Summary of Study ST002367
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 PR001521. The data can be accessed directly via it's Project DOI: 10.21228/M83707 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
| Study ID | ST002367 |
| Study Title | Single cell lipidome analysis of phosphatidylcholines and spingomyelins from prostate cells |
| Study Type | Quantitative single cell lipidomics |
| Study Summary | We have developed a high-throughput method for the detection and quantification of a wide range of phosphatidylcholine (PC) and sphingomyelin (SM) species from single cells that combines fluorescence-assisted cell sorting (FACS) with automated chip-based nanoelectrospray ionization (nanoESI) and shotgun lipidomics. Using this method we can detect and perform relative quantitation on more than >50 different PC and SM species from immortalised human cells, and can easily distinguish between tumorigenic and non-tumorigenic prostate cell lines. |
| Institute | Victor Chang Cardiac Research Institute |
| Laboratory | Cellular Bioenergetics Laboratory |
| Last Name | Hancock |
| First Name | Sarah |
| Address | Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia |
| s.hancock@victorchang.edu.au | |
| Phone | +61414537526 |
| Submit Date | 2022-10-30 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | MS(Dir. Inf.) |
| Release Date | 2023-10-19 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001521 |
| Project DOI: | doi: 10.21228/M83707 |
| Project Title: | Single cell lipidomics |
| Project Type: | Quantitative lipidomics |
| Project Summary: | Analysis of lipids from single cells isolated by FACS. |
| Institute: | Victor Chang Cardiac Research Institute |
| Laboratory: | Cellular Bioenergetics Laboratory |
| Last Name: | Hancock |
| First Name: | Sarah |
| Address: | Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW, Australia 2010 |
| Email: | s.hancock@victorchang.edu.au |
| Phone: | +61414537526 |
| Funding Source: | PdCCRS |
| Project Comments: | Study 1 of 2 |
Subject:
| Subject ID: | SU002456 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | cell number |
|---|---|---|
| SA237170 | PCa-A04 | fifty_cells |
| SA237171 | PCa-A12 | fifty_cells |
| SA237172 | PCa-A02 | fifty_cells |
| SA237173 | PCa-A05 | fifty_cells |
| SA237174 | PCa-A01 | fifty_cells |
| SA237175 | PCa-A11 | fifty_cells |
| SA237176 | PCa-A03 | fifty_cells |
| SA237177 | PCa-A10 | fifty_cells |
| SA237178 | PCa-A06 | fifty_cells |
| SA237179 | PCa-A08 | fifty_cells |
| SA237180 | PCa-A07 | fifty_cells |
| SA237181 | PCa-A09 | fifty_cells |
| SA237167 | PCa-H03 | N/A |
| SA237168 | PCa-H02 | N/A |
| SA237169 | PCa-H01 | N/A |
| SA237182 | PCa-F01 | single_cell |
| SA237183 | PCa-E12 | single_cell |
| SA237184 | PCa-F02 | single_cell |
| SA237185 | PCa-F03 | single_cell |
| SA237186 | PCa-F05 | single_cell |
| SA237187 | PCa-E11 | single_cell |
| SA237188 | PCa-F04 | single_cell |
| SA237189 | PCa-F06 | single_cell |
| SA237190 | PCa-E05 | single_cell |
| SA237191 | PCa-E04 | single_cell |
| SA237192 | PCa-F07 | single_cell |
| SA237193 | PCa-E06 | single_cell |
| SA237194 | PCa-E07 | single_cell |
| SA237195 | PCa-E09 | single_cell |
| SA237196 | PCa-E08 | single_cell |
| SA237197 | PCa-E10 | single_cell |
| SA237198 | PCa-G04 | single_cell |
| SA237199 | PCa-G08 | single_cell |
| SA237200 | PCa-G07 | single_cell |
| SA237201 | PCa-G06 | single_cell |
| SA237202 | PCa-G09 | single_cell |
| SA237203 | PCa-G10 | single_cell |
| SA237204 | PCa-G12 | single_cell |
| SA237205 | PCa-G11 | single_cell |
| SA237206 | PCa-G05 | single_cell |
| SA237207 | PCa-E03 | single_cell |
| SA237208 | PCa-F11 | single_cell |
| SA237209 | PCa-F10 | single_cell |
| SA237210 | PCa-F09 | single_cell |
| SA237211 | PCa-F12 | single_cell |
| SA237212 | PCa-G01 | single_cell |
| SA237213 | PCa-G03 | single_cell |
| SA237214 | PCa-G02 | single_cell |
| SA237215 | PCa-F08 | single_cell |
| SA237216 | PCa-D08 | single_cell |
| SA237217 | PCa-B12 | single_cell |
| SA237218 | PCa-B11 | single_cell |
| SA237219 | PCa-B10 | single_cell |
| SA237220 | PCa-C01 | single_cell |
| SA237221 | PCa-C02 | single_cell |
| SA237222 | PCa-C05 | single_cell |
| SA237223 | PCa-C04 | single_cell |
| SA237224 | PCa-C03 | single_cell |
| SA237225 | PCa-B09 | single_cell |
| SA237226 | PCa-B08 | single_cell |
| SA237227 | PCa-B03 | single_cell |
| SA237228 | PCa-B02 | single_cell |
| SA237229 | PCa-B01 | single_cell |
| SA237230 | PCa-B04 | single_cell |
| SA237231 | PCa-B05 | single_cell |
| SA237232 | PCa-B07 | single_cell |
| SA237233 | PCa-B06 | single_cell |
