Isotopic ratios:

The pattern of peaks comes into existence for a molecular ion frequently indicates the presence of specific halogens like chlorine or bromine. This is since each of these elements has a significant proportion of two naturally occurring isotopes. Because the position of the peaks in the mass spectrum depends upon the mass of each individual molecular ion, molecules consisting of different isotopes will appear at different positions on the spectrum. Chlorine takes place naturally as two isotopes (³⁵Cl and ³⁷Cl) in the ratio 3: 1. The meaning of this is that the spectrum of a compound consisting of a chlorine atom will have two peaks for the molecular ion. The two peaks will be two mass units apart along with a ratio of 3: 1. For instance ethyl chloride will have two peaks for C₂H₅ ³⁵Cl and C₂H₅ ³⁷Cl at m/e 64 and 66 in a ratio of 3: 1.

The naturally abundant isotope for carbon is ¹²C. Though, the ¹³C isotope is also present at a level of 1.1%. This can effect in a peak one mass unit above the molecular ion. For methane, the relative ratios of the peaks because of ¹²CH₄ and ¹³CH₄ are 98.9: 1.1, and thus the peak for ¹³CH₄ is extremely small. Though, as the number of carbon atoms increase in a molecule, there is a greater probability of a molecule consisting of a ¹³C isotope. For instance, the mass spectrum for morphine depicts a peak at m/e 308 and a smaller peak at m/e 309 which is about a fifth as intense. The peak at m/e 308 is because of morphine containing carbon atoms of isotope 12. The peak at 309 is because of morphine where one of the carbon atoms is ¹³C (that is ¹³C¹²C₁₆H₁₈NO₃).

The intensity of the peak can be rationalized like this. The natural abundance of ¹³C is 1.1%. In morphine there are 17 carbon atoms and thus this raises the probabilities of a ¹³C isotope being present by a factor of 17. Though, the peak at 309 is almost 18% the intensity of the molecular ion at 308.