A novel strategy based on carboxy group derivatization is presented for specific characterization of phosphopeptides. By tagging the carboxy group with 1-(2-pyrimidyl) piperazine (PP), the ion charge states of phosphopeptides can be largely enhanced, showing great advantages for sequencing phosphorylated peptides with electron-transfer dissociation MS. Besides, after PP-derivatization, most non-specific bindings can be avoided by eliminating the interaction between the carboxy group and TiO(2), greatly improving the specificity of TiO(2)-based phosphopeptide enrichment strategy. Moreover, being tagged with a hydrophobic group, the retention time of phosphopeptides in RPLC can be prolonged, overcoming the difficulty of separating phosphopeptides in RPLC-based approach. Together with several other advantages, such as ease of handling, rapid reaction time, broad applicability and good reproducibility, this PP-derivatization method is promising for high-throughput phosphoproteome research.