Shao, Wenguang, Guo, Tiannan ORCID: 0000-0003-3869-7651, Toussaint, Nora C., Xue, Peng, Wagner, Ulrich, Li, Li, Charmpi, Konstantina, Zhu, Yi, Wu, Jianmin ORCID: 0000-0002-8876-128X, Buljan, Marija, Sun, Rui, Rutishauser, Dorothea ORCID: 0000-0003-2303-103X, Hermanns, Thomas, Fankhauser, Christian Daniel, Poyet, Cedric, Ljubicic, Jelena, Rupp, Niels, Ruschoff, Jan H., Zhong, Qing ORCID: 0000-0002-5340-301X, Beyer, Andreas ORCID: 0000-0002-3891-2123, Ji, Jiafu, Collins, Ben C., Liu, Yansheng, Ratsch, Gunnar, Wild, Peter J. and Aebersold, Ruedi (2019). Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins. Nat. Commun., 10. LONDON: NATURE PUBLISHING GROUP. ISSN 2041-1723

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Abstract

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.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Shao, WenguangUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Guo, TiannanUNSPECIFIEDorcid.org/0000-0003-3869-7651UNSPECIFIED
Toussaint, Nora C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Xue, PengUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wagner, UlrichUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Li, LiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Charmpi, KonstantinaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhu, YiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wu, JianminUNSPECIFIEDorcid.org/0000-0002-8876-128XUNSPECIFIED
Buljan, MarijaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Sun, RuiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Rutishauser, DorotheaUNSPECIFIEDorcid.org/0000-0003-2303-103XUNSPECIFIED
Hermanns, ThomasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Fankhauser, Christian DanielUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Poyet, CedricUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ljubicic, JelenaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Rupp, NielsUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ruschoff, Jan H.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhong, QingUNSPECIFIEDorcid.org/0000-0002-5340-301XUNSPECIFIED
Beyer, AndreasUNSPECIFIEDorcid.org/0000-0002-3891-2123UNSPECIFIED
Ji, JiafuUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Collins, Ben C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Liu, YanshengUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ratsch, GunnarUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wild, Peter J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Aebersold, RuediUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-138027
DOI: 10.1038/s41467-019-10513-5
Journal or Publication Title: Nat. Commun.
Volume: 10
Date: 2019
Publisher: NATURE PUBLISHING GROUP
Place of Publication: LONDON
ISSN: 2041-1723
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
QUANTIFICATION; MUTATIONS; MS/MSMultiple languages
Multidisciplinary SciencesMultiple languages
Refereed: Yes
URI: http://kups.ub.uni-koeln.de/id/eprint/13802

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