The most common histological preparative technique is formalin-fixed, paraffin embedded tissue. Some epitopes are more sensitive to fixation and embedding than others and can be masked (hidden) from the addition of affinity reagents. Various antigen retrieval methods exist to unmask a given epitope. These are not applicable to frozen sections. The optimal method will have to determined on a case by case basis. Crosslinking when fixating and embedding can prevent antigen degradation or physical relocation within the cell/tissue. It also eliminates bacterial contamination. Frozen sections can often lose morphological integrity, whereas paraffin embedded sections tend to retain it over multiple sections. Paraffin embedded sections will cause cell/tissue shrinkage that results in higher antigen density over a given section. Always be aware of the fact that your tissues/cells may contain various components that could interfere with your staining technique, such as endogenous enzymes (alkaline phosphatase, peroxidases), endogenous biotin and Fc receptors.
