Laser desorption-ionization mass spectrometry (LDI-MS) is used to determine Hg(II) ions by using thymine-modified chitosan-coated magnetic nanoparticles (TCTS). TCTS nanoparticles are characterized using transmission electron microscopy, X-ray diffraction, UV-vis absorption, infrared spectroscopy and LDI-MS. TCTS acts as a preconcentration probe, supports surface enhanced LDI-MS (SELDI-MS) and acts as a capping agent for Hg(II). The separation of Hg(II) via this method combined with SELDI-MS provides a sensitive and selective tool for inexpensive and fast (5 min) detection of Hg(II) with limit of detection down to 0.05 nmol for environmental samples such as tap and sea water.