Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Photoproximity labeling of cell surface phosphoproteins

ABSTRACT: A method for photoproximity labeling targeting cell surface phosphotyrosine residues to identify cell surface phosphoproteins

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Breast Cancer

SUBMITTER: Corleone Delaveris

LAB HEAD: Jim Wells

PROVIDER: PXD071183 | Pride | 2026-03-12

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20240315_20240826_SrcHCLC_CombinedFirst5files_CirclePlot.csv	Csv
	20240315_SrcHCLC_CombinedFirst5files_noDecoys_Over50.xlsm	Xls
	20240315_TPC_CD_XLMS_1ug_2_output20240826.csv	Csv
	20240315_TPC_XLMS_DSSO_mAb_180min_60k30k_MaxIT70_IW1p6_sceHCD_1ug_2.raw	Raw
	20240315_TPC_XLMS_DSSO_mAb_180min_60k30k_MaxIT70_IW1p6_sceHCD_1ug_3.raw	Raw

Items per page:

1 - 5 of 58

Similar Datasets

Chemoproteomics reveals immunogenic and tumor-associated cell surface substrates of ectokinase CK2α

Project description:We engineered a cell-tethered version of the extracellular kinase CK2α, demonstrated it was active on cells under tumor-relevant conditions, and profiled its substrate scope using a chemoproteomic workflow.

2024-07-16 | PXD050801 | Pride

Tracking Ebolavirus genomic drift in a replicating virus with a resequencing microarray

Project description:This study demonstrates the ability of a Ebolavirus resequencing microarray to determine the sequence of the Zaire ebolavirus glycoprotein that has been engineered into the place of the surface protein of a recombinant vesicular stomatitis virus expressing green fluorescent protein (rVSV-EBOVgp-GFP). The rVSV-EBOVgp-GFP was cultured in VERO-E6 cells for three passages either in the presence of a monoclonal antibody that blocks infection (KZ52) or in control cultures with no antibody. Culture supernatant and cell lysate was collected before passaging and after each passage. RNA was extracted from each sample and the sequence of the Ebola glycoprotein in each sample was determined by the Ebola resequencing microarray.

2021-01-30 | E-MTAB-10008 | biostudies-arrayexpress

Na2CO3-responsive phosphoproteins in Puccinellia tenuiflora leaves

Project description:Reversible protein phosphorylation also play crucial roles in plant salt resistance. In our syudy, 62 Na2CO3-responsive phosphoproteins were found in leaves by isobaric tags for relative and absolute quantification (iTRAQ) labeling. These Na2CO3-responsive phosphoproteins were sorted into seven functional categories. Among them, most of photosynthetic proteins including 11 light harvesting proteins, five PS II protein, and ten Calvin cycle-related protein (i.e. RuBisCO activase, RuBisCO large subunit, glyceraldehyde-3-phosphate dehydrogenase, and Phosphoglycerate kinase), three ATP synthase subunits, and other carbohydrate and energy metabolism related proteins were identified increased in phosphorylation level. While two starch and sucrose metabolism related protein (e.g. UDP-glucose 6-dehydrogenase), one stress response protein, one membrane and transporting protein, and most of gene expression, protein synthesis and turnover related proteins were identified inhibited phosphorylation under Na2CO3 treatment. In addition, calmodulin, inactive receptor kinase, VWA copine domain containing protein, and tetraspanin family protein participate in signaling pathways were identified enhanced phosphorylation under Na2CO3.

2021-08-30 | PXD005471 | Pride

Comparative Qualitative Phosphoproteomics Analysis Identifies Shared Phosphorylation Motifs and Associated Biological Processes in Flowering Plants

Project description:In this work we carried out a comparative bioinformatics analysis of pre-existing phosphoproteomics data in the public domain: PXD000033 and PXD000421 (Arabidopsis. thaliana) and PXD002222 and PXD000923 (O. sativa; rice). The aim of the analysis was to profile two model species representing the largest subclasses in flowering plants the dicot Arabidopsis thaliana and the monocot Oryza sativa, to understand the extent to which phosphorylation signaling and function is conserved across evolutionary divergent plants. From data set re-analysis, we identified 6,537 phosphopeptides from 3,189 phosphoproteins in Arabidopsis and 2,307 phosphopeptides from 1,613 phosphoproteins in rice. The relative abundance ratio of serine, threonine, and tyrosine phosphorylation sites in rice and Arabidopsis were highly similar: 88.3: 11.4: 0.4 and 86.7: 12.8: 0.5, respectively. In addition, tyrosine phosphorylation shows features different from those of the serine and threonine phosphopeptides and was found to be more frequent in doubly-phosphorylated peptides in Arabidopsis. We identified protein sequence motifs in the two species to explore the similarities, finding nineteen pS motifs and two pT motifs that are shared in rice and Arabidopsis; among them are five novel motifs that have not previously been described in both species. The majority of shared motif-containing proteins were mapped to the same biological processes with similar patterns of fold enrichment, indicating high conservation of these pathways. We also identified shared patterns of crosstalk between phosphoserines with motifs pSXpS, pSXXpS and pSXXXpS, where X is any amino acid, in both species indicating this is an evolutionary conserved signaling mechanism in flowering plants.

2018-04-13 | PXD007979 | Pride

Quantitative iTRAQ-based proteomic analysis of phosphoproteins and ABA-regulated phosphoproteins in maize leaves under osmotic stress.

