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MS analysis of phosphopeptides enriched from BRG1-phospho mutants

ABSTRACT: Phosphopeptides enriched from stable clones expressing wild-type, phosphorylation-mimic (brg1-S1452D), or non-phosphorylatable BRG1 (brg1-S1452A) were analyzed by Q Exactive Quadrupole-Orbitrap LC-MS.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Ayuko Kimura

PROVIDER: PXD022680 | JPOST Repository | Wed Nov 24 00:00:00 GMT 2021

REPOSITORIES: jPOST

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			Action	DRS
	160822QE_Brg1_phos_MM_1.raw	Raw
	160822QE_Brg1_phos_MM_2.raw	Raw
	160822QE_Brg1_phos_MM_3.raw	Raw
	160822QE_Brg1_phos_WT_1.raw	Raw
	160822QE_Brg1_phos_WT_2.raw	Raw

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1 - 5 of 11

Publications

Phosphorylation of Ser1452 on BRG1 inhibits the function of the SWI/SNF complex in chromatin activation.

Kimura Ayuko A Arakawa Noriaki N Kagawa Hiroyuki H Kimura Yayoi Y Hirano Hisashi H

Journal of proteomics 20210706

BRG1, one of core subunits of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancers. Previously, we reported significant downregulation of the phosphorylation level of BRG1 on Ser<sup>1452</sup> (<10%) in cell lines derived from ovarian clear cell carcinoma with frequent recurrence and acquired drug resistance. In this study, we tried to elucidate the roles of BRG1 phosphorylation, using cell lines expressing wild-type, phosphorylation-mimic (brg1-S<sup>1452</sup>D), or non- ...[more]

PMID: 34237461

Similar Datasets

Proteomic analysis using BRG1-phosphorylation mutants

Project description:Proteins extracted from stable clones expressing wild-type, phosphorylation-mimic (brg1-S1452D), or non-phosphorylatable BRG1 (brg1-S1452A) were trypsin-digested and analyzed by Q Exactive Quadrupole-Orbitrap LC-MS.

2021-11-24 | PXD022681 | JPOST Repository

HeLa phosphoproteomics - TiO2-enriched phosphopeptides

Project description:TiO2-enriched phosphopeptides

2011-08-08 | PRD000526 | Pride

Discontinuous pH gradient-mediated separation of TiO2-enriched phosphopeptides.

Project description:Global profiling of phosphoproteomes has proven to be a great challenge due to the relatively low stoichiometry of protein phosphorylation and poor ionization efficiency in mass spectrometers. Effective, physiologically relevant, phosphoproteome research relies on the efficient phosphopeptide enrichment from complex samples. Immobilized metal affinity chromatography and titanium dioxide chromatography can greatly assist selective phosphopeptide enrichment. However, the complexity of resultant enriched samples is often still high, suggesting that further separation of enriched phosphopeptides is required. We have developed a pH gradient elution technique for enhanced phosphopeptide identification in conjunction with titanium dioxide chromatography. Using this process, we demonstrated its superiority to the traditional "one-pot" strategies for differential protein identification. Our technique generated a highly specific separation of phosphopeptides by an applied pH gradient between 9.2 and 11.3. The most efficient elution range for high-resolution phosphopeptide separation was between pHs 9.2 and 9.4. High-resolution separation of multiply phosphorylated peptides was primarily achieved using elution ranges greater than pH 9.4. Investigation of phosphopeptide sequences identified in each pH fraction indicated that phosphopeptides with phosphorylated residues proximal to acidic residues, including glutamic acid, aspartic acid, and other phosphorylated residues, were preferentially eluted at higher pH values.

| S-EPMC3002755 | biostudies-literature

Phosphoproteomics quantitative characterization in Jurkat E6.1 and Jurkat Gamma1.

