Summary of Study ST000246

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 IDST000246
Study TitleLipid Extraction Efficiency Comparison
Study TypeLipid Extraction Efficiency Comparison
Study SummaryAliquots of Jurkat T-lymphocyte cells were extracted using the Folch or Matyash method at different total volumes and run in triplicate to calculate the extraction efficiency for each method.
University of Florida
DepartmentDept. of Chemistry/SECIM
LaboratoryBiomedical Mass Spectrometry Lab
Last NameUlmer
First NameCandice
AddressR3-226 Academic Research Building, Department of Biochemistry and Molecular Biology, PO Box 100245, Gainesville, FL 32610-0245
Phone(352) 392-0515
Submit Date2015-09-15
Num Groups4
Total Subjects12
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Uploaded File Size2.2 G
Analysis Type DetailLC-MS
Release Date2016-12-22
Release Version1
Candice Ulmer Candice Ulmer application/zip

Select appropriate tab below to view additional metadata details:


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:SU000266
Subject Type:Human cells
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 cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Extraction Method
Showing results 1 to 4 of 4


Collection ID:CO000257
Collection Summary:-
Sample Type:Cells - Jurkat, Clone E6-1
Collection Method:Centrifugation
Collection Frequency:1200 rpm
Collection Duration:5 min
Volumeoramount Collected:10 mL of cell suspension
Storage Conditions:-80°C
Tissue Cell Quantity Taken:1e6 cells


Treatment ID:TR000277
Cell Storage:Liquid Nitrogen, 5% DMSO
Cell Growth Container:10 cm2 culture dish
Cell Media:RPMI 1640
Cell Envir Cond:95% humidity, 5% CO2
Cell Harvesting:centrifugation

Sample Preparation:

Sampleprep ID:SP000271
Sampleprep Summary:Cells were extracted using either the Folch or Matyash method. The total volume of MeOH in each extraction method was varied (0.5 mL or 2.0 mL) while the ratio of MeOH to the other solvents was maintained.
Sampleprep Protocol Filename:SOP_LipidExtractionProtocol.pdf
Processing Method:cell lysis
Processing Storage Conditions:on ice
Extraction Method:Folch or Matyash lipid extraction method
Extract Concentration Dilution:1e6 cells were extracted with the solvent systems explained in the Sample Prep Summary
Sample Resuspension:100 μL of IPA
Sample Spiking:internal standards: lysophosphatidylcholine (LPC 17:0 and LPC 19:0), phosphatidylcholine (PC 17:0/17:0 and PC 19:0/19:0), phosphatidylethanolamine (PE 15:0/15:0 and PE 17:0/17:0), phosphatidylserine (PS 14:0/14:0 and PS 17:0/17:0), and phosphatidylglycerol (PG 14:0/14:0 and PG 17:0/17:0), triacylglyceride (TG 15:0/15:0/15:0 and TG 17:0/17:0/17:0)
Cell Type:Jurkat, Clone E6-1

Combined analysis:

Analysis ID AN000384
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 RS
Column Supelco Analytical Titan C18
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Units Peak Area


Chromatography ID:CH000276
Chromatography Summary:Reversed Phase
Methods Filename:m_lipid_pos_switch_100
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Supelco Analytical Titan C18
Column Pressure:1241 bar (max)
Column Temperature:30 C
Flow Gradient:32% B at 0 min, 40% B at 1 min, a hold at 40% B until 1.5 min, 45% B at 4 min, 50% B at 5 min, 60% B at 8 min, 70% B at 11 min, and 80% B at 14 min
Flow Rate:0.5 mL/min
Injection Temperature:4 C
Sample Injection:2 μL
Solvent A:40% water/60% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Solvent B:90% isopropanol/8% acetonitrile/2% water; 0.1% formic acid; 10 mM ammonium formate
Analytical Time:21 min
Randomization Order:3,10,12,11,8,6,5,4,7,9,2,1
Chromatography Type:Reversed phase


MS ID:MS000330
Analysis ID:AN000384
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
Capillary Temperature:320
Dry Gas Flow:30
Mass Accuracy:<2 ppm
Spray Voltage:3.5 kV
Desolvation Gas Flow:.raw
Scan Range Moverz:100-1500
Skimmer Voltage:15 V
Acquisition Parameters File:QE1_CZU_08_sequence