Project description:Raw files corresponding to LC-MS-based relative quantification of oxidized lipids in Pfa1 cells and mouse liver samples subjected to ferroptosis. Data were acquired in parallel reaction monitoring (PRM) MS/MS mode.
Project description:Raw files corresponding to the epilipidomic dataset for identification and relative quantification of oxidized complex lipids in the blood plasma of lean and obese individuals.
Project description:Raw files corresponding to the epilipidomic dataset for identification and relative quantification of oxidized complex lipids in the blood plasma of lean and obese individuals.
Project description:Lipids are important structural and functional components of the skin. Alterations in the lipid composition of the epidermis can lead to diminished barrier function of the skin and are associated with diseases like atopic dermatitis. SHARPIN-deficient cpdm mice develop a chronic dermatitis with similarities to atopic dermatitis in humans. Here, we used a new mass spectrometry analytical strategy named multiple reaction monitoring (MRM) profiling to rapidly identify discriminative lipid ions. Shorter fatty acyl residues and increased relative amounts of sphingosine ceramides were observed in cpdm epidermis compared to wild type mice. These changes were accompanied by downregulation of the Fasn gene which encodes fatty acid synthase. Fast screening of more than 300 ion pairs (representing a parent molecule and a fragment) related to diverse lipids allowed phenotypical profiling and discrimination of cpdm and wild type mice. Tentative attribution of the most significant ion pairs was confirmed by product ion screening (MS/MS). Relative quantification of sphingosine ceramides CerAS(d18:1/24:0)OH, CerAS(d18:1/16:0)OH and CerNS(d18:1/16:0) could discriminate between the two groups with 100% accuracy, while the free fatty acids cerotic acid, 16-hydroxy palmitic acid, and docosahexaenoic acid (DHA) had a 96.4% of accuracy. MRM profiling is proposed as an accelerated prospective biomarker discovery approach.
Project description:<p>Characterization of botanical extracts by mass spectrometry-based metabolomics analysis helps in determining the phytochemical composition that underlies their bioactivity and potential health benefits, while also supporting reproducibility of effects in clinical trials. The quantification of seven withanolides in Withania somnifera using three mass-spectrometry methods was evaluated using Deming regression. Two high-resolution time-of-flight mass spectrometry methods were used, one operating in data-dependent acquisition mode and the other in parallel-reaction-monitoring mode with an inclusion list. The two high-resolution time-of-flight mass spectrometry methods were compared to a multiple-reaction-monitoring method. We evaluated in-source fragmentation of steroidal glycosides and optimized the methods accordingly. A novel software approach to integrating parallel-reaction-monitoring data acquired with an inclusion list was developed. Combining and comparing quantitative results allowed for quantitative specificity, good precision, and adjustment of instrument source conditions for optimal quantification by multiple-reaction-monitoring mass spectrometry, an analytical method that is widely accessible in analytical and phytochemical laboratories.</p><p><br></p><p><strong>Linked R Script</strong></p><p>An R script for PRM data analysis collected with an inclusion list is available in <a href='https://github.com/marneylc/prm' rel='noopener noreferrer' target='_blank'>Github</a>.</p>
Project description:Development, implementation, and evaluation of a new data acquisition scheme called internal standard triggered-parallel reaction monitoring (IS-PRM) to increase the scale of targeted quantitative experiments while retaining high detection and quantification performance. All the details about the dataset, the associated sample preparation and liquid chromatography coupled to tandem mass spectrometry methods, and the data processing procedures are provided in the manuscript by Gallien et al., entitled "Large-Scale Targeted Proteomics Using Internal Standard Triggered-Parallel Reaction Monitoring", Molecular and Cellular Proteomics.
Project description:T cell metabolic fitness plays a pivotal role in anti-tumor immunity and metabolic deregulation causes T cell dysfunction in cancer. We identify that CD36 limits anti-tumor CD8+ T cell effector functions through lipid peroxidation. In murine tumors, oxidized phospholipids (OxPLs) were highly abundant and CD8+ TILs increased uptake and accumulation of lipids and lipid peroxidation. Functionally ‘exhausted’ CD8+ TILs increased CD36 expression and CD36-deficient CD8+ TILs had more robust anti-tumor activity and cytokine production than wild-type cells. We further show that CD36 promotes uptake of oxidized low-density lipoproteins (OxLDL), induces lipid peroxidation in CD8+ TILs, and enhances p38 kinase phosphorylation. Moreover, we found that OxLDL inhibits CD8+ T cell functions in a CD36/p38-dependent manner. Furthermore, glutathione peroxidase 4 (GPX4) over-expression lowers lipid peroxidation and restores functionalities in CD8+ TILs. These results define a key role for an oxidized lipid-CD36-p38 axis in promoting intratumoral CD8+ T cell dysfunction.
Project description:The abundance of N-terminal fragments starting from V21 (pV21–W33), S22 (pS22–W33), S23 (pS23–W33), and G24 (pG24–W33) along with three control peptides (Ctrl1, pH81–Y95; Ctrl2, pR106–L118; Ctrl3, pH113–L123) were measured by parallel reaction monitoring (PRM), an MS/MS-based targeted quantification method using high-resolution MS. Targeted MS/MS scans were acquired by a time-scheduled inclusion list, and time alignment and relative quantification of the transitions of three biological replicates were performed with PinPoint version 1.4 (Thermo Fisher Scientific).