The best antibody results are obtained from antigens that present
the most number of desirable epitopes. Your choice should be based on the following information:

Protein antigens provide

• most number of linear epitopes
• most number of structural epitopes
• highest chance of generating antibodies that are useful in a wide range of applications

however

• could have homology with unwanted family members
• could have homology with unwanted and unrelated proteins
• not useful for PTM specific antibodies
• must be >80% pure to avoid cross-reactivity
• must be in sufficient quantity for a programme, eg 1mg for rabbit polyclonal programmes

Peptide antigens provide

• easy access to new antibodies
• antibodies can be easily affinity purified against the peptide
• access to PTM specific antibodies such as phosphospecific antibodies
• can be designed to be highly specific for a single protein isoform

however

• are linear epitopes
• require good peptide design knowledge for success - such as what we have :)

Peptide antibodies are today a very viable alternative to anti-protein programmes. A peptide antibody programme offers the advantages of being able to immunize with highly purified material and to affinity purify the antibodies against the peptide.