Ptal-N*01:01 mass spectrometry results
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ
ORGANISM(S): Pteropus Alecto (black Flying Fox)
TISSUE(S): T Cell
DISEASE(S): Covid-19
SUBMITTER: 
Suqiu Wang
LAB HEAD: Nianzhi Zang
PROVIDER: PXD046952 | Pride | 2024-05-02
REPOSITORIES: Pride
Similar Datasets
Project description:The RPLD-MS system was used to obtain peptides that bind to bat MHC I molecules, and their sequences were sequenced by mass spectrometry, based on which the peptide sequences obtained were used to predict the peptide delivery
2024-05-02 | PXD047090 | Pride
Project description:The RPLD-MS system was used to obtain peptides that bind to bat MHC I molecules, and their sequences were sequenced by mass spectrometry, based on which the peptide sequences obtained were used to predict the peptide delivery
2024-05-02 | PXD047017 | Pride
Project description:Morphine, a commonly used antinociceptive drug in hospitals, is known to cross the blood-brain barrier (BBB) by first passing through brain endothelial cells. Despite its pain-relieving effect, morphine also has detrimental effects, such as the potential induction of redox imbalance in the brain. However, there is still insufficient evidence of these effects on the brain, particularly on the brain endothelial cells and the extracellular vesicles that they naturally release. Indeed, extracellular vesicles (EVs) are nanosized bioparticles produced by almost all cell types and are currently thought to reflect the physiological state of their parent cells. These vesicles have emerged as a promising source of biomarkers by indicating the functional or dys-functional state of their parent cells and, thus, allowing a better understanding of the biological processes involved in an adverse state. However, there is very little information on the mor-phine effect on human brain microvascular endothelial cells (HBMECs), and even less on their released EVs. Therefore, the current study aimed at unraveling the detrimental mechanisms of morphine exposure (at 1, 10, 25, 50 and 100 µM) for 24 h on human brain microvascular endothe-lial cells as well as on their associated EVs. Isolation of EVs was carried out using an affini-ty-based method. Several orthogonal techniques (NTA, western blotting and proteomics analy-sis) were used to validate the EVs enrichment, quality and concentration. Data-independent mass spectrometry (DIA-MS)-based proteomics was applied in order to analyze the proteome modu-lations induced by morphine on HBMECs and EVs. We were able to quantify almost 5500 pro-teins in HBMECs and 1500 proteins in EVs, of which 256 and 148, respectively, were found to be differentially expressed in at least one condition. Pathway enrichment analysis revealed that the “cell adhesion and extracellular matrix remodeling” process and the “HIF1 pathway”, a pathway related to oxidative stress responses, were significantly modulated upon morphine exposure in HBMECs and EVs. Altogether, the combination of proteomics and bioinformatics findings high-lighted shared pathways between HBMECs exposed to morphine and their released EVs. These results put forward molecular signatures of morphine-induced toxicity in HBMECs that were also carried by EVs. Therefore, EVs could potentially be regarded as a useful tool to investigate brain endothelial cells dysfunction, and to a different extent, the BBB dysfunction in patient cir-culation using these “signature pathways”.
2023-03-11 | PXD038516 | Pride
Project description:A battery of spliceosome-associated proteins has been identified in microRNA (miRNA) biogenesis; however, the underlying mechanisms remain elusive. The intron lariat spliceosome (ILS) complex is highly conserved among eukaryotes and its disassembly marks the end of a canonical splicing cycle. In this study, we show that two conserved disassembly factors of the ILS complex, ILP1 and NTR1, positively regulate microRNA biogenesis through facilitating transcriptional elongation in Arabidopsis. ILP1 and NTR1 form a stable complex and co-regulate alternative splicing of more than a hundred genes across the genome including the core circadian gene LHY and some pri-miRNAs. Dysfunction in either ILP1 or NTR1 result in reduced RNA polymerase II occupancy at elongated regions of MIR chromatins, without affecting MIR promoter activity, pri-miRNA decay and DCL1 processing. Our results provide insights into the molecular mechanisms of spliceosomal machineries in non-coding RNA regulation.
2019-11-12 | PXD011542 | Pride
Project description:We investigate a range of methods for solubilizing modern and archaeological silks and demonstrate a protocol using mass spectrometry-based proteomics to successfully differentiate modern samples of Bombyx, Antheraea, and Samia -produced silks matching samples to species level. We also analyzed archaeological silks from excavations at the ancient city of Palmyra, Syria, and provide evidence that these silks were produced by A. mylitta, which is the first direct evidence supporting the production and trade of Indian wild silk in antiquity.
