LC-MS/MS analysis of peptide methionine sulfoxides stereoisomers
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)
SUBMITTER: 
Cristian Munteanu
LAB HEAD: Cristian (V.A.) Munteanu
PROVIDER: PXD077492 | Pride | 2026-05-04
REPOSITORIES: Pride
Dataset's files
Items per page: 5 1 - 5 of 119 |
Publications
A new strategy to separate peptide methionine sulfoxides stereoisomers for potential immunotherapy application.
Stănescu Lucian-Mihai LM Aramă Corina-Cristina CC Chirițoiu Gabriela N GN Petrescu Andrei J AJ Petrescu Ștefana M ȘM Munteanu Cristian V A CVA
Analytical and bioanalytical chemistry 20260501
Peptide-based immunotherapy is a promising cancer treatment due to its scalability and patient-centered approach; therefore, there is an increasing focus on discovering neoantigens or modified peptides which could elicit a better immune response. We recently found that the methionine sulfoxide variant of YMDGTMSQV, an immunogenic tyrosinase derived epitope, elicits a stronger immune response compared to the native one. Here, we address the separation of six MHC I-restricted tyrosinase-derived pe ...[more]
Similar Datasets
Project description:Ultra-violet (UV) and high-intensity visible (VIS) radiation are environmental stressors known to harm photosynthetic organisms through the generation of reactive intermediates that damage photosynthetic machinery. This study shows the potential of using a thermoacidophilic red alga of the order Cyanidiales to model in situ algal gene expression dynamics as a function of UV exposure and seasonal shifts in UV-VIS intensity. These algae exhibit a dynamic seasonal biomass fluctuation referred to as 'mat decline' where viability drastically decreases as seasonal UV-VIS irradiance intensity increases. In Yellowstone National Park (YNP), temporal experiments coupling UV irradiance manipulations (filtering) with whole-community transcription profiling revealed significant cyanidial gene expression changes occurring as a result of exposure to UV, and that patterns of response adjust across low and high irradiance time periods. Separate analyses examined genes responding to either increasing seasonal UV or VIS intensity, or by the combined effects of both irradiance wavelengths (UV and VIS). Results not only corroborated known physiological changes to solar irradiance, but also suggested the strategies employed to deal with excess VIS and UV intensity may be highly integrated. Finally, a suite of comparative analyses determined the relative utility of environmental transcriptomics technologies in studying ecologically-relevant expression patterns. Results suggest in situ expression profiles will improve understanding of how photosynthetic organisms are responding to environmental stressors as they are observed in nature. 16 samples with 3 biological replicates each.
2014-03-31 | E-GEOD-37673 | biostudies-arrayexpress
Project description:Proteinopathies are protein misfolding diseases that have an underlying factor that effect the conformation of proteoforms. A factor hypothesised to play a role in these diseases is the incorporation of non-protein amino acids into proteins, with a key example being the therapeutic drug levodopa. The presence of levodopa as a protein constituent has been explored in several studies but it has not been examined in a global proteomic manner. This paper provides a proof-of-concept method for enzymatically creating levodopa containing proteins using the enzyme tyrosinase, provides spectral evidence of in vitro incorporation and the induction of the unfolded protein response due to levodopa.
2022-02-17 | PXD025759 | Pride
Project description:Peptide-Spectrum Match (PSM) Validation with Internal Standards (P-VIS) is an objective approach to validating individual PSMs. A biological sample is analyzed by LC-MS/MS and the data are searched using a traditional approach such as a database search or de novo sequencing. A PSM of interest is identified, and a synthetic version of the putative peptide is obtained. Internal standard peptides (ISPs) are spiked into both the biological sample and the validation peptide sample and both samples are analyzed by LC-MS/MS. Using PSM_validator (https://github.com/Delong-Lab/PSM_validator/releases), an open-source program we created to implement the P-VIS workflow, both the fragmentation spectrum and the chromatographic retention time for the peptide of interest in the biological sample are compared to those of the validation peptide. The same comparisons are made for each of the ISPs, and these results are used to establish a prediction interval for valid matches. If the values for the comparisons between the biological and validation peptide fall within the prediction intervals, the match is considered valid. This submission contains the data and P-VIS results from a study aimed at benchmarking the P-VIS workflow.
