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.

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Study IDST001691
Study TitleLC-MS untargeted lipidomics of primary human fibroblasts
Study TypeLC-MS untargeted lipidomics of fibroblasts
Study SummaryWe 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 NameCapolupo
First NameLaura
AddressRoute Cantonale
Emaillaura.capolupo@epfl.ch
Phone+41 21 693 42 79
Submit Date2021-02-10
Raw Data AvailableYes
Raw Data File Type(s).raw
Analysis Type DetailLC-MS
Release Date2021-05-01
Release Version1
Laura Capolupo Laura Capolupo
https://dx.doi.org/10.21228/M8698W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA15665501_01FibroblastSphin1_n1p_A_1methylamine treatment
SA15665602_02FibroblastSphin2_n1p_A_1methylamine treatment
SA15665703_03FibroblastTotal1_n1p_A_1total lipid extract
SA15665804_04FibroblastTotal2_n1p_A_1total 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 ( 2.6lm, 2.1 × 50 mm2)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Hybrid Orbitrap Elite
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 ( 2.6lm, 2.1 × 50 mm2)
Chromatography Type:HILIC

MS:

MS ID:MS002558
Analysis ID:AN002761
Instrument Name:Hybrid Orbitrap Elite
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Check protocol file
Ion Mode:POSITIVE
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