Summary of Study ST000140

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 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.
Institute
University of Florida
DepartmentDept. of Chemistry/SECIM
LaboratoryBiomedical Mass Spectrometry Lab
Last NameUlmer
First NameCandice
AddressP.O. Box 117200, Gainesville, FL 32611
Emailczulmer@chem.ufl.edu
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
https://dx.doi.org/10.21228/M8DW2B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

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
Email:ryost@aa.ufl.edu
Phone:(352) 392-0515
Funding Source:JDRF Research Grant

Subject:

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

Factors:

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:

Collection ID:CO000144
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:

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 Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode POSITIVE
Units Peak area

Chromatography:

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:0.1% formic acid in water
Solvent B: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:

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