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Identification of sulfhydryl-containing proteins and further evaluation of the selenium- tagged redox homeostasis-regulating proteins:Identification of cysteine sites using tandem orthogonal proteolysis strategy (TOP-ABPP).

ABSTRACT: We sought to identify exact modified cysteine sites by Se-probes using TOP-ABPP strategy and the acid cleavable azide-biotin tag was used to enrich and release the modified peptides for LC-MS/MS analys

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

DISEASE(S): Disease Free

SUBMITTER: Zhongyao Jiang

LAB HEAD: Zhenzhe Chen

PROVIDER: PXD046852 | Pride | 2023-12-07

REPOSITORIES: Pride

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			Action	DRS
	R1DPDSyne1.raw	Raw
	R1DPDSyne2.raw	Raw
	R1NPSPyne1.raw	Raw
	R1NPSPyne2.raw	Raw
	R1NPSSyne1.raw	Raw

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Identification of sulfhydryl-containing proteins and further evaluation of the selenium-tagged redox homeostasis-regulating proteins:Identification of sulfhydryl-containing proteins and further evaluation of the selenium-tagged redox homeostasis-regulating proteins:Identification of sulfhydryl-containing proteins and further evaluation of the selenium-tagged redox homeostasis-regulating proteins:Mass Spectrometry (MS)-based quantitative profiling of Se-probes-reactive proteins

Project description:We performed MS-based quantitative profiling of Se-probes-reactive proteins by ABPP using stable isotope reductive dimethylation method.

2023-12-07 | PXD046856 | Pride

Identification of sulfhydryl-containing proteins and further evaluation of the selenium- tagged redox homeostasis-regulating proteins:Identification of cysteine sites using competitive rdTOP-ABPP strategy.The competitive rdTOP-ABPP strategy be used to reidentify the cysteine sites labeled by Se-SMs.

Project description:The competitive rdTOP-ABPP strategy be used to reidentify the cysteine sites labeled by Se-SMs.

2023-12-07 | PXD046847 | Pride

grape berry vacuole proteomic - Quantitative Proteome Analysis Reveals Changes in the Protein Landscape During Grape Berry Development With a Focus on Vacuolar Transport Proteins

Project description:The vacuole occupies a large portion of plant cell volume, it is especially true to fruit tissues. Berry flesh cell vacuole serves as storage organelle for water, sugars, acids, secondary metabolites and others, which largely determining berry quality (Fontes et al., 2011a, b; Shiratake and Martinoia, 2007, Conde et al., 2006). However, the molecular basis of these compartmentation processes is still poorly understood. As in many species, the major bottle neck to study these aspects in grapevine is to obtain highly purified vacuoles with a good yield (Fontes et al., 2010). Up to date, several vacuole or tonoplast proteome researches were applied on a few plants mainly on Arabidopsis thaliana, vacuoles or tonoplast were derived from mesophyll cells (Carter et al., 2004, Endler et al., 2006, Schulze, et al., 2012) or cell culture (Jaquinod et al 2006, Shimaoka et al 2004), cauliflower buds (Schmidt et al., 2007) and sugar beet taproots (Jung et al., 2015). Though the grape berry protoplasts and intact vacuoles were successfully isolated from Cabernet Sauvignon berry suspension-cultured cells (Fontes et al., 2010), the vacuoles isolated from grape berry or different development and ripening stages of grape berry mesocarp tissues were not achieved.

2019-11-12 | PXD010556 | Pride

USF2 interacted proteins in HEK293T cells

Project description:We found that USF2 is repressor of lysosomal genes. To find the interacting co-repressor complex of USF2, we performed USF2 complex purification and mass spectrography.

2024-09-11 | PXD050434 | Pride

Targeted AURKA degradation: Towards new therapeutic agents for neuroblastoma

Project description:Aurora kinase A (AURKA) is a well-established target in neuroblastoma (NB) due to both its catalytic functions during mitosis and its kinase-independent functions, including stabilization of the key oncoprotein MYCN. We present a structure-activity relationship (SAR) study of MK-5108-derived PROTACs against AURKA by exploring different linker lengths and exit vectors on the thalidomide moiety. PROTAC SK2188 induces the most potent AURKA degradation (DC50,24h 3.9 nM, Dmax,24h 89%) and shows an excellent binding and degradation selectivity profile. Treatment of NGP neuroblastoma cells with SK2188 induced concomitant MYCN degradation, high replication stress/DNA damage levels and apoptosis. Moreover, SK2188 significantly outperforms the parent inhibitor MK-5108 in a cell proliferation screen and patient-derived organoids. Furthermore, altering the attachment point of the PEG linker to the 5-position of thalidomide allowed us to identify a potent AURKA degrader with a linker as short as 2 PEG units. With this, our SAR-study provides interesting lead structures for further optimization and validation of AURKA degradation as a potential therapeutic strategy in neuroblastoma

2023-02-27 | PXD040391 | Pride

Label-free analysis of HCV-associated hepatic fibrosis

Project description:A differential label-fee proteomics approach was performed using 27 biopsies from patients with HCV-associated hepatic fibrosis. For statistical analysis the patients were grouped into a low and a high fibrosis group. The low fibrosis group contained 13 patients of fibrosis stages 0, 1 and 2, whereas the high fibrosis group contained 14 patients of fibrosis stages 3 and 4 (fibrosis stages according to Batts-Ludwig classification).

