Summary of Study ST002150

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 PR001363. The data can be accessed directly via it's Project DOI: 10.21228/M8J708 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	ST002150
Study Title	Sphingomyelin depletion inhibits CXCR4 dynamics and CXCL12-mediated directed cell migration in human T cells
Study Summary	Sphingolipids, ceramides and cholesterol are integral components of cellular membranes, and they also play important roles in signal transduction by regulating the dynamics of membrane receptors through their effects on membrane fluidity. Here, we combined biochemical and functional assays with single-molecule dynamic approaches to demonstrate that the local lipid environment regulates CXCR4 organization and function and modulates chemokine-triggered directed cell migration. Prolonged treatment of T cells with neutral sphingomyelinase promoted the complete and sustained breakdown of sphingomyelins and the accumulation of the corresponding ceramides, which altered both membrane fluidity and CXCR4 nanoclustering and dynamics. Under these conditions CXCR4 retained some CXCL12-mediated signaling activity but failed to promote efficient directed cell migration. Our data underscore a critical role for the local lipid composition at the cell membrane in regulating the lateral mobility of chemokine receptors, and their ability to dynamically increase receptor density at the leading edge to promote efficient cell migration
Institute	Universidad CEU San Pablo
Last Name	Gonzalez-Riano
First Name	Carolina
Address	km 0, Universidad CEU-San Pablo Urbanización Montepríncipe. M-501
Email	carolina.gonzalezriano@ceu.es
Phone	646251045
Submit Date	2022-04-22
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	LC-MS
Release Date	2022-05-09
Release Version	1

Select appropriate tab below to view additional metadata details:

Combined analysis:

Analysis ID	AN003520	AN003521
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Agilent 1290 Infinity II	Agilent 1290 Infinity II
Column	Agilent InfinityLab Poroshell 120 EC–C18, 3.0 × 5 mm, 2.7 μm	Agilent InfinityLab Poroshell 120 EC–C18, 3.0 × 5 mm, 2.7 μm
MS Type	ESI	ESI
MS instrument type	QTOF	QTOF
MS instrument name	Agilent 6546 QTOF	Agilent 6546 QTOF
Ion Mode	POSITIVE	NEGATIVE
Units	AREA	AREA

MS:

MS ID:	MS003278
Analysis ID:	AN003520
Instrument Name:	Agilent 6546 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	The Agilent 6545 QTOF mass spectrometer equipped with a dual AJS ESI ion source was set with the following parameters: 150 V fragmentor, 65 V skimmer, 3500 V capillary voltage, 750 V octopole radio frequency voltage, 10 L/min nebulizer gas flow, 200 °C gas temperature, 50 psi nebulizer gas pressure, 12 L/min sheath gas flow, and 300 °C sheath gas temperature. Data were collected in positive and negative ESI modes in separate runs, operated in full scan mode from 50 to 1800 m/z with a scan rate of 3 spectra/s. A solution consisting of two reference mass compounds were used throughout the whole analysis: purine (C5H4N4) at m/z 121.0509 for the positive and m/z 119.0363 for the negative ionization modes; and HP-0921 (C18H18O6N3P3F24) at m/z 922.0098 for the positive and m/z 980.0163 (HP-0921+acetate) for the negative ionization modes. These masses were continuously infused into the system through an Agilent 1260 Iso Pump at a 1 mL/min (split ratio 1:100) to provide a constant mass correction. Ten Iterative-MS/MS runs were performed for both ion modes at the end of the analytical run. They were operated with an MS and MS/MS scan rates of 3 spectra/s, 40–1800 m/z mass window, a narrow (∼ 1.3 amu) MS/MS isolation width, 3 precursors per cycle, and 5000 counts and 0.001% of MS/MS threshold. Five iterative-MS/MS runs were set with a collision energy of 20 eV, and the subsequent five runs were performed at 40 eV. References masses and contaminants detected in blank samples were excluded from the analysis to avoid inclusion in the iterative-MS/MS.
Ion Mode:	POSITIVE

MS ID:	MS003279
Analysis ID:	AN003521
Instrument Name:	Agilent 6546 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	The Agilent 6545 QTOF mass spectrometer equipped with a dual AJS ESI ion source was set with the following parameters: 150 V fragmentor, 65 V skimmer, 3500 V capillary voltage, 750 V octopole radio frequency voltage, 10 L/min nebulizer gas flow, 200 °C gas temperature, 50 psi nebulizer gas pressure, 12 L/min sheath gas flow, and 300 °C sheath gas temperature. Data were collected in positive and negative ESI modes in separate runs, operated in full scan mode from 50 to 1800 m/z with a scan rate of 3 spectra/s. A solution consisting of two reference mass compounds were used throughout the whole analysis: purine (C5H4N4) at m/z 121.0509 for the positive and m/z 119.0363 for the negative ionization modes; and HP-0921 (C18H18O6N3P3F24) at m/z 922.0098 for the positive and m/z 980.0163 (HP-0921+acetate) for the negative ionization modes. These masses were continuously infused into the system through an Agilent 1260 Iso Pump at a 1 mL/min (split ratio 1:100) to provide a constant mass correction. Ten Iterative-MS/MS runs were performed for both ion modes at the end of the analytical run. They were operated with an MS and MS/MS scan rates of 3 spectra/s, 40–1800 m/z mass window, a narrow (∼ 1.3 amu) MS/MS isolation width, 3 precursors per cycle, and 5000 counts and 0.001% of MS/MS threshold. Five iterative-MS/MS runs were set with a collision energy of 20 eV, and the subsequent five runs were performed at 40 eV. References masses and contaminants detected in blank samples were excluded from the analysis to avoid inclusion in the iterative-MS/MS.
Ion Mode:	NEGATIVE