A blocking peptide (also peptide competitor or neutralising peptide) is the free synthetic peptide corresponding to the immunogen sequence used to raise a given antibody. It is supplied alongside the antibody for one purpose: to demonstrate that an observed signal comes from the intended epitope.
How the control works
The antibody is pre-incubated with a molar excess of the peptide — commonly a several-fold to hundred-fold excess, optimised empirically — before being applied to the blot, plate or section. If the signal is epitope-specific it should be abolished or strongly reduced; bands that persist are non-specific or reflect a distinct cross-reactive epitope. Both the blocked and unblocked conditions must be run side by side on the same sample, and the peptide-only condition is worth including to confirm that the peptide itself contributes no signal.
Limitations should be stated plainly: the control proves epitope dependence, not that the stained protein is the protein you assume. An unrelated protein sharing that short linear epitope would behave identically. Genetic knockout or knockdown remains the stronger specificity control; peptide blocking is the practical one.
Related terms and material
polyclonal vs monoclonal · purified IgG · ELISA · native sequence. Reference material: antibodies, peptide libraries. Further reading: antibodies in peptide research.