Project description:Phosphorylation is a reversible post-translational modification, playing a vital role in protein function. In T cells, protein phosphorylation is the key mechanism regulating T cell receptor – driven signaling pathways. In order to gain insights into the phosphoproteome evolution of T cell activation, we performed a large-scale quantitative phosphoproteomics study of Jurkat E6.1 (wild type) and Jurkat gamma1 (Phospholipase gamma1 null) cell clones upon costimulation with anti-CD3 and anti-CD28 antibodies at times ranging from 15 min to as long as 120 min. In total, we identified 5585 phosphopeptides belonging to 2008 phosphoproteins from both cell clones. We detected 130 and 114 novel phosphopeptides in Jurkat E6.1 and Jurkat gamma1 clones, respectively. A significantly lower number of proteins containing regulated phosphorylation sites were identified in Jurkat gamma1 in comparison to Jurkat E6.1, reflecting the vital role of Phospholipase gamma1 in T cell signaling. Several new phosphorylation sites from lymphocyte-specific protein tyrosine kinase (LCK) were identified. Of these, Serine-121 showed significant changes in JE6.1 while only small changes in the Jgamma1 clone.

2015-11-10 | PXD002871 | Pride

Wild-type Heterogeneity Contributes to Clonal Variability in Genome-Edited Cells

Project description:Phenotypic variability among different knockout clones of the same gene is a common problem confounding the establishment of robust genotype-phenotype correlations. Optimized genome editing protocols to enhance reproducibility include measures to reduce off-target effects. However, even if current state-of-the-art protocols are applied phenotypic variability is frequently observed. Here we identify heterogeneity of wild-type cells as an important and often neglected confounding factor in genome-editing experiments. We demonstrate that isolation of individual wild-type clones from an apparently homogenous stable cell line uncovers significant phenotypic differences between clones. Strikingly, we observe hundreds of differentially regulated transcripts when comparing two populations of wild-type cells. Heterogeneity of wild-type cells thus contributes to variability in genome-edited cells when these are generated through isolation of clones. We show that the generation of monoclonal isogenic wild-type cells prior to genomic manipulation reduces phenotypic variability.

2022-02-18 | GSE196762 | GEO

In-Depth Analyses of B Cell Signaling Through Tandem Mass Spectrometry of Phosphopeptides Enriched by PolyMAC.

Project description:Tandem mass spectrometry (MS/MS) has enabled researchers to analyze complex biological samples since the original concept inception. It facilitates the identification and quantification of modifications within tens of thousands of proteins in a single large-scale proteomic experiment. Phosphorylation analysis, as one of the most common and important post-translational modifications, has particularly benefited from such progress in the field. Here we showcase the technique through in-depth analyses of B cell signaling based on quantitative phosphoproteomics. As a complement to the previously described PolyMAC-Ti (polymer-based metal ion affinity capture using titanium) reagent, we introduce here PolyMAC-Fe, which utilizes a different metal ion, Fe(III). An extensive comparison using the different available MS/MS fragmentations techniques was made between PolyMAC-Fe, PolyMAC-Ti and IMAC (immobilized metal ion affinity chromatography) reagents in terms of specificity, reproducibility and type of phosphopeptides being enriched. PolyMAC-Fe based chelation demonstrated good selectivity and unique specificity toward phosphopeptides, making it useful in specialized applications. We have combined PolyMAC-Ti and PolyMAC-Fe, along with SILAC-based quantitation and large-scale fractionation, for quantitative B cell phosphoproteomic analyses. The complementary approach allowed us to identify a larger percentage of multiply phosphorylated peptides than with PolyMAC-Ti alone. Overall, out of 13,794 unique phosphorylation sites identified, close to 20% were dependent on BCR signaling. These sites were further mapped to a variety of major signaling networks, offering more detailed information about the biochemistry of B cell receptor engagement.

| S-EPMC4417941 | biostudies-literature

JPST000031-3 TiO2-enriched phosphopeptides from thymocytes [Reanalysis: JPST000031]

Project description:Changes in phosphorylation of specific sites were examined by TiO2-based phosphopeptide enrichment from wild-type and PKD2/3-deficient thymocytes followed by LC-MS/MS analysis. [Original project description]

2023-03-11 | RPXD034762 | JPOST Repository

JPST000031-1 TiO2-enriched phosphopeptides from thymocytes [Reanalysis: JPST000031]

2023-03-11 | RPXD034760 | JPOST Repository

JPST000031-2 TiO2-enriched phosphopeptides from thymocytes [Reanalysis: JPST000031]

2023-03-11 | RPXD034761 | JPOST Repository

Expression data from hela cells stable clones overexpressing TFEB-GFP

Project description:In order to identify the effects of TFEB overexpression on the hela cells transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the hela TFEB stable clones Transcriptome analysis of hela stable clones overexpressing TFEB-GFP

2018-09-07 | GSE73055 | GEO

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