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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000140 |
| Study Title | Cell Rinsing Solution Comparison |
| Study Type | Cell Rinsing Solution Comparison |
| Study Summary | Aliquots 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 |
| Department | Dept. of Chemistry/SECIM |
| Laboratory | Biomedical Mass Spectrometry Lab |
| Last Name | Ulmer |
| First Name | Candice |
| Address | P.O. Box 117200, Gainesville, FL 32611 |
| czulmer@chem.ufl.edu | |
| Phone | (352) 392-0515 |
| Submit Date | 2015-03-02 |
| Num Groups | 5 |
| Total Subjects | 15 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Uploaded File Size | 3.1 G |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-03-03 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|
| SA007941 | amm_acetate | 0.3% ammonium acetate |
| SA007942 | amm_form | 0.3% ammonium formate |
| SA007943 | nacl | 0.9% NaCl |
| SA007945 | hepes | 100 mM HEPES |
| SA007944 | pbs | 1 M PBS |
| Showing results 1 to 5 of 5 |
Collection:
| 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:
| 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: | 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:
| 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 |