2015-03-30 | PXD001474 | Pride

Loss of hepatic miR-33 improves metabolic homeostasis and liver function without altering body weight or atherosclerosis

Project description:miR-33 is an intronic microRNA within the gene encoding the SREBP2 transcription factor. Like its host gene, miR-33 has been shown to be an important regulator of lipid metabolism. Inhibition of miR-33 has been shown to promote cholesterol efflux in macrophages by targeting the cholesterol transporter ABCA1, thus reducing atherosclerotic plaque burden. Inhibition of miR-33 has also been shown to improve high-density lipoprotein (HDL) biogenesis in the liver and increase circulating HDL-C levels in both rodents and nonhuman primates. However, evaluating the extent to which these changes in HDL metabolism contribute to atherogenesis has been hindered by the obesity and metabolic dysfunction observed in whole-body miR-33–knockout mice. To determine the impact of hepatic miR-33 deficiency on obesity, metabolic function, and atherosclerosis, we have generated a conditional knockout mouse model that lacks miR-33 only in the liver. Characterization of this model demonstrates that loss of miR-33 in the liver does not lead to increased body weight or adiposity. Hepatic miR-33 deficiency actually improves regulation of glucose homeostasis and impedes the development of fibrosis and inflammation. We further demonstrate that hepatic miR-33 deficiency increases circulating HDL-C levels and reverse cholesterol transport capacity in mice fed a chow diet, but these changes are not sufficient to reduce atherosclerotic plaque size under hyperlipidemic conditions. By elucidating the role of miR-33 in the liver and the impact of hepatic miR-33 deficiency on obesity and atherosclerosis, this work will help inform ongoing efforts to develop novel targeted therapies against cardiometabolic diseases.

2021-02-11 | PXD023471 | Pride

Quantitative Secretome Analysis of Activated Jurkat Cells

Project description:A quantitative label-free secretome analysis protocol using a click chemistry-based approach for the enrichment of secreted glycoproteins was adapted for and applied to a T cell model. There, Jurkat cells were activated via PMA/ionomycin and the dynamic modulation of the T cell secretome was investigated and compared to the dynamic modulation of the T cell proteome of the same model.

2016-10-10 | PXD004280 | Pride

Nogo-B co-IP-MS experiment in mouse liver and pancreas

Project description:Co-immunoprecipitation with either rabbit normal IgG or anti-Nogo-B antibody followed by mass spectrometry (co-IP-MS) in the liver and pancreas of wild-type C57BL/6J mice.

2024-07-27 | PXD046104 | Pride

Glioblastoma biomarkers in urinary extracellular vesicles reveal the potential for a ‘liquid gold’ biopsy

Project description:Background: Biomarkers that reflect glioblastoma tumour activity and treatment response are urgently needed to help guide clinical management, particularly for recurrent disease. As the urinary system is a major clearance route of circulating extracellular vesicles (EVs; 30-1000 nm nanoparticles) we explored whether sampling urinary-EVs could serve as a simple and non-invasive liquid biopsy approach for measuring glioblastoma-associated biomarkers. Methods: Fifty urine specimens (15-60 ml) were collected from 24 catheterised glioblastoma patients immediately prior to primary (n=17) and recurrence (n=7) surgeries, following gross total resection (n=9), and from age/gender-matched healthy participants (n=14). EVs isolated by differential ultracentrifugation were characterised and extracted proteomes were analysed by high-resolution data-independent acquisition liquid chromatography tandem mass spectrometry (DIA-LC-MS/MS). Results: Overall, 6857 proteins were confidently identified in urinary-EVs (q-value≤0.01), including 94 EV marker proteins. Glioblastoma-specific proteomic signatures were determined, and putative urinary-EV biomarkers corresponding to tumour burden and recurrence were identified (FC≥|2|, adjust p-val≤0.05, AUC>0.9). Conclusion: In-depth DIA-LC-MS/MS characterisation of urinary-EVs substantiates urine as a viable source of glioblastoma biomarkers. The promising ‘liquid gold’ biomarker panels described here warrant further investigation.

2024-04-18 | PXD046511 | Pride

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