Peak lists for the database search were produced in the Mascot generic format using BioWorks 3.3.1 (Thermo Finnigan, San Jose, CA) and DTASuperCharge V 1.31 (SourceForge), and the derived peak lists were searched using the Mascot 2.2.04 search engine (Matrix Science, London, UK) against a real and false IPI human database (V3.56, including 153, 078 protein entries). The following search criteria were employed: full tryptic specificity was required; two missed cleavages were allowed; Carbamido-methylation was set as fixed modification, whereas Oxidation (M), Phospho (ST), and Phospho (Y) were considered as variable modifications. Precursor ion mass tolerances were 10 ppm for all MS acquired in the Orbitrap mass analyzer, fragment ion mass tolerance was 0.5 Da for all MS 2 spectra acquired in the LTQ. Mass spectra of identified phosphopeptides with peptide score .10 were further processed and validated with the MSQuant 1.5 software for post-translational modification (PTM) score analysis [48] . Two filters criteria for phosphopeptide identification were applied: 1) Peptide score threshold was 17; 2) The total threshold of PTM score and peptide score was 36. All fragmentation spectra were manually verified using the criteria as described by Mann et al [48] . For phosphopeptides with multiple potential phosphorylation sites, the probabilities for phosphorylation at each site were calculated from the PTM scores as described [48] . Phosphorylation sites that were occupied with probability .0.75 were reported as class I phosphorylation sites. For class II sites, localization probability was between 0.75 and 0.25. Phosphorylation sites with localization probability ,0.25 were discarded. The identified phosphopeptides were further processed with MSQuant 1.5 for statistics evaluation as well as quantization.