QE files 1601 - 1615 for data set 1
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Anthony Persechini
PROVIDER: MSV000083787 | MassIVE | Thu May 16 12:03:00 BST 2019
REPOSITORIES: MassIVE
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Project description:In vivo cross-linking and ribonucleoprotein-immunopurification experiments followed by microarray analysis of bound RNAs (X-RIP-chip). Cells expressing recombinant tandem-affinity purification (TAP)-tagged Trf4 protein were cross-linked with formaldehyde, and Trf4-containing ribonucleoprotein complexes were recovered by affinity selection on IgG-coupled beads (see linked protocol). As a control for non-specifically enriched RNAs, the same experiment was done with untagged WT cells and with cells expressing Fpr1-TAP, a peptidyl-prolyl-cis-trans-isomerase not expected to bind RNA. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Antigenic peptide used in IP: Protein A derivative Computed
2010-06-24 | E-GEOD-16105 | biostudies-arrayexpress
Project description:In vivo cross-linking and ribonucleoprotein-immunopurification experiments followed by microarray analysis of bound RNAs (X-RIP-chip). Cells expressing recombinant tandem-affinity purification (TAP)-tagged Trf4 protein were cross-linked with formaldehyde, and Trf4-containing ribonucleoprotein complexes were recovered by affinity selection on IgG-coupled beads (see linked protocol). As a control for non-specifically enriched RNAs, the same experiment was done with untagged WT cells and with cells expressing Fpr1-TAP, a peptidyl-prolyl-cis-trans-isomerase not expected to bind RNA. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Antigenic peptide used in IP: Protein A derivative
2009-07-15 | GSE16105 | GEO
Project description:Affinity purification of deubiquitinase DUB2 from Leishmania mexicana promastigotes. Myc tagged DUB2 was purified from cross linked Leishmania parasites in 3 independent replicates and compared to affinity purification of an unrelated myc tagged protein by label free quantification.
2020-04-07 | MSV000085242 | MassIVE
Project description:Protein occupancy is a means of identifying all the regions in the genome that are bound to proteins. A simple protocol is used whereby cross-linked chromatin is digested with DNase to remove all non-crosslinked, naked, DNA. To distinguish the regions that are bound by RNA polymerase from the rest, a ChAPseq (chromatin affinity precipitation) with TAP-tagged alpha subunit of RNApol, was performed.
2016-04-01 | E-MTAB-3783 | biostudies-arrayexpress
Project description:Mass spectrometry data of peptide–RNA cross-links derived from complex biological systems. Yeast (pre-)mRNPs were isolated by TAP tag purification of Cbp20; human protein–RNA complexes were assembled on an aptamer tagged pre-mRNA. Isolated complexes were UV irradiated. For each of the aforementioned experiments, a non-irradiated control was prepared. Yeast RBPs cross-linked in vivo after labeling with 4-thio-uridine (4SU) were isolated with oligo d(T). All samples were enriched for cross-linked heteroconjugates prior to LC-MS analysis.
2014-08-07 | PXD000513 | Pride
Project description:To identify transcripts enriched in ventomedial hypothalamus (VMH) neurons that contain both Lepr and Slc17a6, we used translating affinity ribosome purification combined with RNA-seq (TRAP-seq) from Lepr-Cre;Slc17a6-Flpo mice.
