Summary of Study ST001691
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 PR001087. The data can be accessed directly via it's Project DOI: 10.21228/M8698W 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 | ST001691 |
| Study Title | LC-MS untargeted lipidomics of primary human fibroblasts |
| Study Type | LC-MS untargeted lipidomics of fibroblasts |
| Study Summary | We did LC-MS untargeted lipidomics of primary human fibroblasts to have a comprehensive overview of their lipidome in positive ion mode |
| Institute | École polytechnique fédérale de Lausanne (EPFL) |
| Last Name | Capolupo |
| First Name | Laura |
| Address | Route Cantonale |
| laura.capolupo@epfl.ch | |
| Phone | +41 21 693 42 79 |
| Submit Date | 2021-02-10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-05-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001087 |
| Project DOI: | doi: 10.21228/M8698W |
| Project Title: | Untargeted lipidomics of primary human skin fibroblasts |
| Project Type: | MS qualitative untargeted lipidomics of human fibroblasts |
| Project Summary: | Untargeted lipidomics of primary human skin fibroblasts to identify their lipidome in positive ion mode |
| Institute: | École polytechnique fédérale de Lausanne (EPFL) |
| Laboratory: | UPDANGELO |
| Last Name: | Capolupo |
| First Name: | Laura |
| Address: | Route Cantonale, Lausanne, Vaud, 1015, Switzerland |
| Email: | laura.capolupo@epfl.ch |
| Phone: | +41 21 693 42 79 |
Subject:
| Subject ID: | SU001768 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA156655 | 01_01FibroblastSphin1_n1p_A_1 | methylamine treatment |
| SA156656 | 02_02FibroblastSphin2_n1p_A_1 | methylamine treatment |
| SA156657 | 03_03FibroblastTotal1_n1p_A_1 | total lipid extract |
| SA156658 | 04_04FibroblastTotal2_n1p_A_1 | total lipid extract |
| Showing results 1 to 4 of 4 |
Collection:
| Collection ID: | CO001761 |
| Collection Summary: | Cells were washed with cold PBS, scraped and collected after centrifugation in -80° untill the MS analysis |
| Sample Type: | Fibroblasts |
Treatment:
| Treatment ID: | TR001781 |
| Treatment Summary: | No treatment has been done on the cells |
Sample Preparation:
| Sampleprep ID: | SP001774 |
| Sampleprep Summary: | Total lipid extracts were prepared using a standard MTBE protocol followed by a methylamine treatment for total lipid analysis by mass spectrometry 7. Briefly, cell pellet was resuspended in 100 μL H2O. 360 μL methanol and 1.2 mL of MTBE were added and samples were placed for 10 min on a vortex at 4 °C followed by incubation for 1 h at room temperature on a shaker. Phase separation was induced by addition of 200 μL of H2O. After 10 min at room temperature, samples were centrifuged at 1000 g for 10 min. The upper (organic) phase was transferred into a glass tube and the lower phase was re-extracted with 400 μL artificial upper phase [MTBE/methanol/H2O (10:3:1.5, v/v/v)]. The combined organic phases were dried in a vacuum concentrator. Lipids where then resuspended in 500 μL of CHCl3 and divided in two aliquots for a further methylamine treatment for sphingo- and glycosphingolipids analysis. In details, 500 μL of freshly prepared monomethylamine reagent [methylamine/H2O/nbutanol/ methanol (5:3:1:4, (v/v/v/v)] was added to the dried lipid extract and then incubated at 53 °C for 1 h in a water bath. Lipids were cooled to room temperature and then dried. The dried lipid extract was then extracted by n-butanol extraction using 300 μL water-saturated nbutanol and 150 μL H2O. The organic phase was collected, and the aqueous phase was reextracted twice with 300 μL water-saturated n-butanol. The organic phases were pooled and dried in a vacuum concentrator. |
Combined analysis:
| Analysis ID | AN002761 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Shimadzu Prominence UFPLC xr system |
| Column | Kinetex (50 x 2.1mm,2.6um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap |
| Ion Mode | POSITIVE |
| Units | abundance |
Chromatography:
| Chromatography ID: | CH002041 |
| Chromatography Summary: | Liquid chromatography on a HILIC Column |
| Methods Filename: | laura_capolupo_20210210_062234_PR_CH_Chromatography_methods.pdf |
| Instrument Name: | Shimadzu Prominence UFPLC xr system |
| Column Name: | Kinetex (50 x 2.1mm,2.6um) |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS002558 |
| Analysis ID: | AN002761 |
| Instrument Name: | Thermo Orbitrap Elite Hybrid Ion Trap-Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Check protocol file |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | laura_capolupo_20210210_062234_PR_CH_Chromatography_methods.pdf |
