Rationale Cold EI is defined as electron ionization of cold molecules in supersonic molecular beams (SMB). Gas chromatography/mass spectrometry (GC/MS) with Cold EI provides informative mass spectra, which combine the usual library-searchable EI fragment ions with enhanced molecular ions for improved library-based identification probabilities. However, in some cases, such as in the analysis of complex petrochemical matrices, a soft ionization method that provides only molecular ions is desirable. Methods GC/MS with Cold EI was used with a fly-through ion source at selected electron energies, including at low electron energies, in an attempt to observe molecular ions alone. Results We explored low electron energy Cold EI and found that once the sample compound is cooled by the supersonic expansion it can be reheated via reflected scattered helium atoms near the skimmer. Furthermore, once a labile molecular ion is formed it can undergo undesirable collision-induced dissociation (CID) in the same way as in tandem mass spectrometry (MS/MS), and the magnitude of such CID can be significant for labile molecular ions such as those of hydrocarbons. In order to reduce these adverse effects we reduced the helium pressure at the ion source and MS vacuum chamber by increasing the nozzle-skimmer distance. Cold EI at low electron energies was explored with a squalane isomer (C30H62) and with n-C24H50. Conclusions It was found that an increased nozzle-skimmer distance resulted in a noticeable increase in the abundance ratio of molecular ions to low mass fragment ions. Consequently, Cold EI at low electron energies and a large nozzle-skimmer distance converts EI into Soft Cold EI while further approaching the ideal of a molecular ion only ionization method.