Combinatorial peptide libraries offer an expedient source of structurally diverse molecules that could serve as lead compounds in the development of drug therapies to toxins. The libraries have typical structures of X1 - X2 - hinge - X3 - X4, where X1 through X4 are near-equimolar mixtures of twelve alpha-L-amino acids and hinge = gamma-aminobutyric acid. Screening of the libraries for inhibitory activity in assays for botulinum neurotoxins A and B (BoNTIA, BoNTIB) and saxitoxin uncovered potent library subsets. For effective screening of the peptide libraries, improved methods of analysis were sought. We report on development of a capillary electrophoresis laser-induced fluorescence (CE LIF) method for measuring BoNTIA peptidase activity and for screening peptide libraries for inhibitory effects. A second analytical method for quantitation of BoNTIA assays was employed based on fluorescence resonance energy transfer (FRET). The FRET assay is homogeneous phase, i.e., no separation step is required. Thus assay time was reduced and throughput increased. The research described in this report was supported by the Technology Investment Fund of Defence R&D Canada.