Epitope Mapping Service via HDX MS.
RapidHDX-MS™ is our mass spectrometry based epitope mapping service, that can identify the binding site of an antibody to its corresponding antigen with the highest confidence and resolution. Our HDX MS service can study complex binding, identify linear and conformational epitopes. Integrated MAbSilico AI enables us to scale up to 100’s of mAbs at a time.
HDX-MS Service – How It Works.
The HDX-MS Epitope Mapping Workflow
Hydrogen-Deuterium-eXchange Mass Spectrometry (HDX-MS) measures the exposure levels of amide hydrogen atoms on the surface of a protein or protein complex. The first step causes the exposed hydrogen atoms to be readily exchanged with deuterium. Hydrogen atoms that are buried within the protein structure – for instance at the binding site of an antibody-antigen complex – are not exchanged as readily. By examining the peptides using Bottom-up mass spectrometry, and comparing them with the amino acid sequence, it is then possible to determine which regions are the binding locations between the interacting partners.
- Labeling – incubate different fractions with D2O solution in a time series
- Quench – chill and control temperature to prevent further exchange or back-exchange
- Digest – prepare peptides for analysis
- LC-MS/MS
- Data processing – determine deuterium uptake of digested peptides acid and identify binding site(s)
- Comparison – compare similar samples – e.g. antibodies with similar sequences


NEW – Integrating AI with our HDX-MS Epitope Mapping Service
In epitope screening analyses, 100’s of antibodies are first sorted into bins based on their predicted epitopes using MAbSilico AI. Subsequently, HDX-MS experiments confirm epitope predictions and increase resolution. These experimentally determined epitope maps are fed back to the AI to refine the epitope predictions for related antibodies. In single antibody-antigen analyses, MAbSilico AI generated epitope predictions can guide experimenters to more detailed study of certain regions, or simply increase confidence in the results.
Applications of our HDX-MS Services
While our RapidHDX-MS™ service is commonly used for epitope mapping in an antibody-antigen interaction, it can also be used to study other protein-protein interactions, protein conformation changes, multi-protein complexes, small molecule interactions with proteins, disulfide linked proteins, glycosylation sites, protein interactions with DNA or RNA, disordered proteins, etc. Note that the AI-powered workflows are only available for antibody-antigen interactions at this time.

Advantages of Our HDX-MS Services.
High Resolution Epitopes Even for Large Ab:Ag Complexes.




Quality and Expertise in Epitope Mapping.
With over 7 years of experience in HDX-MS services, we are capable of working with a variety of analytes and ligands, and novel projects. No two projects are ever the same and so experimental conditions are always individually optimized for overall project success.

