Deterioration of biomolecules in clinical tissues is an inevitable pre-analytical process, which affects molecular measurements and thus potentially confounds conclusions from cohort analyses. While mRNA degradation has been studied extensively, the extent of protein degradation in human tissues and its implication for molecular classification remain largely unexplored. Here, we comprehensively compare the degradation patterns of mRNA and protein in a prostate cancer tissue cohort. We subject 68 pairs of adjacent prostate tissue samples to RNA-Sequencing (RNA-Seq) or proteomic analysis by pressure cycling technology (PCT) coupled with SWATH mass spectrometry. 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. We benchmark the PIN algorithm using a set of ground-truth samples in which the levels of proteome degradation were artificially controlled and independently validated, and assess the relative degree of mRNA and protein degradation in adjacent samples. Our results indicate that the PIN score faithfully indicates the degree of protein degradation of a sample and is robust across different types of clinical samples and mass spectrometric measurement methods. We show 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, even if the corresponding samples show substantial transcript degradation and establish the PIN score as a generic and accurate indicator of sample quality for proteomic analyses. Our results thus provide important information and resources for proteomic measurements in clinical cohort studies.