Trace elements play a vital role in life activities. The abnormal level of trace elements, alteration of their speciations, changes of expression, location, structure and function of specific metalloenzyme and metalloprotein are often related to some pathological states, even are the key factors for pathogenesis. Thus the high-throughput analysis of the location, concentration, chemical form of metals in organism is an important subject in life science. In this review, various approaches to extraction and separation of metal-containing proteins are introduced and compared with emphasis on the application of different electrophoresis techniques to separation of metalloproteins. The influence of all these analysis processes to metals associated with proteins is also evaluated, along with the possible approaches to improvement of these processes.