Summary of Study ST000140

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 PR000125. The data can be accessed directly via it's Project DOI: 10.21228/M8DW2B This work is supported by NIH grant, U2C- DK119886.


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Study IDST000140
Study TitleCell Rinsing Solution Comparison
Study TypeCell Rinsing Solution Comparison
Study SummaryAliquots of Jurkat T-lymphocyte cells were washed with 5 different rinsing solutions (0.3% amm. formate, 0.3% amm. acetate, 0.9% NaCl, 1 M PBS, 100 mM PBS) and ran in triplicate to monitor the effect of ion suppression on the electrospray ionization signal.
University of Florida
DepartmentDept. of Chemistry/SECIM
LaboratoryBiomedical Mass Spectrometry Lab
Last NameUlmer
First NameCandice
AddressP.O. Box 117200, Gainesville, FL 32611
Phone(352) 392-0515
Submit Date2015-03-02
Num Groups5
Total Subjects15
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Uploaded File Size3.1 G
Analysis Type DetailLC-MS
Release Date2016-03-03
Release Version1
Candice Ulmer Candice Ulmer application/zip

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Project ID:PR000125
Project DOI:doi: 10.21228/M8DW2B
Project Title:Mammalian Suspension-Cultured Cellular Metabolomics Workflow
Project Type:Metabolomics, Lipidomics, Untargeted
Project Summary:A workflow was optimized for the sample preparation of a single suspension-cultured cell pellet for both metabolomics and lipidomics analysis. Jurkat T-lymphocyte cells were washed with various rinsing solutions and the lipids extracted using different lipid extraction protocols to allow for the most reproducible and quantitative method.
Institute:University of Florida
Department:Dept. of Chemistry/SECIM
Laboratory:Biomedical Mass Spectrometry Lab
Last Name:Yost
First Name:Richard
Address:P.O. Box 117200, Gainesville, FL 32611
Phone:(352) 392-0515
Funding Source:JDRF Research Grant


Subject ID:SU000159
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Cell Biosource Or Supplier:ATCC - Supplier
Subject Comments:P?+10
Cell Primary Immortalized:immortalized
Cell Passage Number:P?+10
Cell Counts:P?+10
Species Group:Human


Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id rinsing_solution
SA007941amm_acetate0.3% ammonium acetate
SA007942amm_form0.3% ammonium formate
SA007943nacl0.9% NaCl
SA007945hepes100 mM HEPES
SA007944pbs1 M PBS
Showing results 1 to 5 of 5


Collection ID:CO000144
Collection Summary:-
Sample Type:Jurkat cells, Clone E6-1
Collection Method:Centrifugation
Collection Frequency:1200 rpm
Collection Duration:5 min.
Storage Conditions:-80°C
Tissue Cell Quantity Taken:1e6 cells


Treatment ID:TR000162
Cell Storage:Liquid Nitrogen, 5% DMSO
Cell Growth Container:10 cm2 culture dish
Cell Media:RPMI 1640
Cell Envir Cond:95% humidity, 5% CO2

Sample Preparation:

Sampleprep ID:SP000157
Sampleprep Summary:80% MeOH metabolite extraction
Sampleprep Protocol ID:SOP_PP_02
Sampleprep Protocol Filename:SOP_PP_02_CZU.pdf
Processing Method:cell lysis
Processing Storage Conditions:on ice
Extraction Method:80% MeOH
Extract Concentration Dilution:1e6 cells/ 2 mL of extraction solvent
Sample Resuspension:30 μL 0.1% formic acid in water
Sample Spiking:internal standards: (1) L-tryptophan-2,3,3-d3; (2) creatine-d3; (3) d-leucine-d10; (4) caffeine-d3
Cell Type:Jurkat, Clone E6-1

Combined analysis:

Analysis ID AN000222
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 RS
Column ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Units Peak area


Chromatography ID:CH000154
Chromatography Summary:Reversed phase
Methods Filename:PFP-metabolomics-pos-350
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
Column Pressure:800 bar (max)
Column Temperature:30 C
Flow Rate:0.35 mL/min
Injection Temperature:4 C
Sample Injection:5 μL
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile
Analytical Time:18 min
Randomization Order:3,5,7,2,12,10,15,9,13,14,4,8,6,1,11
Chromatography Type:Reversed phase


MS ID:MS000173
Analysis ID:AN000222
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
Capillary Temperature:320
Dry Gas Flow:45
Mass Accuracy:<2 ppm
Spray Voltage:3.5 kV
Scan Range Moverz:70-700
Skimmer Voltage:15 V
Acquisition Parameters File:QE1_CZU_17_SEQUENCE