A system was developed in our laboratory to couple capillary electrophoresis with mass spectrometry. The capillary electrophoresis system was equipped with a high voltage supply, and a microcontroller with assembly language programming was developed for the computational control of the system. The MS system was a commercial Thermo Finningan LCQ ion trap mass spectrometer. The robustness of the coupled system was evaluated using standard protein samples (lysozyme, aprotinin, and bovine albumin) and tryptic digests of lysozyme. The system showed positive results in terms of robustness, allowing for the separation of digested proteins and the identification of 33% of the total amino acids in a protein (6 of the 18 expected peptides). The limit of detection was in the order of 1 picomole (signal-to-noise ratio), which was considered satisfactory for this system. The system shows high versatility in tandem coupling and combinations with other analytical procedures.