In this study, targeted parallel reaction monitoring assays for phosphopeptides were configured by mining data from large-scale experiments. The capabilities of the method were assessed by performing several benchmarking experiments. The accuracy of retention time prediction using a large-scale database was assessed by using BSA peptides or human phosphopeptides to predict the retention time of distinct peptides in a subsequent run. Data-driven phosphopeptide sequence and charge state was compared to heuristics-based selection using unscheduled PRM assays. Phosphoproteome analysis was performed in technical quadruplicate using parallel reaction monitoring, data-independent acquisition, and data-dependent acquisition. A label-free quantitative parallel reaction monitoring experiment was performed on phosphopeptides enriched from cells stimulated -/+ IGF-1 (n=6).