Amorphous silicon thin-film transistors have been prepared and used to drive a microchannel electrophoresis device for protein identification. The complete system was fabricated on a glass substrate using only three photomasks. Proteins of three different sizes (14.2, 29, and 45 kDa) were successfully separated from a microliter solution and in situ identified in a short period of 1000 s. The thin film transistor also suppressed the current perturbation of the microchannel electrophoresis device in the early operation stage. This low-cost chip is potentially applicable to the identification of micro or nano amount of biomolecules from a complicated solution.