It seems that, however, conformation of peptides on MAP is less flexible, and antibodies obtained by MAP often recognize protein less often than by conventional KLH conjugation. In addition, there is no free peptide produced when making MAP, making it difficult to remove polylysine core directed antibodies. Purification of MAP by HPLC is difficult, and MAP is provided without mass verification due do its heterogeneity and large molecular size.

Multiple antigen peptide application is one potent way to produce high-titer anti-peptide antibodies and synthetic peptide vaccines. This system utilizes the a- and e-amino groups of lysine to form a backbone to which multiple peptidechains can be attached. Depending on the number of lysine tiers, different numbers of peptide branches can be synthesized. This eliminates the need to conjugate the antigen to a protein carrier.