Protein expression profiling of CLL B cells using replicate off-line strong cation exchange chromatography and LC–MS/MS

In this study we use replicate 2D-LC–MS/MS analyses of crude membranes from B cells derived from a patient with chronic lymphocytic leukemia (CLL) to examine the protein expression profile of CLL B cells. Protein identifications made by replicate 2D-LC–MS/MS analysis of tryptic peptides from detergent solubilized B cell membrane proteins, as well as replicate LC–MS/MS analysis of single off-line strong cation exchange chromatography (SCX) fractions, were analyzed. We show that despite the variance in SCX, capillary LC, and the data-dependent selection of precursor ions, an overlap of 64% between proteins identified in replicate runs was achieved for this system.