Hi.
Does anyone know how much difference in a protein sequence there "is allowed" before the antibody doesn't detect the protein? If there is a 1-2 amino acid difference between the peptide the AB has been raised against and the sequence in the protein you want to detect, can the AB still bind maybe with a lower affinity?

This all depends on what epitope is recognized by the Ab. If you change a single AA of an epitope then the Ab will not recognize it. If the AA change is away from the epitope and doesn't affect conformation of the protein (maybe less of an issue with small peptides) then the change is likely to have no effect.

My guess is that on a small peptide you stand a high chance of messing with binding if you substitute AA.