The identification of tumor related cell membrane protein targets is important in understanding tumor progression, the development of new diagnostic tools, and potentially for identifying new therapeutic targets. Here we present a novel strategy for identifying uniquely expressed proteins using cell specific aptamers. Using an intact viable B-cell Burkitt’s lymphoma cell line (Ramos cells) as the target, we have selected aptamers that recognize cell membrane proteins with high affinity. Among the selected aptamers that showed unique recognition patterns with different cell lines of leukemia, the aptamer TD05 showed binding only with Ramos cells. By chemically modifying TD05 to covalently crosslink with its target on Ramos cells and to capture and enrich the target receptors using streptavidin coated magnetic beads followed by mass spectrometry, we were able to identify membrane bound Immunoglobin Heavy mu chain (IGHM) as the target for TD05 aptamer. IGHM is a major component of B-Cell antigen receptor (BCR) which is uniquely expressed in B-Cells. This study demonstrates that this two-step strategy, the development of high-quality aptamer probes and then the identification of their target proteins, can be used to discover new disease-related potential markers and thus enhance tumor diagnosis and therapy. The aptamer based strategy will enable effective molecular elucidation of disease related biomarkers and other interesting molecules.