Matrix-assisted laser desorption/ionization combined with time-of-flight mass spectrometry (MALDI/TOF-MS) was used for the analysis of low molecular mass compounds. Three classes of molecules were studied: organic acids, salts of oxyanions and amine-based chelating compounds. Mass spectra from samples of citric, propionic, butyric, oxalic and stearic acid; ethylenediaminetetraacetic acid (EDTA), N-(2-hydroxyethyl) ethylenediaminetriacetic acid (HEDTA), ethylenediamine N,N′-diacetic acid (EDDA) and nitrilotriacetic acid (NTA); and sulfate, nitrate, nitrite and phosphate salts were obtained. These species were analyzed alone and as mixtures in both the positive and negative ion modes. The organic acids and oxyanion salts displayed much stronger signals in the negative ion detection mode whereas chelating compounds, which contain basic amine functional groups, yielded stronger signals in the positive ion mode. This implies that detection sensitivity is often better for a particular ion mode in the analysis of small molecules containing limited classes of functional groups. In all analyses, the presence of high concentrations of sodium was found to quench the MALDI signals. To increase the detection sensitivity, some samples were processed through an ion-exchange column to remove sodium ions. This step was found to enhance the signal by two orders of magnitude over untreated samples. © 1997 by John Wiley & Sons, Ltd.