Early detection and targeted therapy represent a novel regimen of cancer management. The understanding of receptor tyrosine kinases in tumorigenesis at the molecular level has led to the first generation of kinase inhibitors for anticancer therapy that targets a specific kinase or pathway. While the therapeutic advantage is obvious, targeted therapy often relapses and results in drug resistance for advanced cancers. To achieve feasible early detection and better efficacy of therapeutics targeting multiple pathways, significantly more biomarkers and drug targets are in demand, especially for individualized therapy. Recent advances in phosphoprotein enrichment and MS technologies for quantitative phosphoproteome analysis provide great opportunities in the identification and validation of kinases as drug targets. The MS-based phosphoproteomic technologies would be useful tools as well for the identification of phosphosignatures unique to a specific type or subtype of cancer and drug responsive biomarkers. This review summarizes the major kinases acting as cancer biomarkers and drug targets, the advances of MS-based phosphoproteomic technologies, and some potential values and challenges of this emerging phosphoproteomics-based biomarker and drug target discovery field. Strategies for global, targeted, and quantitative phosphoproteomics are discussed, and some recent interesting applications are also evaluated.