Frequently Asked Questions

1. What makes epitopic different?

Epitopic’s epitope fingerprinting focuses on the rapid Identification of antibody epitopes by statistical means from a naïve library. For more information about our methods and approaches, please check the pages under Technologies.

2. Why is epitope fingerprinting different to epitope mapping?

Epitope mapping is the identification of antibody epitopes as part of a protein sequence or on the landscape of a protein structure. epitopic's epitope fingerprinting delivers in addition an insight into the allowed variations and structural features as they can only be obtained, when hundreds of different binding peptide variants are derived from a wet lab experiment.

3. What is the application range of epitope fingerprinting?

Epitopic provides analyses of epitopes of mono/polyclonal antibodies, even in sera.

4. Can epitopic’s epitope fingerprinting identify “structural” and discontinuous epitopes?

Discontinuous epitopes are usually not a problem, because we produce data beyond the normal output of an Ala-scan. “Structural” epitopes requiring special constraint structures, like those flanked by cysteine disulfide bridges or simply in ordinary loop structures are within the range of sequences favored in our libraries. “Structural” epitopes comprising conserved and short continuous stretches of amino acids have been identified in many cases.

5. Peptide arrays have failed, can epitopic do better?

In allergy projects at Fraunhofer IZI in Leipzig peptide arrays have been compared to epitope fingerprinting. The result was that the array missed all structural and even continuous epitopes discovered by the fingerprinting technology.

6. Why can’t one simply purchase a commercial phage display library and do epitope-fingerprinting at home?

Our libraries are of unmatched diversity and epitopic is using a special software to exploit their special features. It took ten years and projects of all kinds to reach the present level.

7. Prime interests of our customers:

a. Epitope sequence
b. Comparison of monoclonal antibodies
c. Identification of binding peptides for QC
d. Competing peptides with different affinities to the antibody for diagnostics
e. Binding peptides to predefined target structures
f. Patentability of an antibody

8. How much material is required?

10-20 µg antibody is already perfect in most cases, purity usually does not matter. For mixtures like polyclonal serum please inquire regarding the details. Use our contact form to get in touch with us.

9. Which quality of the materials is required?

Quality is of importance with respect to the integrity of the antibody. Clean versus decomposed materials from the same mAb clone but different providers can result in dramatic differences in the precision an epitope can be defined. Which is obvious, when taking into account our everyday experiences with westernblots or ELISAs.

10. How long must you wait for results?

That is depending on the setup of the project/experiments. For one monoclonal Antibody the standard analysis takes around 2-3 weeks. For more antibodies, the time needed will increase, but usually not more than 4-6 weeks. For questions concerning your project idea, please use the contact form to get in touch with us.

11. What is as typical project outcome?

The final report covers all epitopes of the delivered antibodies. The epitopes are usually defined at the amino acid level, a resolution otherwise only achieved by Ala-scan. The report includes sequences, alignments and a summary and analysis of the results. If there are more epitopes found, they will also be described or named in the report. For brief examples see here.

12. What is the typical project structure?

Usually, it is a twostep project:
a. In a first step selections are carried out and the resulting NGS-data is checked for matching QC-criteria. If the antibody is of limited quality and the QC is not passed, the customer will only pay the upfront fee covering this step.
b. In a second step, often in close exchange with the customer, the data is analyzed and further processed to identify the epitopes and, where necessary, peptides for all kinds of applications. See here.

13. How do we compare to other methods?