| SA237234 | PCa-C06 | single_cell |
| SA237235 | PCa-C07 | single_cell |
| SA237236 | PCa-D07 | single_cell |
| SA237237 | PCa-D06 | single_cell |
| SA237238 | PCa-D05 | single_cell |
| SA237239 | PCa-D09 | single_cell |
| SA237240 | PCa-D10 | single_cell |
| SA237241 | PCa-E01 | single_cell |
| SA237242 | PCa-D12 | single_cell |
| SA237243 | PCa-D11 | single_cell |
| SA237244 | PCa-D04 | single_cell |
| SA237245 | PCa-D03 | single_cell |
| SA237246 | PCa-C10 | single_cell |
| SA237247 | PCa-C09 | single_cell |
| SA237248 | PCa-C08 | single_cell |
| SA237249 | PCa-C11 | single_cell |
| SA237250 | PCa-C12 | single_cell |
| SA237251 | PCa-D02 | single_cell |
| SA237252 | PCa-D01 | single_cell |
| SA237253 | PCa-E02 | single_cell |
| Showing results 1 to 87 of 87 |
Collection:
| Collection ID: | CO002449 |
| Collection Summary: | Samples were obtained from established immortalised adherent human tumorigenic (DU145, LNCaP & PC3) and non-tumorigenic (PNT1) cell lines. Cells were cultured in RPMI (R5886, Sigma-Aldrich) supplemented with 2 mM L-glutamine and 10% heat-inactivated fetal calf serum and incubated at 37°C in 5% CO2. Cell media was changed every three days and cells were passaged regularly at ~80-90% confluency by trypsinization. Cell lines were regularly screened for mycoplasma infection. |
| Sample Type: | Prostate |
Treatment:
| Treatment ID: | TR002468 |
| Treatment Summary: | Cells were grown as per collection data with no treatment being applied. |
Sample Preparation:
| Sampleprep ID: | SP002462 |
| Sampleprep Summary: | Samples were prepared by using fluorescence-assisted cell sorting (FACS) to sort either pooled fifty cells or singly-isolated cells into a single well on a 96 well plate. Full sample prep details are provided in the attached protocol. |
| Sampleprep Protocol Filename: | MWB_sampleprep_protocol.pdf |
Combined analysis:
| Analysis ID | AN003862 |
|---|---|
| Analysis type | MS |
| Chromatography type | None (Direct infusion) |
| Chromatography system | none |
| Column | none |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | ABI Sciex 5500 QTrap |
| Ion Mode | POSITIVE |
| Units | Peak Area (cps) |
Chromatography:
| Chromatography ID: | CH002860 |
| Instrument Name: | none |
| Column Name: | none |
| Chromatography Type: | None (Direct infusion) |
MS:
| MS ID: | MS003603 |
| Analysis ID: | AN003862 |
| Instrument Name: | ABI Sciex 5500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | NanoESI mass spectrometry of lipid extracts was performed using a hybrid triple quadrupole linear ion trap mass spectrometer (QTRAP® 5500, SCIEX, Framingham, MA, USA) equipped with an automated chip-based nanoelectrospray source (TriVersa Nanomate®, Advion Biosciences, NY, USA). Spray parameters were set at a gas pressure of 0.4 psi and a voltage of 1.2 kV. PC and SM data were acquired in positive ion mode using a precursor ion scan of m/z 184 at a scan rate of 200 Da/s across a mass range of 640 – 850 m/z. Declustering potential was set at 100 V, entrance potential at 10 V, collision energy at 47 V, and collision cell exit potential at 8V (31). Aspiration of 10 μl of sample from each well generated a stable spray time of ≥30 minutes. Lipids were identified from acquired data using Lipidview™ software (v1.2b, SCIEX, Framingham, MA, USA). Processing settings in Lipidview™ were set at a mass tolerance of 0.5 Da, with a minimum intensity of 0.1% and a minimum signal-to-noise ratio of 4. Smoothing and deisotoping of lipid species were enabled. Lipid species were identified from target lists (see attached protocol files), and peak area for each detected lipid species was then exported. These data underwent further processing in R, including background subtraction and relative quantification from internal standards. Lipid nomenclature follows recommendations for the level of molecular detail known (as per Liebisch et al. 2013 J Lipid Res); and in the present study we report lipids as class (e.g., PC or SM) followed by the total number of carbons and carbon-carbon double bonds present within the fatty acids separated by a colon (e.g., a PC with 34 carbons and 1 double bond as PC 34:1). At the level of identification available by the technique used in this study some ambiguity exists between isobaric PC species containing either odd-chain or ether-linked fatty acid species, and in the absence of further structural detail we chose to report such species as ether-linked only where overlap exists. |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | MWB_Lipidview_target_list.txt |
