If the peptide has a free amino or thiol group, you can detect it by reacting the plasmid with a fluorescent dye that is amine- or thiol-reactive. After the reaction, separate the plasmid from any free dye, and then test the plasmid for fluorescence using a spectrofluorometer, fluorescence plate reader, or by running it on an agarose gel and using a fluorescence imager.

Dear Adam,

thank you very much for the answer. My peptide is having ala-gly-ala-gly. It dont have free amine containing amino acid.