Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ubiquitinome Profiling: Optimizing the enrichment and Data-Independent Analysis for Deeper Insights into Targeted Protein Degradation

ABSTRACT: Targeted protein degradation has emerged as a highly promising therapeutic strategy for a wide range of diseases, including cancer and neurodegenerative disorders. The ubiquitin-proteasome system, which is responsible for protein degradation, plays a critical role in this process. Gaining comprehensive insights into the landscape of ubiquitination events is essential for the development of effective targeted protein degradation approaches. In recent years, data-independent analysis (DIA) has gained significant popularity as a robust and unbiased approach for quantitative proteomics. By leveraging on this method, we have developed a cutting-edge workflow that combines diGly antibody-based enrichment with an optimized Orbitrap-based data-independent acquisition method for the identification of ubiquitylated peptides.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Gajanan Sathe

LAB HEAD: Prof Gopal Sapkota

PROVIDER: PXD059978 | Pride | 2026-06-09

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	61415_GG_R1.raw	Raw
	61415_GG_R1.raw.quant	Raw
	61415_GG_R2.raw	Raw
	61415_GG_R2.raw.quant	Raw
	61415_GG_R3.raw	Raw

Items per page:

1 - 5 of 30

Similar Datasets

Ubiquitinome Profiling: Optimizing the enrichment and Data-Independent Analysis for Deeper Insights into Targeted Protein Degradation

Project description:Targeted protein degradation has emerged as a highly promising therapeutic strategy for a wide range of diseases, including cancer and neurodegenerative disorders. The ubiquitin-proteasome system, which is responsible for protein degradation, plays a critical role in this process. Gaining comprehensive insights into the landscape of ubiquitination events is essential for the development of effective targeted protein degradation approaches. In recent years, data-independent analysis (DIA) has gained significant popularity as a robust and unbiased approach for quantitative proteomics. By leveraging on this method, we have developed a cutting-edge workflow that combines diGly antibody-based enrichment with an optimized Orbitrap-based data-independent acquisition method for the identification of ubiquitylated peptides.

2026-06-09 | PXD059788 | Pride

Ubiquitinome Profiling: Optimizing the enrichment and Data-Independent Analysis for Deeper Insights into Targeted Protein Degradation

2026-06-09 | PXD057960 | Pride

Data-independent acquisition approach for comprehensive ubiquitinome profiling in targeted protein degradation

Project description:Targeted protein degradation (TPD) has emerged as a highly promising therapeutic strategy for a wide range of diseases, including cancer and neurodegenerative disorders. The ubiquitin-proteasome system, which is responsible for protein degradation, plays a critical role in this process. Gaining comprehensive insights into the landscape of cellular ubiquitylation events is essential for the development of selective and efficient targeted protein degradation approaches. In recent years, data-independent acquisition (DIA) approach has gained significant popularity as a robust and unbiased approach for quantitative proteomics. By leveraging DIA, we have developed a cutting-edge workflow that utilizes diGly antibody-based enrichment followed by an optimized Orbitrap-based DIA method for the identification of ubiquitylated peptides. Through the implementation of our workflow, we have identified over 40,000 diGly precursors corresponding to more than 7,000 proteins in a single measurement from cells exposed to a proteasome inhibitor, highlighting an exceptional throughput. By applying our optimized workflow, we successfully identify ubiquitylation sites on substrate proteins in various TPD approaches, thereby helping establish mode of action for TPD. Our workflow therefore holds tremendous potential for rapidly establishing mode of action for various TPD modalities, such as for PROTACs and molecular glues.

2026-06-09 | PXD061232 | Pride

Data-independent acquisition approach for comprehensive ubiquitinome profiling in targeted protein degradation

