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MetabolomicsMulti-omics and biophysical phosphoproteomics uncover functional phosphorylation networks of BRAFV600E-driven signaling

Dysregulated kinase activity drives oncogenic signalling, perturbs cellular homeostasis, and promotes tumour progression. Despite major success in targeting kinases therapeutically, the downstream consequences of kinase inhibition and the mechanisms underlying drug resistance remain incompletely ...

2025-12-09 | MTBLS7390 | MetaboLights
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 
2023-05-17 | PXD037870 |
ProteomicsPhosphoproteomics sample preparation impacts biological interpretation of signalling responses
Quantitative data-dependent acquisition phosphoproteomics (DDAP) has revolutionised cell signaling studies. However, the impact of the specific DDAP sample preparation method on the phosphoproteome quantified is unclear as each study quantifies only a fraction of the phosphoproteome. Here, we compar...
ORGANISM(S): Mus musculus (Mouse) 
2021-12-25 | PXD025376 | Pride
Phosphoproteomics Tio2 Mouse High-throughput phosphoproteomics Scxphos Sample preparation Highphos Comparative analysis 
ModelsEDN signalling models
Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data
2019-08-19 | MODEL1904170001 | BioModels
ProteomicsFAS Inhibited Proteomics and Phosphoproteomics Profiling of Colorectal Cancer Spheroids shows Activation of Ferroptotic Death Mechanism
Colorectal cancer (CRC) is projected to become the third most diagnosed and third most fatal cancer in the United States by 2024, with early onset CRC on the rise. Research is constantly underway to discover novel therapeutics for the treatment of various cancers to improve patient outcomes and surv...
ORGANISM(S): Homo sapiens (Human) 
2024-08-10 | PXD050987 | Pride
Phosphoproteomics Mass spectrometry Colorectal cancer Cancer Proteomics Data-independent acquisition Spheroids 
ProteomicsProteoViz: A toolset for interactive analysis of phosphoproteomics data
Quantitative proteomics generates large datasets with increasing depth and quantitative information. Even after data processing and statistical analysis, interpreting the results and relating their significance back to the system of study remains challenging. Often, this process is performed by sc...
ORGANISM(S): Homo sapiens (Human) 
2020-05-07 | PXD015606 | Pride
Phosphoproteomics Shiny Tmt 
ProteomicsPhosphoproteomics Data of pancreatic cancers cells treated with anlotinib
Aberrant regulation of angiogenesis involves in the growth and metastasis of tumors, but angiogenesis inhibitors fail to improve overall survival of pancreatic cancer patients in previous phase III clinical trials. A comprehensive knowledge of the mechanism of angiogenesis inhibitors against pancrea...
ORGANISM(S): Homo sapiens (Human) 
2021-09-09 | PXD023345 | Pride
Phosphoproteomics data Anlotinib Pancreatic cancer 
UnknownPhosX: data-driven kinase activity inference from phosphoproteomics experiments.
Not available
S-EPMC11630834 | biostudies-literature
ProteomicsPhosphoproteomics identifies determinants of PAK inhibitor sensitivity in AML cells
Background The p21 activated kinases (PAK) are frequently dysregulated in cancer and have central roles in oncogenic signalling, prompting the development of PAK inhibitors (PAKi) as anticancer agents. However, such compounds have not reached clinical use because, at least partially, there is a lim...
ORGANISM(S): Homo sapiens (Human) 
2025-05-07 | PXD056514 | Pride
Acute myeloid leukaemia Phosphoproteomics Machine learning Kinase inhibitors Pak inhibitors Target therapy Pf-3758309 Proteomics Biomarkers Cancer 
UnknownA data-independent acquisition-based global phosphoproteomics system enables deep profiling.
Not available
S-EPMC8099862 | biostudies-literature
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