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Comparative analysis of mRNA degradation and protein degradation in prostate tissues indicates high stability of proteins

ABSTRACT: To benchmark the PIN algorithm that quantifies the extent of protein degradation in samples, we generated a set of “ground truth” samples, in which the levels of proteome degradation were known and independently validated by western blotting. Protein extracts of HeLa Kyoto cells were treated with the low specificity protease Proteinase K at different protease concentrations.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Hela Cell

DISEASE(S): Cervical Cancer

SUBMITTER: Wenguang Shao

LAB HEAD: Ruedi Aebersold

PROVIDER: PXD013622 | Pride | 2019-06-12

REPOSITORIES: Pride

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Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins.

Shao Wenguang W Guo Tiannan T Toussaint Nora C NC Xue Peng P Wagner Ulrich U Li Li L Charmpi Konstantina K Zhu Yi Y Wu Jianmin J Buljan Marija M Sun Rui R Rutishauser Dorothea D Hermanns Thomas T Fankhauser Christian Daniel CD Poyet Cedric C Ljubicic Jelena J Rupp Niels N Rüschoff Jan H JH Zhong Qing Q Beyer Andreas A Ji Jiafu J Collins Ben C BC Liu Yansheng Y Rätsch Gunnar G Wild Peter J PJ Aebersold Ruedi R

Nature communications 20190607 1

Deterioration of biomolecules in clinical tissues is an inevitable pre-analytical process, which affects molecular measurements and thus potentially confounds conclusions from cohort analyses. Here, we investigate the degradation of mRNA and protein in 68 pairs of adjacent prostate tissue samples using RNA-Seq and SWATH mass spectrometry, respectively. To objectively quantify the extent of protein degradation, we develop a numerical score, the Proteome Integrity Number (PIN), that faithfully mea ...[more]

PMID: 31175306

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