Summary of Study ST002373

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001526. The data can be accessed directly via it's Project DOI: 10.21228/M8FH84 This work is supported by NIH grant, U2C- DK119886.


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 IDST002373
Study TitleExtracellular metabolome of activated CD8+ T cells
Study SummaryWT OT-I CD8+ T cells were activated with plate-bound anti-CD3 and soluble anti-CD28. Blank media or media post 10hr, 30hr or 48hr cell culture were collected for mass spectrometry analysis.
Johns Hopkins University
Last NameXu
First NameWei
Address1650 Orleans Street, Baltimore, MD 21287, USA.
Submit Date2022-11-29
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2023-11-28
Release Version1
Wei Xu Wei Xu application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR001526
Project DOI:doi: 10.21228/M8FH84
Project Title:Extracellular metabolome of activated CD8+ T cells
Project Summary:WT OT-I CD8+ T cells were activated with plate-bound anti-CD3 and soluble anti-CD28. Blank media or media post 10hr, 30hr or 48hr cell culture were collected for mass spectrometry analysis.
Institute:Johns Hopkins University
Last Name:Xu
First Name:Wei
Address:1650 Orleans Street, Baltimore, MD 21287, USA.


Subject ID:SU002462
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


Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA23733910hr_M_0110hr blank media
SA23734010hr_M_0310hr blank media
SA23734110hr_M_0210hr blank media
SA23734230hr_M_0330hr blank media
SA23734330hr_M_0230hr blank media
SA23734430hr_M_0130hr blank media
SA23734548hr_M_0248hr blank media
SA23734648hr_M_0148hr blank media
SA23734748hr_M_0348hr blank media
SA23734810hr_WT_02media post 10hr cell activation
SA23734910hr_WT_03media post 10hr cell activation
SA23735010hr_WT_01media post 10hr cell activation
SA23735130hr_WT_01media post 30hr cell activation
SA23735230hr_WT_03media post 30hr cell activation
SA23735330hr_WT_02media post 30hr cell activation
SA23735448hr_WT_03media post 48hr cell activation
SA23735548hr_WT_02media post 48hr cell activation
SA23735648hr_WT_01media post 48hr cell activation
Showing results 1 to 18 of 18


Collection ID:CO002455
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 ID:TR002474
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. Blank media post 10, 30, 48 hours in the incubator or media post 10, 30, 48 hr activated CD8+ T cell culture were collected for MS analysis.

Sample Preparation:

Sampleprep ID:SP002468
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 AN003868
Analysis type MS
Chromatography type HILIC
Chromatography system Shimadzu Prominence UFLC
Column Waters XBridge BEH Amide XP HILIC (150 x 2.1mm,2.5um)
MS instrument type QTRAP
MS instrument name ABI Sciex 5500 QTrap
Units AUC


Chromatography ID:CH002866
Instrument Name:Shimadzu Prominence UFLC
Column Name:Waters XBridge BEH Amide XP HILIC (150 x 2.1mm,2.5um)
Chromatography Type:HILIC


MS ID:MS003609
Analysis ID:AN003868
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:QTRAP
MS Comments:The optimized MS parameters were: ESI voltage was +5,000 V in positive ion mode and -4,500 V in negative ion mode; dwell time was 3 ms per SRM transition and the total cycle time was 1.57 seconds. Peak integration for each targeted metabolite in SRM transition was processed with MultiQuant software (v2.1, AB Sciex). The preprocessed data with integrated peak areas were exported from MultiQuant and re-imported into Metaboanalyst software for further data analysis (statistical analysis, principal component analysis, generating heatmap, enrichment analysis, etc.).