Identifying palmitoylated proteins
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Kidney
SUBMITTER: 
Bin Huang
LAB HEAD: Yin chengqian
PROVIDER: PXD051426 | Pride | 2024-12-19
REPOSITORIES: pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 2-BP-1.msf | Msf | |||
| 2-BP-1.raw | Raw | |||
| 2-BP-2.msf | Msf | |||
| 2-BP-2.raw | Raw | |||
| 2-BP-3.msf | Msf |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
Project description:Analysis of proteins interacting with GPX4 in A375 and 293T cells infected with lentiviruses encoding empty vector or Flag-GPX4, using anti-Flag magnetic beads enrichment and LC-MS/MS.
2024-12-19 | PXD051448 | Pride
Project description:The experimental purpose is to investigate the protein interactions involving RBM47 through mass spectrometry experiments.
2023-12-01 | PXD045984 | Pride
Project description:Vesicoureteral reflux (VUR) is a common pediatric condition that predisposes children to renal damage after urinary tract infection (UTI). We profiled the urinary proteome of VUR patients with recurrent UTI and renal scarring to identify potential biomarkers characterizing this condition. Urine was obtained from 22 age-matched controls and 22 patients with low grade VUR (1-3 out of 5), renal scarring, and history of recurrent UTI. Proteins extracted from these samples were analyzed by mass spectrometry for protein identification and quantitation for comparison.
2018-10-05 | PXD010469 | Pride
Project description:The abundance of noncanonical open reading frames present in long noncoding RNAs (lncRNAs) indicates the potential for translational capacity, thereby enabling the generation of multiple functional peptides or proteins. Nevertheless, the existence of peptide or protein products derived from lncRNAs and their specific roles in gastric cancer remain largely unexplored. In this study, we identified HOXA10-HOXA9-derived small protein (HDSP) in gastric cancer by conducting a comprehensive analysis and experimental validation with mass spectrometry and western blotting. HDSP is highly expressed and has oncogenic roles in gastric cancer. Mechanistically, HDSP blocked TRIM25-mediated ubiquitination and degradation by interacting with MECOM. This led to the accumulation of MECOM, which further enhanced the transcription of SPINK1, a gene that promotes cancer through the EGFR signaling pathway. In addition, MECOM promoted the transcription of HOXA10-HOXA9, creating a feedback regulatory loop that activated downstream SPINK1-EGFR signaling. Finally, we found that HDSP knockdown inhibited tumor growth in a patient-derived xenograft (PDX) model, and the infusion of an artificially synthesized HDSP peptide as a neoantigen improved the anti-tumor efficacy of immune cells against gastric cancer in vitro and in vivo. Our findings provide a potential therapeutic target or neoantigen candidate for the treatment of gastric cancer.
2024-05-07 | PXD043737 | Pride
Project description:Dynamic conformational and structural changes in proteins and protein complexes play a central and ubiquitous role in the regulation of protein function, yet it is very challenging to study these changes, especially for large protein complexes, under physiological conditions. Here we introduce a novel isobaric crosslinker, Qlinker, for studying conformational and structural changes in proteins and protein complexes using quantitative crosslinking mass spectrometry (qCLMS). Qlinkers are small and simple, amine-reactive molecules with an optimal extended distance of ~10 Å which use MS2 reporter ions for relative quantification of Qlinker-modified peptides derived from different samples. We synthesized the 2-plex Q2linker and showed that the Q2linker can provide quantitative crosslinking data that pinpoints key conformational and structural changes in biosensors, binary and ternary complexes composed of the general transcription factors TBP, TFIIA, and TFIIB, and RNA polymerase II (pol II) complexes.
2024-11-13 | PXD056825 | Pride
Project description:Hypoxia results in the changes in expression of many genes, the majority of which are mediated via the transcriptional activity of the hypoxia inducible factor (HIF) complex. However, other mechanisms of gene regulation by hypoxia are likely and include control of mRNA stability, regulation of mRNA translation and regulation mediated by micrornas. The aim of this study is to identify microRNAs which expression is regulated by hypoxia. We chose the breast cancer line MCF7 for study as we had previously characterised the expression of the components of the HIF system in that cell line and undertaken an extensive study of the gene expression profile in response to hypoxia, a prolyl hydroxylase inhibitor dimethyloxalylglycine and HIF-1a isoform manipulations (Eldvidge. G.P. et al. (2006) JBC, vol. 281, 22, 15215-15226).
