Phosphoproteomic analysis of primary human multiple myeloma cells

Multiple myeloma (MM) is a malignant disorder of differentiated B cells. Clonal expansion of the tumor results in the excessive production of monoclonal immunoglobulin (Ig) which is a diagnostic feature of this disease. Previous investigations have demonstrated the alteration of the ERK, jun kinase, STAT, and AKT kinase signaling cascades in MM cells, suggesting that deregulated phosphorylation may contribute to MM pathogenesis. However, systematic analysis of the phosphoproteome in MM cells has not been reported. Here, we described a large-scale phosphorylation analysis of primary MM cells. Using a separation strategy involving immunomagnetic bead-positive selection of MM cells, preparative SDS-PAGE for prefractionation, in-gel digestion with trypsin, and titanium dioxide enrichment of phosphopeptides, followed by LC-MS/MS analysis employing a hybrid LTQ-Orbitrap mass spectrometer, we were able to catalog a substantial portion of the phosphoproteins present in primary MM cells. This analysis led to the identification of 530 phosphorylation sites from 325 unique phosphopeptides corresponding to 260 proteins at false positive rate (FPR) of 1.3%. This dataset provides an important resource for future studies on phosphorylation and carcinogenesis analysis of multiple myeloma.