On hidden and visible charges in mass spectrometry: alternative approaches in mass spectral interpretation

Gas chromatography-mass spectrometry (GC-MS) mass spectra of organic molecules contain ions that are generated in the ion-source of GC-MS apparatus. Electron ionization (EI) generates cations; chemical ionization (CI) generates either positive ions (PICI) or negative ions (NICI). GC-EI-MS and GC-NICI-MS mass spectra often contain ions to which the positive or negative charge cannot be definitely assigned to a particular atom of the ionized molecule. In this article, this charge is called hidden in contrast to the clearly assignable visible charge. It is helpful in interpreting EI and NICI mass spectra to consider that, basically, EI is an oxidation reaction and NICI is a reduction reaction that take place in the gas phase in the ion source. The underlying mechanisms of EI and NICI are not fully understood. It is assumed that ionization of molecules is induced by external electrons on certain atoms of the neutral molecules. In general, EI is considered to be a 1-electron oxidation reaction due to ejection of an electron from the molecule caused by a beam of energetic primary electrons (e_P^-) emitted by the cathode. In general, NICI is considered to be a 1-electron reduction reaction due to the uptake/capture of a secondary electron (e_S^-) produced by the EI of a reagent gas such as methane, or of a slowed down primary electron (_sde_P^-). In the present work, the generally accepted and currently widely used approach for the interpretation of EI mass spectra is called the classical approach. The present work proposes an alternative approach for the interpretation of EI and NICI mass spectra. Published GC-EI-MS and GC-NICI-MS mass spectra of organic molecules, including nitrogen-free and nitrogen-containing molecules, such as the tuning compound perfluorotributylamine (PFTBA), were re-analyzed and re-interpreted by the alternative and the classical approach for comparison. Chemical structures of molecules, ions and radicals have been constructed using ChemDraw software. The alternative approach allows both visible and hidden (i.e., non-visible) positive and negative charges on organic molecules in GC-EI-MS and GC-NICI-MS mass spectra to be described. The proposal is in agreement with the laws and rules of chemistry and mass spectrometry.