Interpretation of negative-ion chemical ionization GC-MS and GC-MS/MS mass spectra of perfluorinated organic analyte derivatives: Consideration of reduction reactions in the gas phase.

The main priniciples of gas chromatography-mass spectrometry (GC-MS) and gas chromatography-tandem mass spectrometry (GC-MS/MS) are: 1) separation of mostly derivatized analytes in the lumen of temperature-programmed gas chromatography (GC) fused-silica capillary columns, 2) ionization of gaseous charge-free analyte derivatives in the ion-source by means of electrons (electron ionization, EI) or in combination with a reagent gas such as methane (chemical ionization, CI), and 3) separation of simply ionized analytes or fragments in electric and/or magnetic fields due to their mass-to-charge ratio (m/z). EI generates (radical) cations, whereas CI is used to analyze either simply positively (positive-ion chemical ionization, PICI) or simply negatively charged analytes (negative-ion chemical ionization, NICI). In general, NICI in combination with the use of fluorinated (F) derivatization reagents is used in quantitative analyses as fluorinated analytes are softly ionized thus producing anions in high abundance and of high intensity. In quantitative analyses by GC-NICI-MS and GC-NICI-MS/MS, the position of the negative charge in the detected anions is secondary and in many cases unknown. The question of the position of the negative charge in analyte anions formed by NICI in GC-MS and GC-MS/MS is basically of theoretical interest and poorly addresed. The present article discusses this issue in detail. Previously reported GC-NICI-MS and GC-NICI-MS/MS quantitative methods for different classes of analytes, such as amino acids, fatty acids and drugs alongside their H-, C-, N- and O-isotopologs, after derivatization with fluorinated reagents including pentafluorobenzyl bromide (PFB-Br), pentafluorobenzoyl chloride (PFB-COCl) and pentafluoropropionic anhydride (PFPA) serve as examples and resources of data. ChemDraw Professional software was used to construct chemical structures of analytes and ions found in GC-NICI-MS and GC-NICI-MS/MS mass spectra. The results of the present study provide unique insights into the gas-phase reactions that take place in the ion-source of GC-MS and in the collision-chamber of GC-MS/MS instruments mainly based on the quadrupole (Q) technology. Paradoxically, the negative charge cannot be always assigned in precursor and product ions by standard rules of chemistry, unlike in EI and PICI. For example, PFB esters of fatty acids and eicosanoids (R-COO-PFB) ionize to form their carboxylates with the negative charge being definetly located in the carboxylic groups (R-COO, [M-PFB]). In contrast, methyl ester pentafluoropropionyl derivatives of amino acids ionize readily and abundantly under NICI conditions, yet the negative charge cannot be always asigned with apodictic certainty, even not for the calibrating/tuning compound perfluorotributylamine (PFTBA). The paradox vanishes when considering gas-phase reactions in the ion-source as reduction reactions of secondary electrons with analytes molecules. The present work should be helpful guide in intepreting GC-NICI-MS and GC-NICI-MS/MS mass spectra of derivatized analytes and their isotopologs, as well as in developing analyte-specific quantitative methods for endogenous and exogenous substances including drugs in biological samples.