Abstract: Post-acquisition mass spectral processing can significantly enhance the identification rate from both MS and MS/MS spectra. In this study we focused on how to improve phosphopeptide identification by utilizing the neutral-loss patterns hidden in a large set of tandem mass spectra. We also calibrated the precursor mass to further improve their mass measurement accuracy. The experiments on iPRG2010 data set show that these two types of spectral preprocessing can greatly benefit the phosphopeptide identification using both our developed search engine pFind and the commercial software Mascot.