Tetraalkylammonium salts, commonly used as ion pair reagents in chromatography, were found to react with biological conjugates under desorption chemical ionization conditions in a mass spectrometer. The reactions occur for aromatic glucuronide and glucoside conjugates using solid samples loaded on the direct exposure probe. Evidence is presented that several mechanisms contribute to the degradative alkylation of benzo(a)pyrene glucuronide. This undesirable process can be prevented by using ammonium or trialkylammonium instead of tetraalkylammonium salts in the chromatographic separation. Nucleophilic attack on the tetraalkylammonium cations in the energized condensed phase was found to occur also for some simpler aromatic compounds.