Sulfur content in gas oils is strictly regulated by legal specifications for environmental reasons. Gas oils are composed of various aromatic sulfur compounds, and some of them are known to be very refractory for sulfur removal reactions. Thus, an accurate analysis of sulfur compounds is important to find the appropriate operating conditions of the gas oil hydrotreating processes. Aromatic sulfur compounds contained in 23 gas oils samples were analyzed using APPI(+)-FT-ICR MS considering six replicates. Significant differences were spotted within several processed gas oils. A comparison of one feed and its corresponding effluents also confirmed the well-known refractory character of sulfur compounds such as polyalkylated dibenzothiophenes. To go deeper in the molecular exploration, chemometric tools were applied on this spectral data set including principal component analysis (PCA) and hierarchical cluster analysis (HCA). A unique data rearrangement was performed directly inspired on DBE vs carbon number plots that are systematically used in petroleomics studies. Then, these chemometric tools provided a successful classification of each type of gas oils. The PCA model has also been validated on mixed blends allowing us to conclude that it could be applied to unknown samples in order to identify the process used to produce them. Moreover, the exploration of the generated loadings revealed key types of molecules driving the classification such as C3-DBT which is a dibenzothiophene core with three additional carbon atoms. Indeed, it is known to remain mainly in deeply hydrotreated samples, validating previous observations regarding its potential refractory character. The ability of chemometric tools to extract specific molecular information from ultra-high resolution MS spectra reveals its huge potential for an exhaustive study of highly complex mixtures such as crude oils.