The systematic background of mass spectrometry (MS) was established by using the Valency Interaction Formula theory in an efficient manner. A new graph theoretical method was developed as a pure quantum mechanical survey and applied on a variety of molecules and assemblies to elucidate the quantum mechanical systematics behind mass spectrometry. The topological indexes and graph theoretical methods in chemistry and physics as the striking features of this new method was applied onto the mass spectra of several molecules and assemblies due to the insufficiencies of the obselete fragmentation procedures. These fundamental topological indexes were determined to make quick deductions pictorially on the mass spectra of molecules. The major fragmentation pathways for several molecules, as the striking features of Mass Spectometry, were examined in a pure theoretical way and a priori decomposition products were predicted. The systematic theory was provided in the light of our examination and a great deal of qualitative information was obtained just by knowing which interactions are soft among the others. The results are of general validity in comparison with the experimental data.