Atmospheric pressure Penning ionization mass spectra of methanol were measured as functions of Ar or He gas pressure in the first vacuum chamber, the position of the skimmer, and the voltage applied between the orifice and the skimmer. When the orifice and the skimmer were coaxial with a distance of 4 mm, the distribution of CH3OH2+(CH3OH)n clusters was only weakly dependent on both Ar pressure (in the range of 19-220 Pa) and orifice-skimmer voltage (in the range of 1-45 V). The ion/molecule reaction CH3OH2+ + CH3OH --> CH3+(CH3OH) + H2O was observed in the free jet expansion, especially at high orifice-skimmer voltage values. When the orifice and the skimmer were off-centered and the distance between them was increased to 18 mm, the formation of large CH3OH2+(CH3OH)n clusters, as well as their dissociation, were seen. The endothermic proton transfer reaction, CH3+(CH3OH) + CH3OH --> CH3OH2+ + CH3OCH3, occurred at high orifice-skimmer voltage. The collision-induced dissociation of cluster ions by He gas in the first vacuum chamber was much more efficient than by Ar. These results demonstrated that the mass spectra are highly dependent on skimmer position and on orifice-skimmer voltage and that ions observed by mass spectrometry do not necessarily reflect the abundance of ions produced in the atmospheric pressure ion source.
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