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MetabolomicsMitochondrial NAD+ Deficiency in Vascular Smooth Muscle Impairs Collagen III Turnover to Trigger Aortic Disease

Aortic disease poses a significant mortality risk in adults, yet many of its underlying factors remain undiscovered. In this study, we identify mitochondrial NAD⁺ deficiency as a causal factor. Metabolomics analysis of 73 surgical aortic specimens revealed impaired NAD⁺ salvage and mitochondrial ...

2024-12-04 | MTBLS8062 | MetaboLights
ProteomicsLinking post-translational modifications and protein turnover by site-resolved protein turnover (SPOT) profiling
Proteome-wide measurements of protein turnover have largely ignored the impact of post-translational modifications (PTMs). To address this gap, we employ stable isotope labelling and mass spectrometry to measure the turnover of >120,000 peptidoforms including >33,000 phosphorylated, acetylated and u...
ORGANISM(S): Homo sapiens (Human) 
2021-11-10 | PXD023218 | Pride
Human Ptms Turnover Silac 
ModelsXu2003 - Phosphoinositide turnover
Xu2003 - Phosphoinositide turnover The model reproduces the percentage change of PIP_PM, PIP2_PM and IP3_Cyt as depicted in Figure 1 of the paper. The model also contains the equations for the analysis of PH-GFP experiments, however the initial value of PH_GFP has been set to zer...
2024-09-02 | BIOMD0000000075 | BioModels
TranscriptomicsCATCH-IT method for measuring nucleosome turnover
Direct measurement of nucleosome turnover dynamics by using co-translational incorporation of the methionine (Met) surrogate azidohomoalaine (Aha) into proteins and subsequent ligation of biotin to Aha-containing proteins through the [3+2] cycloaddition reaction between the azide group of Aha and an...
ORGANISM(S): Drosophila melanogaster 
2010-05-27 | E-GEOD-19788 | biostudies-arrayexpress
GenomicsGenome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3
We developed a system to study the DNA replication-independent turnover nucleosomes containing the histone variant H3.3 in mammalian cells. By measuring the genome-wide incorporation of H3.3 at different time points following epitope-tagged H3.3 expression, we find three categories of H3.3-nucleosom...
ORGANISM(S): Mus musculus 
2013-10-23 | E-GEOD-51505 | biostudies-arrayexpress
ProteomicsProtein turnover analysis in Salmonella Typhimurium during infection by dynamic SILAC, Topograph and quantitative proteomics
Protein turnover affects protein abundance and phenotypes. Comprehensive investigation of protein turnover dynamics has the potential to provide substantial information about gene expression. Here we report a large-scale protein turnover study in Salmonella Typhimurium during infection by quantitati...
ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium 
2022-05-17 | PXD033623 | Pride
Proteomics Salmonella typhimurium Dynamic silac Protein turnover 
ProteomicsRibosomal protein turnover under normal condition
The cytosolic ribosome is composed of a large number of distinct protein types and its overall function is responsible for the synthesis of most proteins in plants. Defining the role of each of its protein subunits is a major challenge which is hampered by a lack of consistency in current attributi...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2020-08-17 | PXD012839 | Pride
Arabidopsis cell culture 15n isotopic labelling Protein turnover 80s cytosolic ibosome isolation 
ProteomicsAn Atlas of Proteome and Phosphoproteome Turnover Across Mouse Tissues and Brain Regions
Understanding how different mammalian tissues are regulated is central to biology. Since the same proteins often appear in multiple tissues, protein abundance, turnover, and post-translational modifications, like phosphorylation, are key factors that determine tissue-specific proteome properties. Ho...
ORGANISM(S): Mus musculus (Mouse) 
2025-03-11 | PXD055942 | Pride
Brain region Tmtpro Psilac Dia Phosphoproteome Mouse tissue Protein turnover Proteome 
ProteomicsUbiquitin S65 proteomics: Protein turnover analysis
Ubiquitylation is an essential post-translational modification that regulates numerous cellular processes, most notably protein degradation. Ubiquitin itself can be post-translationally modified by phosphorylation, with nearly every serine, threonine, and tyrosine residue having the potential to be...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2015-07-07 | PXD002205 | Pride
Yeast Orbitrap Phosphorylation Ubiquitin 
ProteomicsProtein turnover rate along the gastrointestinal tract is coordinated by the spatial location and the microbiota
The gastrointestinal tract is covered by a single layer of epithelial cells that, together with the mucus layers, protect the underlying tissue from bacterial invasion. The epithelium has one of the highest turnover rates in the body, renewing every 4-5 days. Using stable isotope labelling, high-res...
ORGANISM(S): Mus musculus (Mouse) 
2020-01-24 | PXD011457 | Pride
Germ-free Colon Mass spectrometry Protein turnover Commensals Lipid metabolism Proteomics Colonization Small intestine Bacteria 
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