Protein or peptide antigen? Advantages and disadvantages

Peptide versus whole protein immunogens for antibody production

What Is an Immunogen?

An immunogen is an antigen used to generate antibodies. Consequently, immunogen design is one of the most important aspects of antibody production: if the immunogen is poorly designed, the purified antibodies will be non-specific or have a low titer. In addition, the immunogen establishes the epitope range of the purified antibody, knowledge of which is critical for experimental design. While there are many facets of immunogen design, we will focus here on the advantages and disadvantages of using a peptide versus a full-length protein as the immunogen for polyclonal antibodies.

Peptide Immunogens

Peptide immunogens can be useful for generating antibodies that will detect a single isoform of a protein; in addition, peptides are useful for generating antibodies that can detect post-translational modifications to specific sites, such as phosphorylation. However, a peptide will not necessarily fold in the same way as the full-length protein, so antibodies generated with a peptide immunogen are more likely to be non-specific or have low affinity. Also, peptide immunogens tend to produce lower affinity antibodies because of the short length of the peptide limits affinity maturation in lymphoid follicles, owing to the reduced number of options for epitopes (1).

Protein Immunogens

When a protein immunogen is used, antibodies can be generated against any region of the protein. Therefore, protein immunogens are best for generating antibodies for experiments that follow a protein while it is modified, such as investigating the processing of a proprotein over time. In addition, there is a high chance that some of the epitopes will be in conserved sequences, so that the resulting antibody may have reactivity across a number of species. Similarly, some regions of the protein may be better for one application than another, so using a protein immunogen often yields antibodies that can work in multiple applications.

Protein Immunogen versus Peptide Immunogen: Which Is Best for You?

In summary, peptide immunogens are ideal for investigating specific protein isoforms and post-translational modified sites, whereas protein immunogens are superior for most other experiments. Proteintech uses both peptide and protein immunogens, depending on which is most appropriate for the particular antibody desired. In addition, we provide the immunogen sequences for all our antibodies, so that you can determine which will be most suitable for your experiments.

Find out more about our polyclonal antibodies here.


  1. Follicular dendritic cells: Dynamic antigen libraries