Fig. 1: Identification of PCa enriched proteins.

a Data analysis was based on label-free spectral counting, obtaining an average of 540 and 536 proteins per sample in PCa and BPH tissue proteomes, respectively. Two proteomic data sets were generated (PCa and BPH), taking into account the proteins that were found in at least 50% of the samples of each type of tissue, and that were also not shared between both groups. 109 proteins were enriched in PCa samples, while 140 proteins were enriched in BPH samples. b Tag cloud network of the 109 PCa enriched proteins identified consistently across the proteomics analyses performed in PCa compared to BPH FFPE human tissue samples. The font size increases proportionally to the average PSMs of these proteins across all the PCa samples. The color reflects the same information. c Semi-quantitative analysis of proteins identified by LC ESI–MS/MS classified by the number of PSMs obtained from PCa tissue samples. Results represent the average PSMs for each group. d GO analysis of PCa enriched proteins using the DAVID software which includes only significant categories (−log P ≥ 1.5) from cellular components, biological process, and molecular functions. e Protein levels (PSMs) and gene differential expression (PCa vs. normal adjacent tissue, TCGA-PRAD) of PCa enriched proteins were grouped by GO terms from the biological process category using DAVID software and visualized in proteogram plots. These graphs are circular heat-plots depicting both protein PSMs on the left semicircle and gene expression fold change (as log₂ (fold change)) on the right semicircle, with the center indicating the averages. For the gene expression, a half outer semicircle was added to include each gene’s transcript’s expression level. PSM data were locally generated while gene expression data was gathered from TCGA-PRAD.