Dataset Information

Targeted analysis of endogenous purification of YAP1 in HEK293A cell lines

ABSTRACT: Targeted analysis of endogenous purification of YAP1 in HEK293A cell lines

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Federico Uliana

LAB HEAD: Federico Uliana

PROVIDER: PXD032310 | Pride | 2023-03-04

REPOSITORIES: Pride

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Source:

			Action	DRS
	210423_final_phospho_method_tmp.sky	Other
	210423_final_phospho_method_tmp.sky.view	Other
	210423_final_phospho_method_tmp.skyd	Other
	210425_final_interactor_analysis_method.sky	Other
	210425_final_interactor_analysis_method.sky.view	Other

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Project description:Global high-throughput phosphoproteomic profiling is increasingly being applied to cancer specimens as a means to identify the oncogenic signaling cascades responsible for promoting disease initiation and disease progression; pathways that are often invisible to genomics analysis. Hence, phosphoproteomic profiling has enormous potential to inform and improve individualized anti-cancer treatment strategies. However, to achieve the adequate phosphoproteomic depth and coverage necessary to identify the activated, and hence, targetable kinases responsible for driving oncogenic signaling pathways; affinity phosphopeptide enrichment techniques are required and often coupled with offline high-pressure liquid chromatographic (HPLC) separation prior to nanoflow liquid chromatography–tandem mass spectrometry (nLC-MS/MS). These complex and time-consuming procedures, limit the utility of phosphoproteomics for the analysis of individual cancer patient specimens in real-time, and restrict phosphoproteomics to specialized laboratories often outside of the clinical setting. To address these limitations, here we have optimized a new protocol, phospho-Heavy-labeled-spiketide FAIMS Stepped-CV DDA (pHASED), that employs online phosphoproteome deconvolution using high-field asymmetric waveform ion mobility spectrometry (FAIMS) and internal phosphopeptide standards to provide accurate label-free quantitation (LFQ) data in real-time. Compared with traditional LFQ using shotgun phosphoproteomics workflows, pHASED provided increased phosphoproteomic depth and coverage (phosphopeptides = 4,617 pHASED, 2,789 LFQ), whilst eliminating the variability associated with offline prefractionation. pHASED was optimized using tyrosine kinase inhibitor (sorafenib) resistant isogenic FLT3-mutant acute myeloid leukemia (AML) cell line models. Bioinformatic analysis identified differential activation of the Serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) pathway, responsible for sensing and repairing DNA damage in sorafenib-resistant AML cell line models, thereby uncovering a potential therapeutic opportunity. Herein, we have optimized a rapid, reproducible, and flexible protocol for the characterization of complex cancer phosphoproteomes in real-time; a step towards the implementation of phosphoproteomics in the clinic to aid in the selection of anti-cancer therapies for patients.

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Targeted analysis of endogenous purification of YAP1 in HEK293A cell lines

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