Capillary isoelectric focusing (CIEF) in uncoated and commercially available coated capillaries was applied to the separation of tryptic peptides from bovine and chicken cytochrome (c). This is the first report of peptide mapping by CIEF. Before separation, the pIs of individual peptides expected to be formed during the digest were calculated, and then the separation pattern obtained was correlated with the calculated pIs. This correlation was reasonably good for some peptides, but not as good for others. However, differentiation of the two species digests was easily achieved based on the CIEF map. The major limitation of the method is the fact that uv detection at (280 \mathrm{~nm}) must be employed, meaning that only tryptophan and tyrosine containing peptides will be detected, since the ampholytes used to generate the (\mathbf{p H}) gradient absorb below (280 \mathrm{~nm}). Postcolumn derivatization of the peptides is one solution to this problem. Migration time reproducibility was on the order of (2 %), and run times were less than (20 \mathrm{~min}) for the entire pH gradient range in the uncoated capillary. In the coated capillary, superior resolution was obtained at the expense of longer run times. ic 1993 Academic Press, Inc.