Dataset Information

Isoform-resolved Correlation Analysis Between mRNA Abundance Dynamics and Protein Level Degradation

ABSTRACT: We employed an optimized, sensitive DIA-MS method on a high-resolution Orbitrap platform and re-measured the proteomic samples used in a previous study, in which the heterogeneity of HeLa cells across different research labs was analyzed by a multi-omic approach. Using the same MS sample sets of all HeLa strains we achieved higher sensitivity compared to our previous SWATH-MS results that were acquired on a TripleTOF instrument (5600 model). To benefit from the significantly improved sensitivity of this single-shot DIA-MS for both proteomic and protein turnover analysis, we analyzed the samples originating from six HeLa Kyoto strains and six HeLa CCL2 strains to profile both total protein-level abundances and the proxy protein turnover rates (Kloss, by pulsed SILAC labeling) across cell lines. Our results emphasized the importance of relative mRNA-protein turnover rate correlation analysis. The dataset demonstrate that specific biological processes, cellular organelles, subunits of organelles, and individual protein isoforms may have distinctive degradation rate and the corresponding buffering or concerting protein turnover control across cancer cell lines.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Cervix Carcinoma

SUBMITTER: Barbora Salovska

LAB HEAD: Yansheng Liu

PROVIDER: PXD014847 | Pride | 2020-03-11

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	1FPKM_mapping_table.txt	Txt
	Annotationandsampleinformation_Hela.xlsx	Xlsx
	FPKM1.fasta	Fasta
	HeLa_1FPKM-pSILAC_library.xls	Xls
	HeLa_1FPKM_lblfree_library.xls	Xls

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Isoform-resolved correlation analysis between mRNA abundance regulation and protein level degradation.

Salovska Barbora B Zhu Hongwen H Gandhi Tejas T Frank Max M Li Wenxue W Rosenberger George G Wu Chongde C Germain Pierre-Luc PL Zhou Hu H Hodny Zdenek Z Reiter Lukas L Liu Yansheng Y

Molecular systems biology 20200301 3

Profiling of biological relationships between different molecular layers dissects regulatory mechanisms that ultimately determine cellular function. To thoroughly assess the role of protein post-translational turnover, we devised a strategy combining pulse stable isotope-labeled amino acids in cells (pSILAC), data-independent acquisition mass spectrometry (DIA-MS), and a novel data analysis framework that resolves protein degradation rate on the level of mRNA alternative splicing isoforms and is ...[more]

PMID: 32175694

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