Choosing the proper antigen is one of the most important decisions you will make as you begin your custom antibody project. If you are not sure where to begin, start by considering the nature of your target protein, as well as your desired end-use application. These factors should serve as requisite guides to direct your antigen strategy. For most projects, custom antibody production can be achieved using one of two approaches. The first and most highly recommended uses protein as immunogen. The second strategy relies on the generation of short peptides derived from the native sequence of the target protein for immunization. To determine which strategy is right for your project, an informative guide is provided below.

Why Immunize with Protein Antigens

You need an antibody that works in multiple applications

Your target protein has low sequence similarity to other proteins, is easy to express and purify, and non-toxic

Superior performance in these applications:

Western Blot



Sandwich ELISA

IF/Flow cytomety

Functional Assay


Direct Bind ELISA

Our popular application-guaranteed MonoExpress™ Premium monoclonal antibody production package exemplifies the high success rate of protein antigens by offering the unprecedented guarantee that at least one clone will work in your own experimental system. Also, check out our PolyExpress™ Gold Plus, PolyExpress™ Premium, and PolyExpress™ Premium Plus polyclonal antibody production packages with guaranteed Western blot detection of immunogen protein and delivery 4 weeks faster than any other vendor.  What's more, all packages include protein antigen production so we can get started from just your target sequence.

Why Immunize with Peptide Antigens

  • Your intended antibody applications only include WB, ELISA, or Post-translational modification detection.
  • Your target protein has high sequence similarity to other proteins, is difficult or impossible to express and purify

Appropriate for these applications:

Western Blot


PTM Detection

Peptide antigens are synthetically produced from carefully-selected, short amino acid sequences of the native target protein. They are a popular solution when access to a target protein is limited or unavailable. They are also the ideal antigen for detecting post-translational modification (PTM) sites within the target protein, as they limit the amount of potential epitopes. While fewer potential epitopes is usually a drawback for most antibody projects and applications, when generating a PTM antibody the constrained number of epitopes makes finding reactive antibodies against only the PTM site far more tractable.

Peptide Antigen Limitations

While peptide antigens are attractive due to their cost and speed of generation, it is important to consider their limitations. Where protein antigens are capable of eliciting antibodies against conformational epitopes, antibodies raised against peptide antigens only recognize linear epitopes. Their value is therefore primarily found in the context of PTM detection, although peptide generated antibodies may work in other applications. For example, anti-peptide antibodies may also perform in Western blots and ELISAs. However, the linearized protein must recapitulate the epitopes of the inherently linear peptide antigen used for immunization to assure positive results. The best way to anticipate how a peptide antigen will generate antibodies for eventual detection of native proteins is our OptimumAntigen Design Tool. While no bioinformatics tool can predict results with 100% accuracy, our design tool uses cutting edge algorithms which take into consideration sequence length, hydrophilicity/hydrophobicity, surface orientation, flexibility, and more for optimal peptide sequence selection. To learn more about the special considerations and potential advantages for using peptide antigens, click Here.

Antibody production services using peptide as antigen

If you feel a peptide antigen is right for your project, check out our MonoExpress™ Gold and PolyExpress™ Gold multi-peptide antigen packages or browse our phospho-specific antibody services for highly-specific custom antibodies for protein phosphorylation detection.

Unsure which service line is appropriate for your application? Try our Antibody Service Selection Tool.

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