<p>Natural organic matter (NOM) is a highly complex mixture of natural organic molecules. The hyphenation of liquid chromatography (LC) with ESI-FT-ICR MS for the molecular characterization of NOM have shown to be a promising approach. However, due to changing solvent composition during gradient elution in LC-FT-ICR-MS, ionization conditions also change throughout the chromatographic separation process. In this study, we applied a post-LC column counter gradient (CG) to ensure stable solvent conditions for transient ESI-MS signals. SRFA and a peat pore water samples were used as representative dissolved NOM samples for method development and validation. Our results show that in the isocratic range segment, the TIC intensities of CG was increased by a factor of 1.5 fold, as compared to the standard gradient (SG) method. In addition, the application of the CASI mode for low abundance fractions revealed over 3 times more molecular formulas (especially for CHNO, CHOS, CHNOS formula classes) than in full scan mode. The number of detected highly polar NOM compounds (with elemental ratios H/C < 1, O/C > 0.6) were more than 20 times larger for CG-LC mode as compared to direct infusion (DI) (5715 vs 266 MF).We conclude that the new CG-LC-FT-ICR MS method achieved a novel insight into the highly polar fractions of NOM, which are inaccessible in conventional DI measurements.</p><p>Key words: Natural organic matter (NOM), online LC-FT-ICR MS method, CASI mode, ESI</p><p>&#160;</p>