The investigation of marine dissolved organic matter (DOM) using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) requires the concentration and extraction of the DOM. Reactions between extraction solvent and DOM might influence data evaluation parameters, which are used to compare DOM of different origin. Potential reactions between methanol and solid-phase extracted marine DOM (SPE-DOM) and their influence on FT-ICR MS data were studied on a molecular level. For elemental formula assignments 9 isotopes were included in the evaluation, and different strategies based on isotope ratios and mass peak intervals were applied to achieve data sets of single assignments. DOM was eluted from the sorbent with methanol, methanol-13C-D4 and acetonitrile and stored at 20°C and -20°C. Under both storage conditions H/D exchanges were detected. In addition, esterifications were detected in the extract stored at 20°C, but did not result in significant differences in the mass peak magnitudes. Hence, no changes of the weighted average H/C and O/C ratios or other values such as Kendrick mass defect (KMD) and double bond equivalents (DBE) were observed. Acetonitrile was tested as an alternative solvent. Both, methanol or acetonitrile can be used to extract marine DOM from sorbents if samples are immediately stored at -20°C after the SPE process. However, FT-ICR MS data of DOM samples extracted with different solvents showed substantial differences as expected and should not be directly compared. © 2010 Elsevier B.V.