Dataset Information

Feasibility of phosphoproteomics on left-over sample after RNA extraction (RNA-Bee)

ABSTRACT: In daily practice biomolecules are usually extracted with their own specific protocols for downstream omics analysis. However, when sample material is limited, an all-in-one strategy is preferable. DNA, RNA and proteins can be isolated with phenol guanidine thiocyanate based extraction, yet lysis with Urea is the accepted standard for phosphoproteomic applications. Here we compared Urea with RNA-Bee mediated protein extraction for use in mass spectrometry (MS) based phosphoproteomics analysis of cells and tissues. We profile the DNA damage response after ionizing irradiation of U2OS cells as proof of principle for cultured human cells as well as mouse liver and three different human tissues. We show high overlap and similarity of phosphosite data and kinase activity for RNA-bee extraction when compared to standard Urea approach. Phenol guanidine thiocyanate lysis might thus be an appropriate way for multi-omics or MS profiling workflows in order to obtain several data types from a single sample.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Liver, Epithelial Cell, Skin, Bone Cancer Cell Line

DISEASE(S): Osteosarcoma,Melanoma,Hepatocellular Carcinoma

SUBMITTER: Sander Piersma

LAB HEAD: Connie Ramona Jimenez

PROVIDER: PXD023665 | Pride | 2021-04-22

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	MQ_txt_folder_HCC.zip	Other
	MQ_txt_folder_HCC_RNAB.zip	Other
	MQ_txt_folder_HCC_Urea.zip	Other
	MQ_txt_folder_Melanoma.zip	Other
	MQ_txt_folder_Melanoma_RNAB.zip	Other

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Publications

Feasibility of Phosphoproteomics on Leftover Samples After RNA Extraction With Guanidinium Thiocyanate.

Rolfs Frank F Piersma Sander R SR Dias Mariana Paes MP Jonkers Jos J Jimenez Connie R CR

Molecular & cellular proteomics : MCP 20210402

In daily practice, different types of biomolecules are usually extracted for large-scale "omics" analysis with tailored protocols. However, when sample material is limited, an all-in-one strategy is preferable. Although lysis of cells and tissues with urea is widely used for phosphoproteomic applications, DNA, RNA, and proteins can be simultaneously extracted from small samples using acid guanidinium thiocyanate-phenol-chloroform (AGPC). Use of AGPC for mass spectrometry-based phosphoproteomics ...[more]

PMID: 33819647

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