What are the disadvantages of the peroxidase-antiperoxidase method?

One drawback is that the PAP complex must originate from the same species as the primary antibody. Tissues with high levels of natural peroxidase activity can interfere with the detection process, leading to nonspecific background staining and reduced sensitivity of the assay. The PAP method typically involves multiple incubation steps and thus it is less time-efficient compared to other methods. The PAP method may not be sensitive enough to reliably detect low abundance antigens in protein expression within FFPE tissue samples.