Figure 1. Proteomic and Phosphoproteomic Platform and Characterization.

A. The LuCaP series of 48 patient derived xenografts (PDX) tumors depicted in the table, where 33 Adenocarcinoma (AdCa) either castrated and non-castrated (all) tumors are shown in dark blue and 15 neuroendocrine prostate cancer (NEPC) tumors are shown in orange, n=2-3 biological replicates (BR). The PDXs were processed by extracting proteins and an enzymatic digestion was performed using Trypsin and LysC. Peptides were purified by reversed-phase chromatography. The final peptide pool was ran as the proteome (I.) and in parallel from this peptide pool a sequential metal oxide affinity chromatography was performed to enrich for phosphorylated Serine, Threonine and Tyrosine (II.). Finally, raw data was searched, processed, and analyzed. B. Overall proteome results using 1%FDR for protein identification and p-value adjusted < 0.05 log2 fold change significance. C. Overall proteome results using 1%FDR for phosphoprotein identification and p-value adjusted <0.05 log2 fold change significance and >0.75 phosphosite probability threshold. D. Venn diagram of the proteome and phosphoproteome show the total number of 8,612 master proteins identified when both data sets are overlaid. E. Volcano plot depicting the intensity based average quantification (iBAQ) enriched in NE and AdCa. F. Volcano plot of the phosphoprotein enriched in NE vs AdCa. Grayed line in the x-axis and y-axis are the cut off threshold for NE 2-fold change and for AdCa −2-fold change and p value adjusted to (−log10 FDR), respectively in E-F.