The potential of capillary electrophoresis (CE) for the separation of peptides has been extensively demonstrated in the last decade. Their correct characterization and sequenciation is a difficult task that can be accomplished using CE-mass spectrometry (CE-MS). An important limitation of CE-MS is the buffer choice since it should provide an adequate CE separation without ruining the MS signal. In this work, a new strategy is used to help to solve this limitation based on the combination of two different methodologies. Namely, an ab initio semiempirical model that relates electrophoretic behavior of peptides to their sequence is first used to obtain in a fast and easy way adequate CE buffers compatible with MS analysis. Next, CE-MS is used to separate and characterize peptides via the determination of their relative molecular masses. The usefulness of this procedure is demonstrated analyzing in a single CE-MS run a group of 10 standard peptides of very different nature (i.e., relative molecular masses ranging from 132 to 1037 and isoelectric points ranging from 5.69 to 10.62). It is concluded that the use of this strategy can help to overcome the buffer limitation in CE-MS.