Journal of the American Society for Mass Spectrometry

, Volume 9, Issue 1, pp 1-7

First online:

Direct comparison of infrared and ultraviolet wavelength matrix-assisted laser desorption/ionization mass spectrometry of proteins

  • Shufang NiuAffiliated withRockefeller University
  • , Wenzhu ZhangAffiliated withRockefeller University
  • , Brian T. ChaitAffiliated withRockefeller University Email author 

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In an effort to gain an understanding of the processes governing matrix-assisted laser desorption/ionization (MALDI), we made a direct comparison of ultraviolet (UV)- and infrared (IR)-MALDI linear time-of-flight mass spectra of proteins obtained from the same samples and matrices (on the same sample surface), using two different lasers, each having short duration (<10-ns) pulses, i.e., a tunable wavelength Nd:yttrium aluminum garnet (YAG) pumped optical parametric oscillator laser operating at 2.94 µm and a Nd:YAG laser operating at 355 nm. We observed that (1) the IR-MALDI and UV-MALDI spectra of a given protein from the same matrix were strikingly similar; (2) protein ions produced by IR-MALDI experienced less fragmentation than those produced by UV-MALDI; and (3) photochemical adducts produced during UV-MALDI were absent in IR-MALDI. These results lead us to speculate on the mechanisms for the ionization process in UV- and IR-MALDI. Because photons with a wavelength of ∼3 µm are unlikely to effect electronic excitation of the matrix at the irradiance used for MALDI, we propose that ionization in IR-MALDI occurs as a natural consequence of the solid-to-gas phase transition induced by the IR irradiation, and involves proton transfer reactions in the intermediate phase between solid and gas. The strikingly similar UV- and IR-MALDI mass spectra leads us to the additional proposal that ionization in UV-MALDI may also be a natural consequence of the phase transition and that electronic excitation may not play a primary role in the ionization process.