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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: Dr Prof Gopal Sapkota

PROVIDER: PXD059788 | Pride | 2026-06-09

REPOSITORIES: pride

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			Action	DRS
	HEK293_MG132_6H_urea_DDA_2.raw	Raw
	HEK293_MG132_6H_urea_DDA_2.raw.quant	Raw
	HEK293_MG132_6H_urea_DIA_1.raw	Raw
	HEK293_MG132_6H_urea_DIA_1.raw.quant	Raw
	MG132_6H_ureaDIA_3.raw	Raw

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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.

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