Glycoprotein Signatures for Aggressive Prostate Cancer via SWATH mass spectrometry

The identification of biomarkers indicating the level of aggressiveness of prostate cancer (PCa) addresses an urgent clinical need to minimize the general over-treatment of patients with non-aggressive PCa, which account for the majority of PCa cases. In this study we combined N-glycopeptide isolation and SWATH-MS towards the molecular characterization of tumor malignancy and aggressiveness. Here, we isolated formerly N-linked glycopeptides from normal prostate (n=10), non-aggressive (n=22), aggressive (n=16) and metastatic PCa (n=25) tumor tissues and analyzed the samples by SWATH-MS, an emerging data independent mass spectrometric acquisition method that generates a single MS file containing fragment ion spectra of all ionized species of a sample. The resulting datasets were searched using a targeted data analysis strategy where a priori spectral reference library representing known N-glycosites of the human proteome was used to identify groups of signals in the SWATH-MS data. On-average we identified 1430 N-glycosites from each SWATH map of which 1057 were quantified across all samples. The 220 glycoproteins that showed significant quantitative changes associated diverse biological processes with the level of PCa aggressiveness and metastasis and indicated functional relationships with common PCa genomic mutations.