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Fourier Transform Ion Cyclotron Resonance Mass spectrometry (FTICR MS) is widely used to explore molecular space of humic substances. However, it cannot easily distinguish between structural isomers. We have developed an approach of selective H/D exchange (HDX) coupled to FTICR MS, which provides information about C-H bonds of individual species. This study demonstrates feasibility of comparing structures with common molecular formulas identified in HS from different sources. We believe that combination of different selective isotope abeling techniques will enable identification of individual molecular compartments of natural HS