2022-04-04 | PXD024610 | Pride
Project description:Investigating the origins of sericulture is challenging, as classification of silks by species is currently technically difficult. Here we investigate a range of methods for solubilizing modern and archaeological silks and demonstrate a protocol using mass spectrometry-based proteomics to successfully differentiate modern samples of Bombyx, Antheraea, and Samia -produced silks matching samples to species level. We also analyzed archaeological silks from excavations at the ancient city of Palmyra, Syria, and provide evidence that these silks were produced by A. mylitta, which is the first direct evidence supporting the production and trade of Indian wild silk in antiquity.
2022-04-04 | PXD024606 | Pride
Project description:In contrast to the desiccation tolerant (DT) ‘orthodox’ seeds, the so-called ‘intermediate’ seeds cannot survive complete drying and are short-lived. All species of the genus Coffea produce intermediate seeds but show a considerable variability for the seed DT level, which may help to decipher the molecular basis of seed DT in plants. We thus led a comparative transcriptome analysis of developing seeds in three coffee species with contrasting seed DT levels. Seeds of all species shared a major transcriptional switch during late maturation that governs a general slow-down of metabolism. However, numerous key stress-related genes, including those coding for the late embryogenesis abundant protein EM6 and the osmosensitive calcium channel ERD4, were upregulated during DT acquisition in the two species with high seed DT, C. arabica and C. eugenioides. By contrast, an upregulation of numerous players of the metabolism, transport and perception of auxin was observed in C. canephora seeds with low DT. Moreover, species with high DT showed a stronger down-regulation of the mitochondrial machinery dedicated to the tricarboxylic acid cycle and oxidative phosphorylation. Accordingly, respiration measurements during seed dehydration demonstrated that intermediate seeds with the highest DT levels are better prepared to cease respiration and avoid oxidative stresses.
2020-05-26 | PXD015806 | Pride
Project description:Electrophiles for covalent inhibitors that are suitable for in vivo administration are rare. While acrylamides are prevalent in FDA approved covalent drugs, chloroacetamides are considered too reactive for such purposes. We report sulfamate-based electrophiles that maintain chloroacetamide-like geometry, with tunable reactivity. We prepared sulfamate-based inhibitors for BTK and Pin1 displaying high potency, low intrinsic reactivity and high stability. Finally, we show that sulfamate acetamides can be used for covalent ligand-directed release (CoLDR) chemistry, both for the generation of ‘turn-on’ probes as well as for traceless ligand-directed site-specific labeling of proteins. Using alkyne-modified sulfamate-based probes, we performed proteomics studies with samples enriched with probe-bound proteins, and the sulfamate probes displayed comparable or improved selectivity compared to the parent compounds. Further characterization of off-target using IsoDTB-ABPP confirmed this result. This submission contains the pull down data.
2023-03-11 | PXD038375 | Pride
Project description:Thiol-based redox post-translational modifications have emerged as important mechanisms of signaling and regulation in all organisms. In this context, the small ubiquitous oxido-reductase thioredoxin plays a key role by controlling the thiol-disulfide status of target proteins. Recent redox proteomic studies revealed hundreds of proteins regulated by glutathionylation and nitrosylation in the unicellular green alga Chlamydomonas reinhardtii while much less is known about the thioredoxin interactome in this photosynthetic model organism. Using an affinity purification strategy, we identified 980 thioredoxin targets. They participate in a wide variety of metabolic pathways and cellular processes. This study broadens not only the redox regulation to new enzymes involved in metabolic pathways already known to be regulated by thioredoxins (carbon, lipid and energy metabolism) but also shed light on cellular processes for which data supporting a putative redox regulation in these processes are scarce (aromatic amino-acid biosynthesis, nuclear transport,…).
2017-07-28 | PXD006097 | Pride
Project description:Axonemal dynein ATPases direct eukaryotic ciliary and flagellar beating via adenosine triphosphate (ATP) hydrolysis. The modulatory effect of adenosine monophosphate (AMP) and adenosine diphosphate (ADP) on flagellar beating is not fully understood. Here we describe a deficiency of CFAP45 in both humans and mice that presents a motile ciliopathy featuring situs inversus totalis and asthenospermia. CFAP45-deficient cilia and flagella show normal morphology and axonemal ultrastructure. Proteomic profiling links CFAP45 to an axonemal module including dynein ATPases and adenylate kinase as well as CFAP52, whose mutations cause a similar human ciliopathy. CFAP45 binds AMP in vitro, consistent with structural modelling that identifies an AMP-binding interface between CFAP45 and AK8. Microtubule sliding of dyskinetic sperm from Cfap45-/- mice is partially rescued with the addition of either AMP or ADP with ATP, compared to ATP alone. We propose that CFAP45 supports mammalian ciliary and flagellar beating via an adenine nucleotide homeostasis module.
2020-11-05 | PXD019806 | Pride