There are several strategies available for determining what epitopes of the protein an antibody binds to. All have their mertis - and limitations - but analysing antibody binding by ELISA using an overlapping peptide array is cost effective yet very successful way of performing epitope mapping.
Each individual peptide in the set of overlapping sequences represents a linear and continuous epitope. Most antibodies however bind to conformational epitopes. Nevertheless, the antibody is likely to cross react with the linear peptides that corespond to the parts that make up the conformational epitope. This makes peptide quality of the outmost importance, as errors may hinder binding. There is a lot to say about the production of high quality peptides, but here when we talk about peptide arrays for epitope mapping, it turns out that details such as raw materials and synthesis methodology are key to success.
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