2020-09-21 | PXD020901 | Pride
Project description:Although current mass spectrometry (MS)-based proteomics identifies and quantifies thousands of proteins and (modified) peptides, only a minority of them are subjected to in-depth downstream analysis. With the advent of automated processing workflows, biologically or clinically important results within a study are rarely validated by visualization of the underlying raw information. Although several tools for this are in principle available, they are often not integrated into the overall analysis nor readily extendable with new approaches. To remedy this, we developed AlphaViz, an open-source Python package to superimpose output from common analysis workflows on the raw data for quick and easy visualization and validation of protein and peptide identifications. AlphaViz takes advantage of recent breakthroughs in the deep learning-assisted prediction of experimental peptide properties to allow manual assessment of the expected and measured peptide result deviation. We focused on the visualization of the 4-dimensional data cuboid provided by Bruker TimsTOF instruments, where the ion mobility dimension, besides intensity and retention time, can be predicted and used for verification. We illustrate how AlphaViz can quickly validate or invalidate peptide identifications regardless of the score given to them by automated workflows. Furthermore, we provide a ‘predict mode’ that can locate peptides present in the raw data but not reported by the search engine. This is illustrated with dilution series and the recovery of missing values from experimental replicates. Applied to phosphoproteomics of the EGF-signaling pathway, we show how key signaling nodes can be validated to enhance confidence for downstream interpretation or follow-up experiments. AlphaViz follows accepted standards for open-source software development, including extensive documentation, testing and continuous integration. It features an easy-to-install graphical user interface for end-users and a modular Python package for bioinformaticians. We hope that AlphaViz can help to make validation of critical proteomics results a standard feature in MS-based proteomics.
2022-07-11 | PXD034223 | Pride
Project description:Visfatin (VIS) is a hormone belonging to the adipokines’ group secreted mainly by the adipose tissue. VIS plays a crucial role in the control of energy homeostasis, inflammation, cell differentiation, and angiogenesis. VIS expression was confirmed in the hypothalamic-pituitary-gonadal (HPG) axis structures, as well as in the uterus, placenta, and conceptuses. We assumed that VIS may affect the abundance of proteins involved in the regulation of key processes occurring in the corpus luteum (CL) during the implantation process. In the present study, we performed the high-throughput proteomic analysis (liquid chromatography with tandem mass spectrometry, LC-MS/MS) to examine the influence of VIS (100 ng/mL) on differentially regulated proteins (DRPs) in the porcine luteal cells (LCs) on days 15-16 of pregnancy (implantation period). We have identified 511 DRPs, 276 of them were up-regulated and 235 down-regulated in the presence of VIS. Revealed DRPs were assigned to 162 gene ontology terms. Western blot analysis of five chosen DRPs, ADAM metallopeptidase with thrombospondin type 1 motif 1 (ADAMTS1), lanosterol 14-α demethylase (CYP51A1), inhibin subunit beta A (INHBA), notch receptor 3 (NOTCH3), and prostaglandin E synthase 2 (mPGES2) confirmed the veracity and accuracy of LC-MS/MS method. We indicated that VIS modulates the expression of proteins connected with the regulation of lipogenesis and cholesterologenesis, and, in consequence, may be involved in the synthesis of steroid hormones, as well as prostaglandins’ metabolism. VIS also changes the expression of proteins involved in the insulin signalling pathway. Moreover, we revealed that VIS affects the abundance of protein associated with ovarian cell proliferation, differentiation, and apoptosis, as well as CL new vessel formation and tissue remodelling. Our results seem to confirm the hypothesis concerning the important role of VIS in the regulation of ovarian functions during the peri-implantation period.
