An automated fraction collection interface was developed for coupling CE with MALDI-MS. This fraction collection approach is based on the electrowetting on dielectric (EWOD) phenomenon performed on a digital microfluidic (DMF) board; it does not rely on a MALDI spotter. In this study, a four-peptide mixture was used as a sample test, and the separations were conducted in a portable CE instrument with a 150 mu m o.d. x 50 mu m i.d. capillary and a contactless conductivity detector. The CE instrument was interfaced with a robust DMF board. The CE fractions were directly deposited onto the DMF board at predetermined locations prior to MALDI analysis. The series of experiments determined the lowest concentration that produces a measurable MALDI signal. The concentrations were 0.25, 0.5, 0.05, and 0.05 nmol for bradykinin, angiotensin, ACTH (1839), and insulin, respectively. The contactless conductivity detector limit of detection for the same analytes was 2.5 mu mol.