To quantify the phosphorylation change for each phosphopeptide, we used the MSQuant software to calculate area ratio, defined as the ratio of the ''heavy'' peak area over the ''light'' peak area in the chromatogram (Fig. 2B ). All together, we have achieved quantification of 259 unique phosphorylation sites from 154 unique phosphopeptides corresponding to 132 protein groups. Based on a predefined threshold of 1.5-fold change, 131 phosphosites from 75 unique phosphopeptides corresponding to 72 proteins showed a 1.5-fold or greater change as listed in Table  S2 . In other words, 31% of the total phosphosites detected showed significant alteration after bortezomib treatment, suggesting that dysregulated phosphorylation may play an important role in bortezomib-induced apoptosis.