Molecular Ion Formation in GC-PCI-TOFMS is Moiety Dependent: A Functional Group Limited Observation

Positive chemical ionization (PCI) is used in Gas Chromatography-Mass Spectrometry (GC-MS) as a complementary technique to electron ionization (EI), often enhancing molecular ion information through protonated/deprotonated molecules or through recognition of characteristic adduct species. While PCI frequently improves molecular mass assignment for labile or highly fragmenting analytes, this outcome is not universal. Continued analytical use of PCI reveals compound classes for which PCI does not generate expected molecular ions or common adduction patterns. Understanding these limitations is essential for accurate spectral interpretation and confident structural elucidation. Here, a series of chemical standards, emphasizing alcohols and alkyl halides, was examined to explore correlations between functional moieties and PCI ion formation behavior.