2024-07-03 | PXD047445 | Pride
Project description:Oculocutaneous albinism type 3 (OCA3) is an autosomal recessive disorder caused by mutations in the TYRP1 gene. Tyrosinase-related protein 1 (Tyrp1) is involved in eumelanin synthesis, catalyzing the oxidation of 5,6-dihydroxyindole-2-carboxylic acid oxidase (DHICA) to 5,6-indolequinone-2-carboxylic acid (IQCA). In our work, we are trying to understand the effect of genetic mutations at the level of protein atomic structure and establish a link between the effect of mutations and disease phenotype. Here, for the first time, four OCA3-causing mutations of Tyrp1, C30R, H215Y, D308N, and R326H, were investigated computationally and experimentally to understand Tyrp1 protein stability and catalytic activity. Using the Tyrp1 crystal structure (PDB:5M8L), global mutagenesis was conducted to evaluate mutant protein stability. Consistent with our predictions the foldability parameter, C30R and H215Y should exhibit greater instability, and two other mutants, D308N and R326H, are expected to keep a native conformation. Mass-spectroscopy analysis has confirmed the identity of mutant recombinant variants. SDS-PAGE and Western blot analysis of the purified recombinant proteins confirmed that the foldability parameter correctly predicted the effect of mutations critical for protein stability. C18 data see C4 data.
2023-06-12 | PXD034893 | Pride
Project description:Oculocutaneous albinism type 3 (OCA3) is an autosomal recessive disorder caused by mutations in the TYRP1 gene. Tyrosinase-related protein 1 (Tyrp1) is involved in eumelanin synthesis, catalyzing the oxidation of 5,6-dihydroxyindole-2-carboxylic acid oxidase (DHICA) to 5,6-indolequinone-2-carboxylic acid (IQCA). In our work, we are trying to understand the effect of genetic mutations at the level of protein atomic structure and establish a link between the effect of mutations and disease phenotype. Here, for the first time, four OCA3-causing mutations of Tyrp1, C30R, H215Y, D308N, and R326H, were investigated computationally and experimentally to understand Tyrp1 protein stability and catalytic activity. Using the Tyrp1 crystal structure (PDB:5M8L), global mutagenesis was conducted to evaluate mutant protein stability. Consistent with our predictions the foldability parameter, C30R and H215Y should exhibit greater instability, and two other mutants, D308N and R326H, are expected to keep a native conformation. Mass-spectroscopy analysis has confirmed the identity of mutant recombinant variants. SDS-PAGE and Western blot analysis of the purified recombinant proteins confirmed that the foldability parameter correctly predicted the effect of mutations critical for protein stability.
