In-depth Endogenous Phosphopeptidomics of Serum with Zirconium (IV)-Grafted Mesoporous Silica Enrichment

In this study, we developed an approach using Zirconium (IV)-grafted mesoporous beads to enrich phosphopeptides followed by analysis with a high resolution nanoRPLC-MS/MS system. The new method was first tested with tryptic digests of standard phosphoproteins and HeLa cell lysates, with excellent enrichment performance achieved. The method was further used for endogenous phosphopeptidomic analysis of serum samples from pancreatic ductal adenocarcinoma (PDAC) patients and controls. In total, 329 endogenous phosphopeptides (containing 113 high confidence sites) were identified across samples, by far the largest endogenous phosphorylation dataset catalogued to date. In addition, the method was readily applied for phosphoproteomics of the same set of samples, with 172 phosphopeptides identified and significant changes in dozens of phosphopeptides observed. Taken together, this method serves as a benchmark for analyzing serum phosphorylation events. Given the simplicity and robustness of the proposed method, we envision that it can be readily used for comprehensive phosphorylation studies (i.e., simultaneous endogenous phosphopeptidomics and phosphoproteomics) of serum and other biofluid samples.