2008-03-01 | E-MEXP-1111 | biostudies-arrayexpress
Project description:PURPOSE. Triamcinolone acetonide (TA) and dexamethasone (DEX) are corticosteroids commonly used for ocular inflammation but both can cause ocular hypertension. We investigated the differential gene expression profile of human trabecular meshwork (TM) cells in response to treatment by TA compared to that by DEX. METHODS. Total RNA was extracted from cultured human TM cells treated with TA or DEX and used for microarray gene expression analysis. The microarray experiments were repeated three times. Differentially expressed genes were identified by an empirical Bayes approach and confirmed by real-time quantitative PCR. RESULTS. 0.1 mg/ml TA treatment resulted in 15 genes up-regulated and 12 genes down-regulated while 1mg/ml TA treatment resulted in 36 genes up-regulated and 21 genes down-regulated. These genes were mainly associated with acute-phase response, cell adhesion, cell cycle and growth, growth factor, ion binding, metabolism, proteolysis and transcription factor. Two genes, MYOC and GAS1, were up-regulated and 3 genes, SENP1, ZNF343 and SOX30, were down-regulated by both TA and DEX treatment. Eight differentially expressed genes were located in known primary open angle glaucoma (POAG) loci, including MYOC, SOAT1, CYP27A1, SPOCK, SEMA6A, EGR1, GAS1 and ATP10A. CONCLUSIONS. Differential gene expression profiles of human TM cells treated by TA and DEX, and a dosage effect by TA, were revealed by microarray technology. TA and DEX treatment shared several differentially expressed genes, suggesting a common mechanism to cause ocular hypertension. Some differentially expressed genes located in the known POAG loci are potential candidates for glaucoma genes. A total of 9 samples were used for this study. There were 3 biological replicates for each of 3 treatments.
2008-05-01 | E-GEOD-6298 | biostudies-arrayexpress
Project description:To identify NLRP6-associated proteins in living cells, we applied an APEX2-based labelling method combined with mass spectrometry. In brief, APEX2 was genetically fused to NLRP6. In the presence of hydrogen peroxide, APEX2 catalysed biotin-phenol to become a biotin-phenol radical that covalently bound to NLRP6 neighbouring proteins (<20 nm). The biotinylated proteins were enriched and collected by streptavidin beads. One-dimensional SDS–PAGE followed by liquid chromatography-tandem mass spectrometry (GeLC–MS/MS) was performed to identify the proteins. To detect ubiquitinated p85α, a Flag-tagged p85α plasmid was transfected into cells. The cell lysates were immunoprecipitated with anti-Flag and separated on a 6% SDS–PAGE gel. After in-gel digestion, the resulting peptides were extracted for GeLC–MS/MS analysis.
2023-07-02 | PXD037436 | Pride
Project description:Assay the ubiquitinated protein remmants post depletion or inhibition of the deubiquitinase Usp9x in melanoma cells.
2017-02-20 | PXD005417 | Pride
Project description:Observations of scarce surface ocean concentrations of dissolved zinc (Zn) have raised the possibility that Zn may co-limit the growth of oceanic phytoplankton, yet testing this hypothesis has been difficult because Zn is highly prone to contamination. Biomarkers of micro-nutrient stress can serve as an alternate means to assay, though biomarker proteins for Zn stress in marine algae are currently uncharacterized. In this study we identified two Zn-responsive proteins in four marine diatom species that became abundant under Zn and Co limitation, but were scarce or undetectable in replete conditions. We refer to these proteins as ZCRP-A and ZCRP-B (Zn/Co Responsive Protein A and B). Sequence similarity of ZCRP-A to the Escherichia coli model COG0523 protein YjiA suggests a Zn2+ binding capability using conserved metal binding sites. Cellular localization by fluorescent tagging and overexpression of these proteins showed that ZCRP-B is part of a membrane-bound transport complex and that ZCRP-A serves as a Zn/Co chaperone with a chloroplastic target. These results imply that ZCRP-A and ZCRP-B are important in intracellular Zn trafficking and high-affinity transport, respectively. Metaproteomic detection of ZCRP-A and ZCRP-B homologs in a variety of eukaryotic protists along a South Pacific Ocean transect demonstrated that both proteins were more abundant in the euphotic zone (0-200m) where dZn and dCo were scarce. These findings describe widely distributed marine algal proteins linked to Zn and Co metabolism that together contribute to our understanding of Zn homeostasis in important marine phytoplankton.
2022-03-02 | PXD026953 | Pride