2023-06-12 | PXD034892 | Pride
Project description:Sporadic Burkitt lymphoma (sBL) can be delineated from diffuse large B-cell lymphoma (DLBCL) by a very homogeneous mRNA expression signature. However, it remained unclear whether all three BL variants – sBL, endemic BL (eBL) and immunodeficiency-associated BL (HIV-BL) – represent a uniform biological entity despite their differences in geographical occurrence, association with immunodeficiency and/or incidence of EBV infection. To address this issue, we generated micro RNA (miRNA) profiles from 18 eBL, 31 sBL and 15 HIV-BL cases. In addition, we analyzed the miRNA expression of 86 DLBCL to determine whether miRNA profiles recapitulate the molecular differences between BL and DLBCL evidenced by mRNA profiling. A signature of 38 miRNAs enriched in MYC regulated and NF-kB pathway associated miRNAs was obtained that differentiated BL from DLBCL. The miRNA profiles of sBL and eBL displayed only 6 differentially expressed miRNAs, whereas HIV and EBV infection had no impact on the miRNA profile of BL. In conclusion, miRNA profiling confirms that BL and DLBCL represent distinct lymphoma categories and demonstrates that the three BL variants are representatives of the same biological entity with only marginal miRNA expression differences between eBL and sBL. Archival tumor specimens of 86 diffuse large B-cell lymphoma (DLBCL) and 64 Burkitt lymphoma (BL) patients were obtained. The DLBCL samples have previously been reviewed by a panel of expert hematopathologists and their clinical data were published as part of the RiCOVER-60 trial. The diagnosis of all BL cases was confirmed by histopathology review according to the criteria of the WHO classification. Based on their geographical origin, 31 BL samples were designated as sporadic BL (sBL) and 18 samples as endemic BL (eBL). Fifteen BL cases were diagnosed as immunodeficiency-associated BL (HIV-BL). Of the 18 eBL 14 cases were EBV+ (87.5%), 2 samples were EBV- (12.5%) and for 2 eBL cases the EBV status was unknown. Of the sBL samples 26 were EBV- (86.7%), 4 cases were EBV+ (13.3%) and for 1 case the EBV status was not evaluable. Among the HIV-BL 5 (33.3%) were EBV+, whereas 10 (66.7%) were EBV-.
2011-07-17 | E-GEOD-22420 | biostudies-arrayexpress
Project description:Antrodia Camphorata is well known in Taiwan as a folk medicinal fungus with anticancer and anti-inflammatory effects. In this study, we used a human acute myelogenous leukemia cell line, KG-1, as the experimental model and constructed a high-throughput gene screen integrated platform by using a combination of herbal identification, UV-VIS spectrophotometry, high performance liquid chromatography (HPLC), inductively coupled plasma mass spectrometry (ICPMS), and DNA microarray technology. Based on this science-based platform, we developed a practical quantitative method and also established an organic/inorganic chemical fingerprint for the herbal materials. In the mean while, the global gene expression patterns of the KG-1 cells treated with various A. camphorata mycelia extracts (water and methanol extracts) were compared. Furthermore, several possible biological responses and relevant marker gene would be identified by our high-throughput integrated platform. Keywords: KG-1 treated with AC extracts for 4 days, cDNA microarray, biomarker selection. We used optimal loop design to calculate the gene expression profile. In this design, we used labeled RNA from each sample to labeled three slides for a total of nine arrays. Therefore, the data computations were consisted of 18 measurements (6 samples with 3 replicates) for each of 7334 genes. Besides, duplicated water-treatment samples were used as internal control
2010-06-24 | E-GEOD-3692 | biostudies-arrayexpress
Project description:Accumulation of visceral (VIS) as opposed to subcutaneous (SUB) fat is a predictor of metabolic disorders, insulin resistance, and cardiovascular disease. This is due in part to the limited capacity of VIS fat to buffer lipids allowing them to deposit in insulin-sensitive tissues, thus impairing insulin action. In addition, VIS adipose tissue is more prone to fibrosis and inflammation, which in turn contributes to the pathogenesis of metabolic disease. Mechanisms underlying selective hypertrophic growth and tissue remodeling properties of VIS fat are not well understood. We and others identified subsets of adipose progenitors (APs) unique to VIS fat with differential adipogenic capacity. We named these CD34+ APs VIS low and VIS high based on low or high CD34 expression respectively. Despite sharing the same developmental origin, VIS low APs are adipogenic whereas VIS high APs are not. Furthermore, VIS high APs inhibit adipogenic differentiation of SUB and VIS low APs in vitro through the secretion of soluble inhibitory factor(s) including insulin-like growth factor binding protein 2 (Igfbp2). The number of VIS high APs increased with VIS adipose tissue expansion and their abundance in vivo causes hypertrophic growth, fibrosis, inflammation and impaired glucose and insulin tolerance. This study unveil the presence of APs unique to VIS fat involved in the paracrine regulation of adipogenesis and tissue remodeling.
2024-05-21 | PXD014672 | Pride