We report a novel analytical technique using gas chromatography/atmospheric pressure chemical ionization-mass spectrometry (GC/APCI-MS) or atmospheric pressure gas chromatography-mass spectrometry (APGC-MS), using corona discharge for analyzing nonpolar hydrocarbons, specifically for petroleum biomarkers that are important in geochemical studies of source rocks and crude oils. The advantages of applying MSE for both high- and low-energy collision simultaneously were demonstrated. The enhancement of molecular ions at low-energy MSE would facilitate the linkage with characteristic fragment ions for tandem mass spectrometry (MS-MS) experiments. The combination of quadrupole and time-of-flight (QTOF) mass analyzers renders sufficient and adequate resolution for accurate mass measurement, with measurement errors less than 1 mDa or 5 ppm for all ionic species in the hopane and sterane analyses.