2026-06-09 | PXD060403 | Pride

Mechanism of degrader-targeted protein ubiquitinability

Project description:Small molecule degraders of disease-driving proteins offer a clinically proven modality with enhanced therapeutic efficacy and the potential to tackle previously undrugged targets. Thermodynamically stable and kinetically long-lived degrader-mediated ternary complexes can drive faster, more profound and durable target degradation, however the mechanistic features by which they impact on target ubiquitination remain elusive. Here, we solve cryo-EM structures of the VHL Cullin 2 RING E3 ligase complexed with degrader MZ1, target protein Brd4BD2 and primed for catalysis with its cognate E2-ubiquitin bound. We find that Brd4BD2 adopts a favourable orientation towards the E2 active site. Mass spectrometry illuminates a patch of favourably ubiquitinable lysines on one face of in vitro ubiquitinated Brd4BD2, with Lys456 showing optimal distance and geometry for nucleophilic attack highlighted by cryo-EM. In vitro ubiquitination coupled with cellular degradation and ubiquitinomics confirm the importance of Lys456 and the ‘ubiquitination zone’ lysines. Our results demonstrate the proficiency of MZ1 in directing the substrate towards catalysis, explains the favourability of Brd4BD2 for ubiquitination bu UBE2R1, and reveals the flexibility of the enzyme in capturing sub-optimal lysines. We propose a model for ubiquitinability of degrader-recruited targets that provides a mechanistic blueprint for further rational drug design and optimization.

2024-11-08 | PXD053502 | Pride

Data-independent acquisition approach for comprehensive ubiquitinome profiling in targeted protein degradation

2026-06-09 | PXD060627 | Pride

Ubiquitinome Profiling: Optimizing the enrichment and Data-Independent Analysis for Deeper Insights into Targeted Protein Degradation

2026-06-09 | PXD077594 | Pride

Data-independent acquisition method for ubiquitinome analysis reveals non-degrative regulation of circadian biology

Project description:Protein ubiquitination is involved in virtually all cellular processes. Enrichment strategies employing antibodies targeting ubiquitin-derived diGly remnants combined with mass spectrometry (MS) have enabled investigations of ubiquitin signaling at a large scale. However, so far the power of data independent (DIA) acquisition with regards to sensitivity in single run analysis and data completeness have not yet been explored. We developed a sensitive workflow combining diGly antibody-based enrichment, optimized Orbitrap-based DIA with comprehensive spectral libraries together containing more than 90,000 diGly peptides. This approach identified 35,000 diGly peptides in single measurements of proteasome inhibitor-treated cells â€“ double the number and quantitative accuracy of data dependent acquisition. Applied to TNF-alpha signaling, the workflow comprehensively captured known sites while adding many novel ones. A first systems-wide investigation of ubiquitination of the circadian cycle uncovered hundreds of cycling ubiquitination sites and dozens of cycling ubiquitin clusters within individual membrane protein receptors and transporters, highlighting novel connections between metabolism and circadian regulation.

2020-11-20 | PXD019854 | Pride

Improvement of ubiquitination site detection by Orbitrap mass spectrometry.

Project description: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 24,000 diGly modified peptides in a single sample. We show the efficacy of this strategy for cell lysates from both non-labeled and metabolically labeled (SILAC) mammalian cells. Furthermore, we demonstrate that this optimized strategy is also useful for the in-depth identification of the endogenous, unstimulated ubiquitinome of in vivo samples such as mouse brain tissue. As such, this study presents an addition to the toolbox of the ubiquitination site analysis for the identification of the deep ubiquitinome.

2017-11-14 | PXD007101 | Pride

Active protein ubiquitination regulates xylem vessel functionality

Project description:Xylem vessels function in the long-distance conduction of water in land plants. The NAC transcription factor VASCULAR-RELATED NAC-DOMAIN7 (VND7) is a master regulator of xylem vessel cell differentiation in Arabidopsis (Arabidopsis thaliana). We previously isolated seiv (suppressor of ectopic xylem vessel cell differentiation induced by VND7) mutants, which are suppressor mutants of VND7-inducible xylem vessel cell differentiation. Here, we report that the responsible genes for seiv3, seiv4, seiv6, and seiv9 are protein ubiquitination-related genes encoding PLANT U-BOX46 (PUB46), uncharacterized F-BOX protein, PUB36, and UBIQUITIN-SPECIFIC PROTEASE1, respectively. We also found the decreased expression of genes downstream of VND7 and abnormal xylem transport activity in the seiv mutants. Upon VND7 induction, ubiquitinated levels from 492 and 180 protein groups were up- and down-regulated, respectively. Proteins for cell wall biosynthesis and protein transport were ubiquitinated by the VND7 induction, whereas such active protein ubiquitination was not observed in the seiv mutants. We detected the ubiquitination of three lysine residues in VND7: K94, K105, and K260. Substituting K94 with arginine significantly decreased the transactivation activity of VND7, suggesting that the ubiquitination of K94 is crucial for regulating VND7 activity. Our findings highlight the crucial roles of target protein ubiquitination in regulating xylem vessel activity.

2024-10-17 | PXD048830 | 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