Methods for improving the specificity of assays for botulinum neurotoxins are described. Reporting constructs are provided that include cleavable linker sequence with genetically modified recognition and/or cleavage sites. These linker sequences act as a substrate for a botulinum neurotoxin, with cleavage of the reporting construct providing a detectable signal. When first and second neurotoxins have activity with the same substrate protein, mutation and/or deletion of a recognition and/or cleavage site associated with the second neurotoxin improves the specificity of the detectable signal for the first neurotoxin.