD8+ T cells were activated in [U-13C]glucose for 24 hours. Blank [U-13C]glucose media or media post cell culture were collected for mass spectrometry analysis. Percent contribution of carbon flux from [U-13C]glucose to pyruvate were analyzed. |
| Institute | Johns Hopkins University |
| Last Name | Xu |
| First Name | Wei |
| Address | 1650 Orleans Street, Baltimore, MD 21287, USA. |
| wxu29@jhmi.edu | |
| Phone | 443-220-9936 |
| Submit Date | 2022-11-29 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-11-28 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001525 |
| Project DOI: | doi: 10.21228/M8K71Z |
| Project Title: | Extracellular pyruvate secretion by activated CD8+ T cells revealed by [U-13C]glucose tracing |
| Project Summary: | WT OT-I CD8+ T cells were activated in [U-13C]glucose for 24 hours. Blank [U-13C]glucose media or media post cell culture were collected for mass spectrometry analysis. Percent contribution of carbon flux from [U-13C]glucose to pyruvate were analyzed. |
| Institute: | Johns Hopkins University |
| Last Name: | Xu |
| First Name: | Wei |
| Address: | 1650 Orleans Street, Baltimore, MD 21287, USA. |
| Email: | wxu29@jhmi.edu |
| Phone: | 443-220-9936 |
Subject:
| Subject ID: | SU002461 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6J |
| Age Or Age Range: | 6-8 weeks |
| Gender: | Male and female |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA237333 | blk_001 | blank media |
| SA237334 | blk_003 | blank media |
| SA237335 | blk_002 | blank media |
| SA237336 | Act_003 | media post cell culture |
| SA237337 | Act_001 | media post cell culture |
| SA237338 | Act_002 | media post cell culture |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO002454 |
| Collection Summary: | Blank media or media post cell culture were collected and centrifuged at 1200rpm for 5min. Supernatant were flash frozen in liquid nitrogen until further analysis. |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR002473 |
| Treatment Summary: | CD8+ T cells were isolated from spleens and lymph nodes from WT mice. Cells were activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in the presence of 11mM [U-13C]glucose. Blank media post 24 hours in the incubator or media post 24 hr activated CD8+ T cell culture were collected for MS analysis. |
Sample Preparation:
| Sampleprep ID: | SP002467 |
| Sampleprep Summary: | For measurement of extracellular metabolome, 625 µL of media was added to 375 µL acetonitrile ACN. Samples were stored at -20 °C for at least two hours followed by centrifugation at 14,000xg to precipitate any proteins. 250 µL of the supernatant was mixed with 250 µL of water and added to a 3 kDa molecular weight cut-off filter spin column (Microcon YM-3 Centrifugal Filter, Millipore). Samples were centrifuged at 14,000xg at 4 °C for 30 min. The flow-through was saved for LC-MS/MS analysis. |
Combined analysis:
| Analysis ID | AN003867 |
|---|---|
| Chromatography ID | CH002865 |
| MS ID | MS003608 |
| Analysis type | MS |
| Chromatography type | Ion pair |
| Chromatography system | Agilent 1290 Infinity |
| Column | Agilent Zorbax Extend C18 (150 x 2.1mm,1.8 um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6520 QTOF |
| Ion Mode | NEGATIVE |
| Units | AUC |
Chromatography:
| Chromatography ID: | CH002865 |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Agilent Zorbax Extend C18 (150 x 2.1mm,1.8 um) |
| Chromatography Type: | Ion pair |
MS:
| MS ID: | MS003608 |
| Analysis ID: | AN003867 |
| Instrument Name: | Agilent 6520 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | The optimized ESI Q-TOF parameters for MS experiments were: ion polarity, negative; gas temperature, 325 °C; drying gas, 10 L min-1; nebulizer pressure, 45 psig; capillary voltage, 4,000 V; fragmentor, 140 V; skimmer, 65 V; mass range, 50-1100 m/z; acquisition rate, 1.5 spectra s-1; instrument state, extended dynamic range (1700 m/z, 2 GHz). Spectra were internally mass calibrated in real time by continuous infusion of a reference mass solution using an isocratic pump connected to a dual sprayer feeding into an electrospray ionization source. Data were acquired with MassHunter Acquisition software. A metabolite database with retention times based on the ion-pairing method was developed using Agilent MassHunter PCDL manager software. The isotopologue peak extractions were achieved by Agilent MassHunter Profinder software. |
| Ion Mode: | NEGATIVE |
