cad a22 4500 569303869 20200127092902.0 cr unu---uuuuu 190726e20190607xx s 000 0 eng 10.5167/uzh-171764 doi 10.1038/s41467-019-10513-5 doi (ZORA)oai:www.zora.uzh.ch:171764 (ETHRESEARCH)oai:www.research-collection.ethz.ch:20.500.11850/393657 610 ddc 31175306 pmid Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins [Elektronische Daten] [Wenguang Shao, Tiannan Guo, Nora C Toussaint, Peng Xue, Ulrich Wagner, Li Li, Konstantina Charmpi, Yi Zhu, Jianmin Wu, Marija Buljan, Rui Sun, Dorothea Rutishauser, Thomas Hermanns, Christian Daniel Fankhauser, Cedric Poyet, Jelena Ljubicic, Niels Rupp, Jan H Rüschoff, Qing Zhong, Andreas Beyer, Jiafu Ji, Ben C Collins, Yansheng Liu, Gunnar Rätsch, Peter J Wild, Ruedi Aebersold] Nat Commun openAccess eu-repo 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 measures the degree of protein degradation. Our results indicate that protein degradation only affects 5.9% of the samples tested and shows negligible correlation with mRNA degradation in the adjacent samples. These findings are confirmed by independent analyses on additional clinical sample cohorts and across different mass spectrometric methods. Overall, the data show that the majority of samples tested are not compromised by protein degradation, and establish the PIN score as a generic and accurate indicator of sample quality for proteomic analyses. Creative Commons Attribution 4.0 International http://creativecommons.org/licenses/by/4.0 ethresearch Institute of Pathology and Molecular Pathology zora Urological Clinic zora Shao Wenguang joint author Guo Tiannan joint author Toussaint Nora C. joint author Xue Peng joint author Wagner Ulrich joint author Li Li joint author Charmpi Konstantina joint author Zhu Yi joint author Wu Jianmin joint author Buljan Marija joint author Sun Rui joint author Rutishauser Dorothea joint author Hermanns Thomas joint author Fankhauser Christian Daniel joint author Poyet Cedric joint author Ljubicic Jelena joint author Rupp Niels joint author Rüschoff Jan H. joint author Zhong Qing joint author Beyer Andreas joint author Ji Jiafu joint author Collins Ben C. joint author Liu Yansheng joint author Rätsch Gunnar joint author Wild Peter J. joint author Aebersold Ruedi joint author Nature Communications 10(1):2524 https://www.zora.uzh.ch/id/eprint/171764/1/Wenguang_nature_communications_2019.pdf text/html WWW-Backlink auf das Repository 1 Journal Article PeerReviewed zora ZORA 856 40 https://www.zora.uzh.ch/id/eprint/171764/1/Wenguang_nature_communications_2019.pdf text/html WWW-Backlink auf das Repository ZORA 700 1- Shao Wenguang joint author ZORA 700 1- Guo Tiannan joint author ZORA 700 1- Toussaint Nora C. joint author ZORA 700 1- Xue Peng joint author ZORA 700 1- Wagner Ulrich joint author ZORA 700 1- Li Li joint author ZORA 700 1- Charmpi Konstantina joint author ZORA 700 1- Zhu Yi joint author ZORA 700 1- Wu Jianmin joint author ZORA 700 1- Buljan Marija joint author ZORA 700 1- Sun Rui joint author ZORA 700 1- Rutishauser Dorothea joint author ZORA 700 1- Hermanns Thomas joint author ZORA 700 1- Fankhauser Christian Daniel joint author ZORA 700 1- Poyet Cedric joint author ZORA 700 1- Ljubicic Jelena joint author ZORA 700 1- Rupp Niels joint author ZORA 700 1- Rüschoff Jan H. joint author ZORA 700 1- Zhong Qing joint author ZORA 700 1- Beyer Andreas joint author ZORA 700 1- Ji Jiafu joint author ZORA 700 1- Collins Ben C. joint author ZORA 700 1- Liu Yansheng joint author ZORA 700 1- Rätsch Gunnar joint author ZORA 700 1- Wild Peter J. joint author ZORA 700 1- Aebersold Ruedi joint author ZORA 773 0- Nature Communications 10(1):2524 ETHRESEARCH 856 40 http://hdl.handle.net/20.500.11850/393657 text/html WWW-Backlink auf das Repository (Open access) ETHRESEARCH 700 1- Shao Wenguang joint author ETHRESEARCH 700 1- Guo Tiannan joint author ETHRESEARCH 700 1- Toussaint Nora C. joint author ETHRESEARCH 700 1- Xue Peng joint author ETHRESEARCH 700 1- Wagner Ulrich joint author ETHRESEARCH 700 1- Li Li joint author ETHRESEARCH 700 1- Charmpi Konstantina joint author ETHRESEARCH 700 1- Zhu Yi joint author ETHRESEARCH 700 1- Wu Jianmin joint author ETHRESEARCH 700 1- Buljan Marija joint author ETHRESEARCH 700 1- Sun Rui joint author ETHRESEARCH 700 1- Rutishauser Dorothea joint author ETHRESEARCH 700 1- Hermanns Thomas joint author ETHRESEARCH 700 1- Fankhauser Christian D. joint author ETHRESEARCH 700 1- Poyet Cedric joint author ETHRESEARCH 700 1- Ljubicic Jelena joint author ETHRESEARCH 700 1- Rupp Niels joint author ETHRESEARCH 700 1- Rüschoff Jan H. joint author ETHRESEARCH 700 1- Zhong Qing joint author ETHRESEARCH 700 1- Beyer Andreas joint author ETHRESEARCH 700 1- Ji Jiafu joint author ETHRESEARCH 700 1- Collins Ben C. joint author ETHRESEARCH 700 1- Liu Yansheng joint author ETHRESEARCH 700 1- Rätsch Gunnar; id_orcid 0000-0001-5486-8532 joint author ETHRESEARCH 700 1- Wild Peter J. joint author ETHRESEARCH 700 1- Aebersold Ruedi joint author ETHRESEARCH 773 0- Nature Communications London : Nature Publishing Group 10 (1), p. 2524 2041-1723 BK010053 XK010053 XK010000 ZORA ZORA ZORA Journal Article openAccess ETHRESEARCH ETHRESEARCH ETHRESEARCH Journal Article Open access