; The molecular structure can be determined by taking as reference the molecular ion and then analyzing the fragments or backwards (bottom-up). Mass Spectrometry. Mass spectrometry is based on the possibility of separating a mixture of ions as a function of their mass/charge ratio. It can be used to find relative isotopic abundance, atomic and molecular mass, and the structure of a compound.. Mass Spectrometry is a process by which the atomic mass of atoms or molecules is determined. ; The fragmentation pattern depends on the chemical structure and is typical for every molecule. Key Information & Summary.