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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 
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 
ProteomicsBenchmarking LFQ, SILAC and MS2/MS3-based TMT quantification strategies for large-scale phosphoproteomics
Comprehensive mass spectrometry (MS)-based proteomics is now feasible, but reproducible and multiplexed quantification remains challenging especially for analysis of post-translational modifications (PTMs), such as phosphorylation. Here we compared the most popular quantification techniques for phos...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2018-03-13 | PXD007145 | Pride
Phosphoproteomics Ms3 Ms2 Tmt Silac Lfq Technical Benchmark Quantification 
ProteomicsA systematic comparison of label-free, SILAC and TMT techniques to study early adaption towards inhibition of EGFR signaling in the colorectal cancer cell line Difi
The epithelial growth factor receptor (EGFR) signalling network plays an essential role inproliferation and survival of colorectal cancer cells. For this reason, EGFR is targeted using therapeutic antibodies blocking EGFR signalling (e.g. cetuximab). However, anti-EGFR therapy is rarely curative as ...
ORGANISM(S): Homo sapiens (Human) 
2019-12-11 | PXD014565 | Pride
Phosphoproteomics Tmt Anti-egfr therapy Colorectal cancer Silac Mapk Label-free Erbb3 Adaptive mechanism Cetuximab 
UnknownDetermining DNA-Protein Binding Affinities and Specificities from Crude Lysates Using a Combined SILAC/TMT Labeling Strategy.
Not available
S-EPMC10407929 | biostudies-literature
ProteomicsDetermining DNA-protein binding affinities and specificities from crude lysates using a combined SILAC/TMT labeling strategy
Gene expression is driven by the binding of transcription factors to regulatory elements in the genome, such as enhancers and promoters. A powerful technique to study DNA-protein interactions is affinity purification followed by mass spectrometry. Classic affinity purifications coupled to quantitati...
ORGANISM(S): Homo sapiens (Human) 
2023-10-08 | PXD041674 | Pride
Tmt Silac Dna pulldowns Paqman 
ProteomicsTranslatome Hypoxia-Acidosis, TMT-pulse SILAC
Cells were grown in light (R0K0) SILAC media (AthenaES) for 7 days, they were then incubated in light media for 24 hours in respective condition (normoxia neutral (NN) pH: 7.4; hypoxia neutral (HN)1% O2, pH: 7.4; hypoxia acidosis (HA), 1% O2, pH=6) and pulsed with heavy (R10K8) SILAC media (AthenaES...
ORGANISM(S): Homo sapiens (Human) 
2020-09-28 | PXD015643 | Pride
U87-mg Tmt-pulse silac 
UnknownTime-resolved Analysis of Proteome Dynamics by Tandem Mass Tags and Stable Isotope Labeling in Cell Culture (TMT-SILAC) Hyperplexing.
Not available
S-EPMC5141271 | biostudies-literature
ProteomicsUsing instrument logic to improve identifications in low stoichiometry SILAC/TMT experiments
Pulsed SILAC approaches allow measurement of protein dynamics, including protein translation and degradation. However, its use in quantifying acute changes has been limited due the low labeled peptide stoichiometry. Here, we describe the use of instrument logic to select peaks of interest via target...
ORGANISM(S): Homo sapiens (Human) 
2020-05-29 | PXD018445 | Pride
Silac Protein dynamics Tmt 
ProteomicsEvaluation of deep and dynamic proteomic screening strategies at sub-50Hz scan rate and without automation
In this study, we systematically evaluate sample preparation strategies, data acquisition modes and data-analysis approaches for both labeled and label-free proteomics, with the explicit goal of maximizing throughput and quantitative depth using Orbitrap-based instruments operating below 50Hz scan r...
ORGANISM(S): Homo sapiens (Human) 
2026-03-27 | PXD073468 | Pride
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