Project description:Abscisic acid (ABA) regulates various developmental processes and stress responses in plants. Protein phosphorylation/dephosphorylation is a central post-translational modification (PTM) in ABA signaling. However, the phosphoproteins regulated by ABA under osmotic stress remain unknown in maize. In this study, maize mutant vp5 (deficient in ABA biosynthesis) and wild-type Vp5 were used to identify leaf phosphoproteins regulated by ABA under osmotic stress. Up to 4052 phosphopeptides, corresponding to 3017 phosphoproteins, were identified by Multiplex run iTRAQ-based quantitative proteomic and LC-MS/MS methods. The 4052 phosphopeptides contained 5723 non-redundant phosphosites; 512 phosphopeptides (379 in Vp5, 133 in vp5) displayed at least a 1.5-fold change of phosphorylation level under osmotic stress, of which 40 shared common in both genotypes and were differentially regulated by ABA. Comparing the signaling pathways involved in vp5 response to osmotic stress and those that in Vp5, indicated that ABA played a vital role in regulating these pathways related to mRNA synthesis, protein synthesis and photosynthesis. Our results provide a comprehensive dataset of phosphopeptides and phosphorylation sites regulated by ABA in maize adaptation to osmotic stress. This will be helpful to elucidate the ABA-mediate mechanism of maize endurance to drought by triggering phosphorylation or dephosphorylation cascades.

| S-EPMC4650667 | biostudies-literature

Pitcher fluid protein profiling from Nepenthes spp.

Project description:Pitcher fluids from 3 species of Nepenthes, namely N. ampullaria, N. rafflesiana and their hybrid H. x hookeriana were collected within 24h of opening, filtered, concentrated, processed and trypsin-digested for mass spectrometry analysis using Thermo Easy-nLC Orbitrap Fusion Tribid MS. Analysis was performed in 2 biological replicates of pools of 9 pitchers for each species and analysed in 3 technical replicates each.

2018-11-29 | PXD007599 | Pride

Na2CO3-responsive phosphoproteins in chloroplasts from Puccinellia tenuiflora leaves

Project description:Alkali-salinity exerts severe osmotic, ionic, and high-pH stresses to plants. Photosynthetic machinery is especially sensitive to saline-alkali stress. In addition, reversible protein phosphorylation also play crucial roles in plant salt resistance. While our knowledge on protein phosphorylation events in salt stress response is very limited. Few studies have been published involving photosynthetic protein phosphorylation modulation to improve salt resistance. In the present study, we investigated the Na2CO3-responsive characteristics in Puccinellia tenuiflora chloroplasts using stable isotope dimethyl labeled phosphoproteomic approach. A total of 161 unique phosphopeptides were identified, and 137 phosphopeptides were quantified by dimethyl labeling. Among them, 50 proteins were quantified as Na2CO3-responsive proteins with 57 phosphosites, including 33 increased and 14 decreased. Importantly, 26 phosphosites were newly identified as Na2CO3-responsive phosphoproteins in plants, which were supposed to be crucial for regulating photosynthesis, membrane and transporting, signaling, stress response, and protein synthesis and turnover. Among them, seven light harvesting proteins, six PSII proteins, five PSI proteins, three electron transfer chain proteins, and two Calvin cycle-related proteins were increased, but five ATP synthase subunits and sucrose-phosphate synthase were decreased at phosphorylation level. Besides, Na+/H+ antiporter, villin-2, and two thylakoid organization related proteins were increased at phosphorylation level. Two signaling related proteins and most protein species in charge of gene expression and protein turnover were enhanced at phosphorylation level at 24h after Na2CO3 treatment.

2021-08-30 | PXD005472 | Pride

Identification of JARID2/PRC2 interactome in human embryonic stem cells

Project description:JARID2 is an integral subunit of the chromatin modifier PRC2 (Polycomb Repressive Complex 2). PRC2 methylates lysine 27 in histone H3 and is required for human development. Mutaitons of PRC2 subunits have been frequently found in a variety of adult and pediatric cancer, suggesting that PRC2 critically regulates normal and cancer development. The goal of this project is to identify new regulator or co-factors of PRC2 and study their molecular interactions and activities in order to better understand function and regulation of PRC2 in normal and cancer development.

2020-08-04 | PXD015670 | Pride

Transcriptome and microRNA array analyses reveal a stimulatory effect of the phytochemical shikonin on epithelial–mesenchymal transition (EMT) in mouse skin

Project description:This SuperSeries is composed of the following subset Series: GSE32694: Transcriptome and microRNA array analyses reveal a stimulatory effect of the phytochemical shikonin on epithelial–mesenchymal transition (EMT) in mouse skin [gene expression profile] GSE32695: Transcriptome and microRNA array analyses reveal a stimulatory effect of the phytochemical shikonin on epithelial–mesenchymal transition (EMT) in mouse skin [microRNA expression profile] Refer to individual Series

2011-12-31 | E-GEOD-32696 | biostudies-arrayexpress

Peptoid ligands that bind selectively to phosphoproteins.

Project description:Synthetic equivalents of phosphoprotein-specific antibodies would be valuable reagents for biological research, since these antibodies can often be difficult to produce. Protein phosphorylation is thought to result in significant conformational changes in most substrate proteins. Therefore, one approach might be to simply screen combinatorial libraries for ligands to the phosphorylated state in the hope of isolating a ligand that binds to a pocket created by the conformational shift. In this study, we probe this strategy by screening a peptoid library for ligands to the phosphorylated form of the Brd4 chromatin adaptor and transcriptional coactivator protein. We find that peptoids with high selectivity for binding to the phosphorylation form of Brd4 can indeed be isolated in this screen. Moreover, these ligands do not bind promiscuously to other phospho-proteins. However, attempts to employ these reagents as antibody substitutes in an immunoaffinity purification-like application showed that they do not perform as well as bona fide antibodies and that significant optimization will be required. This study highlights the potential and current limitations of a naïve library screening strategy for phosphoprotein-specific antibody surrogates.

| S-EPMC3591469 | biostudies-literature