In addition, many of the BMS-907351 peptides that are generated by cleavage at hydrophobic residuesare also elevated by the bortezomib treatment. This finding is much different than the results with epoxomicin, a proteasome inhibitor that also shows greatest potency towards the beta-5 site, and which generally causes a decrease in levels of peptides that require cleavage at beta5 sites. Because our previous data with epoxomicin did not include all of the peptides found in the present study, we reanalyzed the epoxomicin data to search for every peptide found in the present study; those that were found are included together with the previously published epoxomicin data in the heat maps in Figure 3. Although both bortezomib and epoxomicin are potent inhibitors of the beta5 proteasome subunit, there are dozens of likely beta-5 products that are decreased by epoxomicin treatment but elevated by bortezomib treatment. Sorting the heat map data by protein precursor reveals that many of the peptides elevated by bortezomib treatment arise from just six proteins: 60S acidic ribosomal protein P2, heat shock 10kDa protein 1, histidine triade nucleotide-binding protein 1, macrophage migration inhibitory factor, nucleophosmin, and protein SET. Collectively, these six proteins account for 65 of the peptides that are greatly elevated upon bortezomib treatment. Previously, it was noted that many of the observed cellular peptides were derived from cytosolic proteins, although peptides were also found that corresponded to mitochondrial and nuclear proteins. To test if the cellular location of the protein correlated with changes in peptides, the number of peptides in each group were compared. As previously found, most of the peptides detected in the present study were derived from cytosolic proteins. Over 100 of these cytosolic protein-derived peptides were greatly elevated by bortezomib treatment, but this represented only,30% of the total number of cytosolic protein-derived peptides, and many peptides derived from cytosolic proteins showed no change or decreased upon treatment. In contrast, the majority of the mitochondrial protein-derived peptides showed a very large increase upon bortezomib treatment, and only a handful did not change or showed a decrease. In previous studies, approximately 50% of the cellular peptides in HEK293T and other 
cell lines were found to represent the Nor C-terminus of the protein. In the present study, approximately 70% of peptides unaffected by bortezomib were Nor C-terminal peptides and only 30% represented internal peptides. In contrast,,80% of the peptides which were greatly elevated by bortezomib represented internal fragments of the proteins. For the analysis shown in Figure 5, both 50 and 500 nM treatments were combined. To determine if the peptides that showed a partial decrease or increase were comparable between these two concentrations of bortezomib, the two groups were analyzed separately. For this analysis, only those peptides detected in both the 50 and 500 nM treatment groups were considered. The 26 peptides which showed a partial Ibrutinib decreasein the 500 nM bortezomib group were similarly affected by treatment with 50 nM bortezomib, indicating that the partial effect was not due to incomplete inhibition of bortezomib at the lower dose. However, those peptides partially increased by 50 nM bortezomib showed a significantly larger increase upon treatment with 500 nM drug. Similar analysis was performed to compare peptides that partially decreased or increased upon treatment with 500 nM bortezomib for 30 or 90 minutes. Levels of peptides that partially decreased after 30 minutes of treatment were not significantly different after 90 minutes of treatment.