Epitope mapping (HDX)

Hydrogen-deuterium exchange mass spectrometry (HDX MS) is a method to study protein structure and its dynamic changes. We can identify the protein interaction site, epitope mapping, and protein active site identification..etc. The principle of this method is to soak the protein into deuterium solution, which the hydrogen of the protein will be exchanged with deuterium in a neuteral environment, and the speed of hydrogen-deuterium exchange at the surface of the protein is faster than the exchange rate inside the protein, using mass spectrometry to identify the different exchange rates between different peptides will allow us to identify the structure of the protein. An easier way to understand this method is to throw two balls that are stuck together into a colored water tub and take them back out, when you pull them apart you will see that the only site that the balls are not colored are the site where they stuck together. This same method can also be used to understand drug-protein
interaction or antibody-protein interaction site.
Place the sample into a deuterium solution to perform hydrogen-deuterium exchange, digest them with protease at seven different time points (10s,30s,60s,300s,600s,1200s,4800s) and use mass spectrometry to analyze and compare with the database to identify the lowest hydrogen-deuterium exchange rate site, that site might be the protein (or drug, antibody)-protein interaction site.


Working day not including delivery time: 5 weeks

(a) Sample type: Purified protein with amino acid sequence and condition of molecules interaction
(b) Sample amount: ≥200 pmol (~10 ug for 50 kDa protein)
(c) Sample concentration: ≥4.5 pmol/uL (~0.23 ug/uL for 50 kDa protein)
(d) Sample purity: ≥90%
(e) Platform: online-Pepsin-LC, Orbitrap HDX-MS

Please click the link below for the specification of Proteomics service​
Sample requirement

1. Summary report. pdf
2. Protein-peptide report. xlsx

Q1. What other applications does HDX have besides analyzing protein-antibody interaction site?
A: HDX can also identify protein-drug interaction site, or protein conformational change site.

Q2. Is it possible for me to identify protein-drug or protein-DNA interaction site?
A: Of course, just provide us the condition of the interaction, and we will evaluate the possibility.

Q3. Can HDX used in identifying the binding region of protein and nucleic acid?
A: Yes, if you can provide the binding condition of the nucleic acid and protein, unless the DNA:Protein ratio is too high to effect the signal of spectormetry (<1:100, molar ratio, the closer the better). The purity of protein must be >90%)

Q4. Do you provide protein-protein binding condition test?
A: No, we do not provide this service.

Q5. What is the application of HDX besides analyzing the binding site of protein and antibody?
A: HDX can also analyze the binding site of protein and drugs, or the site of protein coformational change.