Comprehensive two-dimensional gas chromatography (GC × GC) is a technique which is rapidly gaining importance for the analysis of complex samples, especially within petrochemical matrixes. Until recently GC × GC has been a technique used within analytical laboratories to characterize complex multi-component mixtures such as fuels, perfumes and organic aerosol extracts, which are difficult to analyze using conventional GC or GC-MS techniques. In the present study we will illustrate how GC × GC-qMS can be used as an effective tool to accurately monitor the conversion of a Straight Run Gas Oil (SRGO) on a Cobalt Molybdenum (CoMo) supported on an alumina sulfide catalyst. A SRGO was hydrotreated at various temperatures and liquid hourly space velocities (LHSV). The products were analyzed and attention was paid to the transformation of sulfur and aromatic compounds. Quantitative analyses using GC × GC-qMS were performed and compared to the “Simulated Distillation” and total sulfur analysis illustrating that this technique can provide a comprehensive view of the entire matrix, family of products and their distribution as well as single molecule evolution upon catalytic conversion.