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Small Molecule Analysis by HDX MS

Background & Overview

The combination of hydrogen/deuterium exchange (HDX) and mass spectrometry (MS) is a powerful tool for exploring molecular building blocks, with applications in a wide range of research fields, from metabolomics and fluxomics to materials science and drug design and development. HDX MS can also be used to elucidate molecular structures or to study mechanisms of rapid ion dissociation. Then, by studying dynamic conformational changes, HDX MS is widely used to study protein structure and dynamics, including protein-ligand interactions.

BOC Sciences focuses on HDX MS for the study of small molecule systems, such as synthetic organic molecules, natural products, drugs and metabolites. We address a wide range of chemical and biochemical problems by providing structural and quantitative tools. Our hydrogen-deuterium exchange technology is still in full expansion to efficiently meet the application needs associated with the use of MS.

Fig.1 The different faces of HDX mass spectrometry.Fig.1 The different faces of HDX mass spectrometry.[1]

Our HDX technology

We have a large number of methods available to perform HDX. Mainly divided into solution-phase reversible HDX, stable chemical replacement of hydrogen and deuterium in solution and irreversible enzymatic HDX.

Fig.2 HDX conducted before MS analysis: (A) reversible versus (B) stable.Fig.2 HDX conducted before MS analysis: (A) reversible versus (B) stable.[1]

Solution-phase reversible HDX

Hydrogen atoms bound to heteroatoms such as nitrogen, oxygen and sulfur have unstable properties and can be easily (on millisecond timescales) replaced by deuterons when exposed to deuterating agents such as D2O or MeOD. Solution-phase HDX can mainly be analyzed by LC/MS by using proton-deuterated reagents as mobile phase.

Stable chemical replacement of hydrogen and deuterium in solution

Based on homogeneous or heterogeneous catalysts, post-incorporation is performed by direct replacement of unstable hydrogen with deuterium at stable sites in the molecular structure.

Irreversible enzymatic HDX

Incorporation of deuterium into biopolymers (proteins, DNA, RNA) based on catalytic enzymatic reactions. We can also achieve deuterium labeling of smaller biomolecules in this way.

Our Services

BOC Sciences combines HDX with MS analysis to provide services related to small molecule structural chemistry and systems biology research. Our small molecule analysis services include, but are not limited to:

Compound Characterization & Identification

  • Discrimination of isomers with different numbers of deuterated sites (i.e. compounds with the same elemental composition)
  • Drug metabolite identification during drug design and development
  • Impurity analysis and impurity characterization of novel synthetic drugs
  • Discrimination of labile hydrogen atom classes, including nitrogen-containing compounds and molecules with -OH and -SH functions

Quantitative MS measurements

  • Quantification of drug and pollutant metabolites
  • Endogenous metabolite quantification and metabolomics

Biotransformation research

  • Metabolism and drug design to improve pharmacological properties in the development of new drug candidates
  • Systems biology research

If you are interested in our services, please contact us immediately, then fill in the complete inquiry form, and we will reply to you as soon as possible.


  1. Damont A, et al. Hydrogen/deuterium exchange mass spectrometry in the world of small molecules. Mass Spectrometry Reviews. 2021: e21765.

About DCL™ Platform

BOC Sciences' DCL™ platform provides a deuterium strategy for both high-end custom markets and basic product needs. Our main business areas cover drug development, omics analysis, scientific research testing, and other markets, and strive to promote the development of biomedicine and scientific research.

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