Many important biomarkers for disease diagnosis are present at low concentrations in human serum. These biomarkers are masked in proteomic analysis by highly abundant proteins such as human serum albumin (HSA) and immunoglobulins (IgGs) which account for up to 80% of the total protein content of serum. Traditional depletion methods using macro-scale LC-columns for highly abundant proteins involve slow separations which impart considerable dilution to the samples. Furthermore， most techniques lack the ability to process multiple samples simultaneously. We present a method of protein depletion using superparamagnetic beads coated in anti-HSA， Protein A， and Protein G， manipulated by digital microfluidics (DMF). The depletion process was capable of up to 95% protein depletion efficiency for IgG and HSA in 10 min for four samples simultaneously， which resulted in an approximately 4-fold increase in signal-to-noise ratio in MALDI-MS analysis for a low abundance protein， hemopexin. This rapid and automated method has the potential to greatly improve the process of biomarker identification.