Dataset Information

Ubiquitination in the human proteome: A meta-analysis of publicly available data sets

ABSTRACT: Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme activation. Mass spectrometry-based proteomics has allowed proteome-scale quantification of hundreds of thousands of ubiquitination sites (ubi-sites). However the regulatory roles and functional importance of most ubi-sites remain undefined. Here, we assembled a human reference ubiquitinome of more than 100,000 ubi-sites by harmonizing public proteomics data.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Shengbo Wang

LAB HEAD: Juan Antonio Vizcaino

PROVIDER: PXD068989 | Pride | 2026-06-09

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	2024-04-04-decoys-contam-uniprotkb_proteome_UP000005640.fasta	Fasta
	PXD003936.mzML.zip	Mzml
	PXD003936.sdrf.tsv	Tabular
	PXD003936_Site_PSM_centric.tsv	Tabular
	PXD003936_Site_Peptidoform_centric.tsv	Tabular

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Project description:Progression through neuronal loss of substantia nigra pars compacta with Parkinson’s disease depends on various protein post-translational modifications mainly comprising phosphorylation, ubiquitination, acetylation, and methylation. Phosphorylation and ubiquitination regulate major physiological changes and cellular signaling pathways during dopaminergic neuronal death. Phosphorylation and ubiquitination dyshomeostasis of substantia nigra pars compacta tissue occurs earlier than movement symptom appearance. Although many phosphorylation and ubiquitination sites have been identified through site-specific methods, systematic quantitative proteomic analysis of pre-symptomatic Parkinson’s disease remains unexplored. Using quantitative proteomics, we have globally profiled ubiquitination and phosphorylation in substantia nigra pars compacta tissue of a Parkinson’s disease transgenic mouse model (A30P*A53T α-synuclein, hm2α-SYN-39 mouse strain) at pre-symptomatic stage; Our datasets of 5,351 phosphorylation sites in 2,136 proteins and 3,971 ubiquitination sites in 1,595 proteins provide valuable insight into pre-symptomatic Parkinson’s disease. After in-depth analysis of the relationship between phosphorylation and ubiquitination sites, we concluded that correlation of the relationship increased with decreasing distance. Subsequent bioinformatic analyses, including gene ontology annotation, domain annotation, subcellular localization, KEGG pathway annotation, functional cluster analysis, and motif analysis were performed to annotate quantifiable targets of phosphorylation and ubiquitination sites. Individual simultaneous phosphorylation and ubiquitination proteins that were differentially quantified were screened. The endocytosis pathway is likely regulated by both phosphorylation and ubiquitination at the molecular protein Epn2 (S439 and K135) in early-stage Parkinson’s disease. Therefore, this elucidation of the dysregulation of phosphorylation and ubiquitination has implications for understanding the pathophysiological mechanism of dopaminergic neuron degeneration and for developing novel therapeutics for Parkinson’s disease.

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Ubiquitination in the human proteome: A meta-analysis of publicly available data sets

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