A MALDI mass spectrometer includes a radiation source, such as a gas or solid state laser, that emits a beam of radiation (typically in the UV or IR wavelengths) directed along the central axis of a linear ion trap in which analyte ions and matrix cluster ions are confined. The radiation beam has a wavelength that is strongly absorbed by the matrix cluster ions. The absorption of radiation by the matrix cluster ions produces dissociation of the matrix cluster ion into fragments having mass-to-charge ratios that lie below a mass-to-charge ratio range of interest. Thus, chemical noise associated with matrix cluster ions is reduced or eliminated.
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