A multichannel gel electrophoresis and continuous fraction collection apparatus for high-throughput protein separation and characterization.

We developed a multichannel gel electrophoresis system that continuously collects fractions as protein bands migrate off the bottom of gel columns. The device uses several short linear gel columns, each of a different percent acrylamide, to achieve a separation power similar to that of a long gradient gel. A "Counter Free-Flow" elution technique allows continuous and simultaneous fraction collection from multiple channels at low cost. Using the system with SDS-PAGE, 300 μg samples of protein can be separated and eluted into 48-96 fractions over a mass range of 10-150 kDa in 2.5 h. Each eluted protein can be recovered at 50% efficiency or higher in ∼500 μL. The system can also be used for native gel electrophoresis, but protein aggregation limits the loading capacity to about 50 μg per channel and reduces resolution. This system has the potential to be coupled with mass spectrometry to achieve high-throughput protein identification.