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Hydrogen/Deuterium exchange coupled to high-resolution mass spectrometry has become a powerful analytical approach for structural investigations ofbiomacromolecules and their complexes. Recently new in source HDX methods were developed based on soft ionization techniques, such as electrospray ionization (ESI), with HDX implemented in source. Such an approach allows identification of labile and non-labile hydrogens in organic molecules. Mechanism for in ESI-source HDX of labile and non-labile hydrogens was investigated with standard compounds. New possibilities of in ESI-source HDX for a structural characterization of individual compound in complex mixtures such as crude oil, natural organic matter (NOM) is demonstrated.