The identification of the structure of a chemical compound is perceived as one of the most time consuming and laborious task in chemical analysis. This is often performed through analytical techniques such as mass spectroscopy (MS) and nuclear magnetic resonance (NMR) with MS being used more often due to its higher sensitivity and specificity . In MS, the molecules that are present in a biological sample are first separated using a chromatographic technique, such as liquid chromatography (LC) and gas chromatography (GC), with the latter being used more commonly . After the separation, the molecule is fragmented into positive or negative charged ions using an ionization source such as electron ionization (EI), chemical ionization (CI) and electrospray ionization source (ESI) . What the instrument records is the mass-to-charge (m/z) ratios of the generated fragment ions. The information that is collected from this process is presented in the mass spectrum which is a graph with the m/z of each recorded fragment in the horizontal axis and the relative abundance in the vertical axis. In order to obtain more detailed information on the query structure, a sequential fragmentation process is often used called tandem mass spectrometry . Once the molecule has been fragmented into ions, a set of them, called precursor ions, is selected and further fragmented to generate MS2 (also called MS/MS) spectra. These second-level ions can be fragmented even further giving MS3 spectra and so on. The peaks and their intensity in the resulting spectrum depend not only on the structure of the chemical molecule that is being fragmented but also on the experimental conditions, that is the instrument used, the collision energy, the selected precursor ion and the ionization mode, as it is illustrated in Figure .