2021-05-19 | GSE172202 | GEO
Project description:Apolipoprotein A-I (apoA-I) is cross-linked and dysfunctional in human atheroma. Although multiple mechanisms of apoA-1 cross-linking have been demonstrated in vitro, the in vivo mechanisms of cross-linking are not well established. We have recently demonstrated the highly selective and efficient modification of high-density lipoprotein (HDL) apoproteins by endogenous oxidized phospholipids (oxPLs), including oxoalkenal phospholipids. In the current study, we report that oxoalkenal phospholipids effectively cross-link apoproteins in HDL. We further demonstrate that cross-linking impairs the cholesterol efflux mediated by apoA-I or HDL3 in vitro and in vivo. Using LC-MS/MS analysis, we analyzed the pattern of apoprotein cross-linking in isolated human HDL either by synthetic oxoalkenal phospholipids or by oxPL generated during HDL oxidation in plasma by the physiologically relevant MPO-H2O2-NO2- system. We found that five histidine residues in helices 5-8 of apoA-I are preferably cross-linked by oxPL, forming stable pyrrole adducts with lysine residues in the helices 3-4 of another apoA-I or in the central domain of apoA-II. We also identified cross-links of apoA-I and apoA-II with two minor HDL apoproteins, apoA-IV and apoE. We detected a similar pattern of apoprotein cross-linking in oxidized murine HDL. We further detected oxPL cross-link adducts of HDL apoproteins in plasma and aorta of hyperlipidemic LDLR-/- mice, including cross-link adducts of apoA-I His-165--apoA-I Lys-93, apoA-I His-154--apoA-I Lys-105, apoA-I His-154--apoA-IV Lys-149, and apoA-II Lys-30/apoE His-227. These findings suggest an important mechanism that contributes to the loss of HDL's atheroprotective function in vivo.
2019-12-13 | MSV000084689 | MassIVE
Project description:Dataset for publication submission. MS/MS and MSn analysis of in vivo cross-linked proteasomes purified from Rpn11, Rpt6, and a7-tagged 293 cell lines.
2018-10-20 | MSV000083052 | MassIVE
Project description:Chemical cross-linking coupled with mass spectrometry has emerged as a powerful strategy which enables global profiling of protein interactome with direct interaction interfaces in complex biological systems. The alkyne-tagged enrichable cross-linkers are preferred to improve the coverage of low-abundance cross-linked peptides, combined with click chemistry for biotin conjugation to allow the cross-linked peptides enrichment. Herein, together with in vivo chemical cross-linking by alkyne-tagged cross-linker, we explored the click chemistry-based enrichment approaches on protein and peptide level with three cleavable click chemistry ligands, respectively. By comparison, the approach of protein-based click chemistry conjugation with acid-cleavable tag was demonstrated to permit the most cross-linked peptides identification. The advancement of this strategy enhanced the proteome-wide cross-linking analysis, constructing a 5,518 protein-protein interactions network among 1,871 proteins with wide abundance distribution in cell. Therefore, all these results demonstrated a guideline value of our work for efficient cross-linked peptides enrichment, thus facilitated the in-depth profiling of protein interactome for functional analysis.
2022-07-15 | PXD035355 | JPOST Repository
Project description:Chemical cross-linking coupled with mass spectrometry has emerged as a powerful strategy which enables global profiling of protein interactome with direct interaction interfaces in complex biological systems. The alkyne-tagged enrichable cross-linkers are preferred to improve the coverage of low-abundance cross-linked peptides, combined with click chemistry for biotin conjugation to allow the cross-linked peptides enrichment. However, a systematic evaluation on the efficiency of click approaches (protein-based or peptide-based) and diverse cleavable click chemistry ligands (acid, reduction, photo) for cross-linked peptides enrichment and release is lacking. Herein, together with in vivo chemical cross-linking by alkyne-tagged cross-linker, we explored the click chemistry-based enrichment approaches on protein and peptide level with three cleavable click chemistry ligands, respectively. By comparison, the approach of protein-based click chemistry conjugation with acid-cleavable tag was demonstrated to permit the most cross-linked peptides identification. The advancement of this strategy enhanced the proteome-wide cross-linking analysis, constructing a 5,518 protein-protein interactions network among 1,871 proteins with wide abundance distribution in cell. Therefore, all these results demonstrated a guideline value of our work for efficient cross-linked peptides enrichment, thus facilitated the in-depth profiling of protein interactome for functional analysis.
2022-07-14 | PXD035317 | JPOST Repository