Frequently asked questions
What are epitopes and paratopes, and how does HDX-MS map them?
HDX-MS is Hydrogen-Deuterium Exchange Mass Spectrometry. An epitope is the surface on the antigen that an antibody binds; the paratope is the region of the antibody, largely within the CDRs, that makes contact. HDX-MS locates both by measuring how deuterium uptake changes when the two are bound together compared with each alone.
Can HDX-MS resolve conformational epitopes?
Yes. Because the method reads solution-phase structural changes, it identifies discontinuous conformational epitopes as readily as linear ones.
Does this work for small molecules as well as antibodies?
Yes, and the experiment is the same one. Deuterium uptake of the target is measured alone and in complex, and the regions where uptake shifts mark the binding site.
What if my protein is disordered or won’t crystallize?
HDX-MS does not need a crystal or a folded, rigid target. We have worked with intrinsically disordered proteins for years and can return binding information in cases where crystallography and cryo-EM have not.
How long does a project take?
Most projects are complete three to four weeks after we receive your samples. If you need results sooner, ask us about expedited scheduling.
How much sample do you need?
Plan on roughly 200 µg of antigen and 250 µg of antibody. Proteins should be ≥90% pure and at 1 mg/mL or above, in an HDX-compatible buffer such as phosphate or Tris, and free of detergents. We can often work with lower concentrations, and we confirm buffer compatibility and quantities with you before the project starts.
What do I receive at the end?
You get a coverage map, per-peptide deuterium uptake kinetics, heat maps, and a written analytical report with the full interpretation.