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ProteomicsEvaluation of library-free strategies for phosphoproteomics and ubiquitinomics data-independent acquisition data
Phosphoproteomics and ubiquitinomics data-independent acquisition MS data is generally analyzed using a DDA spectral library. Performance of different library-free strategies of analyzing phosphoproteomics and ubiquitinomics DIA MS data are not evaluated. In this study, we assess three library-free ...
ORGANISM(S): Homo Sapiens 
PXD037870 |
ProteomicsSite-specific K63 ubiquitinomics reveals stabilization of ribosomes in response to oxidative stress
Reprograming of protein synthesis is an essential cellular process to tolerate and resist to stressing conditions. A variety of mechanisms are known to regulate translation at initiation but cells can also control proteins synthesis after the initiation checkpoint. We previously showed that K63 ubiq...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2018-12-06 | PXD004650 | Pride
Ubiquitinomics Yeast Oxidative stress K63 ubiquitin Translation regulation 
ProteomicsUltra-deep and time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale
By simultaneously capturing thousands of ubiquitination sites, mass spectrometry (MS)-based ubiquitinomics provides system-level understanding of ubiquitin signaling. Here we present a scalable workflow for deep and precise in vivo ubiquitinome profiling, coupling an improved sample preparation prot...
ORGANISM(S): Homo sapiens (Human) 
2021-08-06 | PXD023889 | Pride
Ubiquitinomics Data independent acquisition Proteomics Mass spectrometry Usp7 
ProteomicsIntegrative analysis reveals a conserved role for the amyloid precursor protein in proteostasis during aging
Aβ peptides derived from the amyloid precursor protein (APP) have been strongly implicated in the pathogenesis of Alzheimer’s disease. However, the normal function of APP and the importance of that role in neurodegenerative disease is less clear. We recovered the Drosophila ortholog of APP, Appl, in...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2023-10-04 | PXD041862 | Pride
Proteomics Ubiquitinomics Amyloid precursor protein like Appl Drosophila melanogaster 
ProteomicsProteomic and ubiquitinomics of HUH7 cells after treatment of A1
Protein ubiquitination is a crucial post-translational modification that regulates diversecellular processes, including protein degradation and signal transduction. This study employs proteomic and ubiquitinomic analyses to systematically profile the alterations in protein expression and ubiquitinat...
ORGANISM(S): Homo sapiens (Human) 
2025-11-24 | PXD069676 | Pride
A1 Ubiquitinomics Proteomic Huh7 
UnknownUbiquitination-mediated molecular pathway alterations in human lung squamous cell carcinomas identified by quantitative ubiquitinomics.
Not available
S-EPMC9520991 | biostudies-literature
UnknownQuantitative Ubiquitinomics Revealed Abnormal Ubiquitinated ATP7A Involved in Down-Regulation of ACTH in Silent Corticotroph Adenomas.
Not available
S-EPMC9130458 | biostudies-literature
UnknownUbiquitinomics revealed disease- and stage-specific patterns relevant for the 3PM approach in human sigmoid colon cancers.
Not available
S-EPMC10439878 | biostudies-literature
UnknownSite-Specific K63 Ubiquitinomics Provides Insights into Translation Regulation under Stress.
Not available
S-EPMC6465141 | biostudies-literature
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 
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