Automated systems for protein electrophoresis are available for large volumes of samples for electrophoresis. An automated system is capable of separating 10-100 samples simultaneously.

There are several different automated systems and the number of process steps automated varies. Automated steps may include reagent addition, sample application, electrophoresis separation, staining, and detection.

Below is a stained electrophoresis land for one sample analyzed on the automated instrument, SPIFE 3000, Helena Laboratories. The separated proteins are stained with Acid Blue, a Helena Laboratories' stain developed from Coomassie dye.