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: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: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:We examined ubiquitin-linkages on Nrf1 purified from cell lysates of NGLY1-KO cells overexpressing Nrf1-FLAG with HA-FBS2. The ubiquitin linkage types were quantified using the LC-MS/MS-based absolute quantification method, ubiquitin parallel reaction monitoring (Ub-AQUA/PRM).
Project description:In this study, we aimed to refine our understanding of the molecular events associated with the proteomic response to hypoxia in OS cells with different anatomic origins, namely from a primary and metastatic site. There are similarities in biology and treatment of OS in human and canine. We opted to use a canine parental osteosarcoma cell line (POS), which was cultured from a primary canine tumor24; and a highly metastatic POS cell line (HMPOS) that was derived from pulmonary metastatic lesions in mouse POS xenografts. We have chosen a protein-centric study design that combines 1) initially a label-free data dependent acquisition (DDA) method for enabling quantification of larger sets of proteins and global assessment of adaptive responses induced by hypoxia, 2) selection of hypoxia-responsive protein targets and 3) using parallel reaction monitoring (PRM) for quantitative monitoring of signature peptides of hypoxia-responsive protein targets to determine their precise response to hypoxia and to confirm hypoxia-regulated pathways. Functional biochemical assays provide additional validation of the proteomic findings. Taken together, our results describe the hypoxia response of OS cell phenotypes by inducing comprehensive alterations in the proteome biology that are associated with metabolic reprogramming, redox modulation and extra cellular matrix (EMC) remodeling.
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.