Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

OTUD5 complex mass spectrometry

ABSTRACT: DUBs are involved in various pathways and signalling networks by pairing with E3 ubiquitin ligases in protein complexes. In order to test whether OTUD5 associates with an E3 ubiquitin ligase to regulate cell proliferation, the stable Flag-OTUD5/Hep3B cell line was established by transfecting Hep3B cells with plasmids expressing pCIN4-Flag-OTUD5. The cellular factors interacting with OTUD5 were purified by anti-Flag antibody-conjugated M2 beads.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Liver

SUBMITTER: Fangzhou Li

LAB HEAD: Fangzhou Li

PROVIDER: PXD019907 | Pride | 2020-09-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	053165_HF4_Service_BeiDa_Human_profiling_80per_75min_20190802_F1_R1.msf	Msf
	053165_HF4_Service_BeiDa_Human_profiling_80per_75min_20190802_F1_R1.raw	Raw

Items per page:

1 - 2 of 2

Publications

OTUD5 cooperates with TRIM25 in transcriptional regulation and tumor progression via deubiquitination activity.

Li Fangzhou F Sun Qianqian Q Liu Kun K Zhang Ling L Lin Ning N You Kaiqiang K Liu Mingwei M Kon Ning N Tian Feng F Mao Zebin Z Li Tingting T Tong Tanjun T Qin Jun J Gu Wei W Li Dawei D Zhao Wenhui W

Nature communications 20200821 1

Oncogenic processes exert their greatest effect by targeting regulators of cell proliferation. Studying the mechanism underlying growth augmentation is expected to improve clinical therapies. The ovarian tumor (OTU) subfamily deubiquitinases have been implicated in the regulation of critical cell-signaling cascades, but most OTUs functions remain to be investigated. Through an unbiased RNAi screen, knockdown of OTUD5 is shown to significantly accelerate cell growth. Further investigation reveals ...[more]

PMID: 32826889

Similar Datasets

Proteomic analysis of FBXL6 interacting proteome

Project description:FBXL6 is a E3 ubiquitin ligase that we suspected to be involved in mitochondrial functions. We have investigated the specific interactome of this E3 by transfecting HEK cells with Flagged-FBXL6, or with b-gal (control). After flag immunoprecipiation, specific interacting proteome was identified by mass spectrometry and discriminate from control IP.

2023-09-25 | PXD037248 | Pride

Comprehensive landscape of active deubiquitinating enzymes profiled by advanced chemoproteomics

Project description:Enzymes that bind and process ubiquitin, a small 76 amino acid protein, have been recognized as pharmacological targets in oncology, immunological disorders and neurodegeneration. Mass spectrometry technology has now reached the capacity to cover the proteome with enough depth to interrogate entire biochemical pathways including those that contain DUBs and E3 ligase substrates. We have recently characterized the breast cancer cell (MCF7) deep proteome by detecting and quantifying ~10,000 proteins, and within this data set, we can detect endogenous expression of 65 deubiquitylating enzymes (DUBs), whereas matching transcriptomics detected 78 DUB mRNAs. Since enzyme activity provides another meaningful layer of information in addition of the expression levels, we have combined advanced mass spectrometry technology, pre-fractionation and more potent/selective ubiquitin active-site probes with propargyl based electrophiles to profile 74 DUBs including distinguishable isoforms for five DUBs in MCF7 crude extract material. Competition experiments with cysteine alkylating agents, pan-DUB inhibitors ubiquitin combined with probe labelling revealed the proportion of active cellular DUBs directly engaged with probes by label-free quantitative (LFQ) mass spectrometry, demonstrating that USP13, 39 and USP40 are non-reactive to probe, reflecting no, low or restricted enzymatic activity under these cellular conditions. Our extended chemoproteomics workflow increases depth of covering the active DUBome, including isoform-specific resolution, and provides the framework for more comprehensive cell-based small molecule DUB selectivity profiling.

2019-08-31 | GSE134954 | GEO

Proteomics analysis of JOSD2-overexpression in NIH/3T3 cells

Project description:DUBs exert their biological functions through specific substrates. Theoretically, as a substrate protein of JOSD2, its ubiquitination will be cut by JOSD2. In this regard, an analysis of ubiquitinome assay was performed to identify the potential substrates of JOSD2 in NIH/3T3 cells transfected with Flag-vector or Flag-JOSD2 plasmids.

2023-06-30 | PXD043382 | Pride

Identification of proteins that interacted with ESCO2

Project description:The Flag–ESCO2 plasmids were transfected into HEK293T cells, Flag–ESCO2 complexes were co-immunoprecipitated using an anti-Flag antibody. The Flag–ESCO2 complexes was separated using SDS PAGE, and then was identified by combining silver staining and mass spectrometry.

2021-09-10 | PXD023527 | Pride

Mass spectrometry proteomics detecting interaction proteins of Kindlin-2

Project description:We aim to find out the Kindlin-2 interaction proteins. We transfected plasmids Flag or Flag-Kindlin-2 to HKC cell lines and then used Flag-M2 beads to do the coimmunoprecipitation experiments and followed by NuPAGE Tris-Acetate Mini Gels detection and stained by Coomassie brilliant blue. Compared the two groups,and then we will find the proteins interact with Kindlin-2.

2019-12-16 | PXD016008 | Pride

Proteomics-based identification of DUBsubstrates using selective inhibitors

Project description:Deubiquitinating enzymes (DUBs) catalyze the removal of ubiquitin, thereby reversing the activity of E3 ubiquitin ligases and are central to the control of protein abundance and function. Despite the growing interest in DUBs as therapeutic targets, cellular functions for DUBs remain largely unknown and technical challenges often preclude the identification of DUB substrates in a comprehensive manner. Here we demonstrate that recently developed potent DUB inhibitors coupled to mass spectrometry-based proteomics can identify DUB substrates at a proteome-wide scale. We applied this methodology to USP7, a DUB widely investigated as a therapeutic target and identified novel substrates. We demonstrate that USP7 substrates are enriched for DNA repair enzymes and E3 ubiquitin ligases. This work provides not only a comprehensive annotation of USP7 substrates, but a general methodology widely applicable to other DUBs, which is critical for translational development of DUB targeted agents.

2021-01-18 | PXD020882 | Pride

Proteomics-based identification of DUBsubstrates using selective inhibitors

2021-04-06 | PXD020881 | Pride

Proteomics-based identification of DUBsubstrates using selective inhibitors

2021-01-18 | PXD020873 | Pride

Proteomics-based identification of DUBsubstrates using selective inhibitors

2021-01-18 | PXD020865 | Pride

Par3A and Par3B interactome IMCDs

Project description:We assessed the functional role of the cell polarity proteins Par3A and B in inner medullary collecting duct cells (IMCD). Here, we did an interactome analysis from IMCDs after transiently transfecting Par3A or Par3B with a flag tag.

2022-07-07 | PXD018637 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data