Current methods of protein detection are insensitive to detecting subtle changes in oncoprotein activation that underlie critical cancer signaling processes. The requirement for large numbers of cells precludes serial tumor sampling for assessing a response to therapeutics. Therefore, we have developed a nano-fluidic proteomic immunoassay (NIA) to quantify total and low abundance protein isoforms in 4 nanoliters of lysate. Our method could quantify levels of MYC and BCL2 proteins in Burkitt’s versus follicular lymphoma; identify changes in activation of ERK1/2, MEK1, STAT3/5, JNK and caspase 3 in imatinib-treated chronic myelogeneous leukemia (CML) cells; measure a novel change in phosphorylation of an ERK2 isomer in CML patients who responded to imatinib; and detect a decrease in STAT3/5 phosphorylation in lymphoma patients treated with atorvastatin. Therefore, we have described a novel and highly sensitive method for interrogating oncoprotein expression and phosphorylation in clinical specimens for the development of new therapeutics for cancer.