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ProteomicsQuantification of mitochondrial translation by pulse SILAC
We developed a simple method that combined biochemical mitochondria isolation and pulse SILAC approach to monitor the mitochondrial translation. Our approach allows us to quantify 12 out of the 13 mitochondrial translation products, the highest coverage among analogous methods reported, and provide ...
ORGANISM(S): Homo Sapiens (human) 
2022-12-28 | PXD022476 | JPOST Repository
ProteomicsProtein synthesis rate is the predominant regulator of protein expression during differentiation
The protein expression changes was measured at five time points (Exp1: 0, 12, 24 h; Exp2: 6, 12, 48 h) in differentiating THP-1 cell (human) cells and at three time points(0, 12, 24 h) in differentiating C2C12 cells(mouse), using two triple, or one triple Stable isotope labeling by amino acids in ce...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2013-09-10 | PXD000328 | Pride
Differentiation Proteins synthesis Proteomics Silac Protein degradation 
ProteomicsModeling SILAC Data to Assess Protein Turnover in a Cellular Model of Diabetic Nephropathy
Protein turnover rate is finely regulated through intracellular mechanisms and signals that are still incompletely understood but that are essential for the correct function of cellular processes. Indeed, a dysfunctional proteostasis often impacts on the ability of the cell to remove unfolded, misfo...
ORGANISM(S): Homo sapiens (Human) 
2023-02-13 | PXD038541 | Pride
Lc-ms/ms  protein turnover rate  protein half-life  silac  diabetes  nephropathy  fibroblasts 
ProteomicsTime-resolved analysis of proteome dynamics by TMT-SILAC hyperplexing
In this project, a more efficient methodology for obtaining multi-timepoint kinetic data for proteome-wide analyses of protein turnover is developed and used to globally measure the kinetics of protein turnover in primary human fibroblasts (HCA2-hTert). This approach takes advantage of the multiplex...
ORGANISM(S): Homo sapiens (Human) 
2016-12-14 | PXD004725 | Pride
Tmt-silac Protein degrdation Tmt Proteome dynamics Silac Human primary fibroblasts Protein synthesis Hyperplexing 
ProteomicsPulsed-SILAC analysis of protein translation rate changes upon protrusion formation
To assess the impact of protrusion formation on protein synthesis rates on a global scale, we carried out a pulsed-SILAC (pSILAC) analysis in MDA-MB231 cells grown with or without protrusions for 1, 2, 4, and 8 hrs. Briefly, light SILAC labelled cells were seeded on top of 2x 3 micron transwell filt...
ORGANISM(S): Homo sapiens (Human) 
2020-10-20 | PXD021203 | Pride
Pulsed-silac  psilac Mda-mb231  protrusions translation  orbitrap 
ProteomicsProtein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates
Although protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of ribosome flux along open reading frames (ORFs) are not fully understood. Combining measurements of protein synthesis rate with ribosome footprinting data, we he...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2019-09-10 | PXD014357 | Pride
Protein charge Yeast Translation Tasep Ribosomal proteins 
ProteomicsProtein and peptide turnover measurements using pulsed SILAC-TMT approach
We evaluated the feasibility of a workflow combining dynamic SILAC experiments with tandem mass tag (TMT)-labeling of ten pulse time-points. Replicate analysis established that the same reproducibility of turnover rates can be obtained for peptides as for proteins facilitating proteoform resolved in...
ORGANISM(S): Homo sapiens (Human) 
2018-02-09 | PXD008579 | Pride
Degradation rates Protein turnover Proteoforms Posttranslational cleavage Synthesis rates Tmt Splice variants Pulsed silac Posttranslational modification 
ProteomicsSpecific growth rate-dependent proteome resource allocation dynamics in Escherichia coli
Cells usually respond to changing growth conditions with a change in the specific growth rate (μ) and adjustment of their proteome to adapt and maintain metabolic efficiency. Description of the principles behind proteome resource allocation is thus important for understanding metabolic regulation in...
ORGANISM(S): Escherichia coli 
2015-02-27 | PXD001594 | Pride
E. coli label-free specific growth rate dependent data 
ProteomicsEvaluation of the African swine fever virus-induced host shutoff using dynamic stable isotope labeling with amino acids in cell culture (SILAC)
African swine fever is a viral disease of swine caused by the African swine fever virus (ASFV). Currently, ASFV is a serious threat to the global pig industry. A viral strategy to undermine host cell response is to establish a global shutoff of host protein synthesis (virus-induced shutoff, vhs). He...
ORGANISM(S): Sus scrofa domesticus (domestic pig) 
2023-05-31 | PXD039806 | Pride
Silac African swine fever virus Virus host shutoff Vhs 
ProteomicsGlobal, site-resolved analysis of ubiquitylation occupancy and turnover rate reveals systems properties
Ubiquitylation regulates most proteins and biological processes in a eukaryotic cell. However, the site-specific occupancy (stoichiometry) and turnover rate of ubiquitylation have not been quantified. Here we present an integrated picture of the global ubiquitylation site occupancy and half-life. Ub...
ORGANISM(S): Homo sapiens (Human) 
2024-04-15 | PXD037009 | Pride
Human Ubiquitylation Dynamics Ptms Stoichiometry Half-life 
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