CSC technology captures the surface phenotype of ALL cells. (A) Cell surface proteome map of ALL cells: 713 identified membrane-associated proteins were categorized based on their biological function assigned by the PANTHER algorithm (left); the 20 most abundant protein families and superfamilies are displayed (right; protein family assignment according to UniProt KB annotation). (B) Comparison between immunophenotypes described using 2 different technologies. ALL xenograft samples (n = 19) included in the proteomic pipeline were analyzed by FCM for expression of 26 selected glycosylated cell surface proteins (with an exception of nonglycosylated protein CD20 detected here with the Lys-CSC strategy), which are commonly used in clinical diagnostic panels. Shown is the percentage of cases positive for a given marker by FCM and mass spectrometry identification. Proteins with at least 5 independent spectra acquired for a given sample were taken into account.