An automated fraction collection interface has been developed for coupling capillary electrophoresis (CE) with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). This fraction collection approach is based on electromigration and diffusion and does not rely on the presence of a liquid junction, sheath-liquid, electro-osmotic flow, or a superimposed hydrodynamic flow. Neutrally coated capillary with negligible electroosmosis can thus be used to provide high-efficiency separations of biological compounds. The in-capillary separation resolution is totally independent from the spotting process. CE-separated species can be collected either in a multiwell plate or directly on a MALDI target. In the present work, an eight-protein mixture, submitted to trypsin proteolysis, has been used as a sample test and separations have been conducted in 50 μm i.d. neutrally coated capillaries. As compared to direct MALDI MS analysis, the integration of CE improved the number of detected peptides from 36 to 87 and the average sequence coverage from 24% to 38%. Internal calibration was used, and an average mass accuracy of 16.1 ppm is reported. Finally, diffusion-migration numerical simulations of the iontophoretic fraction collection process have been carried out.