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ProteomicsdCas9 targeted chromatin and histone enrichment for mass spectrometry (Catchet-MS) identifies IKZF1 as a novel target for HIV-1 latency reversal
HIV-1 infected patients virally suppressed by antiviral treatment harbor a persistent reservoir of replication competent latent HIV-1 infected cells, which constitute the main roadblock to a cure. A main strategy for HIV cure aims to stimulate viral gene expression in latently infected cells so that...
ORGANISM(S): Homo sapiens (Human) 
2022-05-31 | PXD032975 | Pride
Catchet-ms Ikzf1 Hiv-1 latency reversal 
ProteomicsImprovement of ubiquitination site detection by Orbitrap mass spectrometry.
We describe a modified workflow to enrich for and detect diGly peptides originating from ubiquitinated proteins using immunopurification. Using a combination of several relatively simple modifications in the sample preparation and mass spectrometric detection protocols, we now routinely detect over ...
ORGANISM(S): Homo sapiens (Human) 
2017-11-14 | PXD007101 | Pride
Ubiquitinome Silac Hela Ubiquitination U2os Ubiquitin Orbitrap lumos Digly peptides Mouse brain tissue 
ProteomicsA ubiquitinome analysis to study the functional roles of the proteasome associated deubiquitinating enzymes USP14 and UCH37
The removal of (poly)ubiquitin (Ub) chains at the proteasome is a key step in the protein degradation pathway that determines which proteins are degraded and ultimately decides cell fate. Specific polyubiquitin linkages may lead to distinct cellular effects, with several linkage types associated wit...
ORGANISM(S): Homo sapiens (Human) 
2022-06-30 | PXD030714 | Pride
Ubiquitinome Ubiquitinomics Silac Quantitative mass spectrometry Usp14 Parallel reaction monitoring Proteasome Deubiquitinase (dub) Ubiquitin Uch37/uchl5 
ProteomicsREX1 is the critical target of RNF12 in imprinted X chromosome inactivation in mice.
In mice, imprinted X-chromosome inactivation (iXCI) of the paternal X in the pre-implantation embryo and extra-embryonic tissues is followed by X-reactivation in the epiblast precursors of the inner cell mass (ICM) of the blastocyst, to facilitate initiation of random XCI (rXCI) in all embryonic tis...
ORGANISM(S): Mus musculus (Mouse) 
2018-11-15 | PXD010944 | Pride
Xci Proteomics Silac Rnf12 Mouse Rex1 
ProteomicsCaldendrin regulates spine apparatus localization through myosin V-dependent ER-stabilization in dendritic spines
Excitatory synapses of principal hippocampal neurons are frequently located on dendritic spines. The dynamic strengthening or weakening of individual inputs results in a great structural and molecular diversity of dendritic spines. Active spines with large Ca2+-transients are frequently invaded by a...
ORGANISM(S): Mus musculus (Mouse) Rattus norvegicus (Rat) 
2022-01-27 | PXD029427 | Pride
Spine apparatus Myosin V-dependent er-stabilization Caldendrin Dendritic spines 
ProteomicsUbiquitinome UPS - Quantitative proteomics reveals extensive changes in the ubiquitinome after perturbation of the proteasome by targeted dsRNA mediated subunit knockdown in Drosophila
In eukaryotic cells, short-lived, regulatory and misfolded or denatured proteins are degraded by the ubiquitin–proteasome system (UPS), a highly regulated mechanism including the active marking of proteins for proteasomal degradation by ubiquitin. The UPS is critical in regulating proteostasis and d...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2017-07-03 | PXD002552 | Pride
Ubiquitinome Digly Silac Proteasome Lc-ms/ms 
ProteomicsTranscription-coupled DNA-Protein Crosslink repair by CSB and CRL4(CSA)-mediated degradation
DNA-protein crosslinks (DPCs), arise from enzymatic intermediates, endogenous metabolism or exogenous chemicals like chemotherapeutics. DPCs are highly cytotoxic as they will impede DNA transacting processes such as replication, which is counteracted by proteolysis-mediated DPC removal by the protea...
ORGANISM(S): Homo sapiens (Human) Caenorhabditis elegans 
2024-02-09 | PXD041679 | Pride
Tc-ner Silac Csb Csa 
ProteomicsTumor decellularization reveals proteomic and mechanical characteristics of the extracellular matrix of primary liver cancer
Tumor initiation and progression are critically dependent on interaction of cancer cells with their cellular and extracellular microenvironment. Alterations in the composition, integrity, and mechanical properties of the extracellular matrix (ECM) dictate tumor processes including proliferation, mig...
ORGANISM(S): Homo sapiens (Human) 
2023-03-28 | PXD035261 | Pride
Decellularization  extracellular matrix  primary liver cancer  hepatocellular carcinoma  cholangiocarcinoma 
ProteomicsProteome-wide ubiquitinome profiling reveals substrate-specific dynamics within the USP7 network
USP7 is a deubiquitylating enzyme, a hub of a multi-nodal network, that is involved in tumor suppression, neuro)development, chromatin regulation and the DNA damage response. How USP7 regulates these diverse pathways is still unclear. Here, we used data-independent acquisition and label free quantit...
ORGANISM(S): Homo sapiens (Human) 
2026-09-07 | PXD071773 | Pride
Neurodevelopment Hao-fountain syndrome Ubiquitin Polycomb Usp7 
ProteomicsModelling organ-specific metastatic colonization of cholangiocarcinoma organoids in decellularized lung and lymph nodes
Cholangiocarcinoma (CCA) is a type of liver cancer with an aggressive phenotype and dismal outcome in patients. Current treatment options are limited, with surgical resection or transplantation the only possibility with curative intent. This becomes unavailable if CCA metastasizes to distant organs,...
ORGANISM(S): Homo sapiens (Human) 
2023-01-11 | PXD038191 | Pride
Metastatic colonization  decellularization  cholangiocarcinoma  tumor organoids 
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