High vs low resolution

In low resolution mode, a mass spectrometer gives masses to the nearest integer values. In high resolution mode, the mass of an ion can be determined to 0.0001 of a mass unit. Thus, at low resolution, each of CO, N₂ and C₂H₄ have M^+⋅ at m / z = 28 and so cannot be distinguished. At high resolution, the values would be 27.9949, 28.0062 and 28.0312 respectively so can be distinguished.

Relative Abundance Effects

Most elements exist as more than one isotope and so a sample of a compound will contain molecules, called isotopomers, with each of the possible isotopes in amounts which depend on their relative abundances. The masses of the isotopomers will differ and the mass spectrum will include separate peaks due to each of them.

Chlorine and bromine containing molecules

• Naturally occuring chlorine occurs in two main isotopes: ³⁵Cl and ³⁷Cl with relative abundances of roughly 3:1. A sample of HCl thus contains roughly 67% H³⁵Cl and 33% H³⁷Cl. The mass spectrum of HCl thus contains two molecular ion peaks with m/z 36 and 38 with relative peak heights of 3:1.
• Naturally occuring bromine occurs in two main isotopes: ⁷⁹Br and ⁸¹Br with roughly equal relative abundances . A sample of HBr thus contains roughly equal amounts of H⁷⁹Br and H⁸¹Br. The mass spectrum of HBr thus contains two molecular ion peaks with m/z 80 and 82 with equal peak heights.

As chlorine and bromine are quite common in organic and biochemistry, this can be used to quickly detect their presence:

In organic molecules containing a chlorine or bromine atom, two molecular ions peaks will be observed, separated by 2 mass units and with distinctive relative peak heights of 3:1 (Cl) and 1:1 (Br) respectively.

For molecules containing two or more chlorine or bromine atoms, the patterns get slightly more complex. For example, a naturally occuring sample of Br₂ contains 3 isotopomers: ⁷⁹Br⁷⁹Br, ⁷⁹Br⁸¹Br and ⁸¹Br⁸¹Br. As the isotopes occur with roughly equal abundances, the relative amounts of these isotopomers will be roughly 1:2:1 (as the chance of ⁷⁹Br⁸¹Br occurring will be twice that of the other two). 3 peaks will be produced each separated by 2 mass units and with relative peak heights of 1:2:1. Working out the patterns for other combinations is simply a matter of statistics and probability.

Isotopes effects due to carbon in organic molecules: M+1 peaks.

Naturally occuring carbon contains roughly 99% ¹²C and 1 % ¹³C. A sample of methane thus contains 99% ¹²CH₄, with a mass of 16, and 1% ¹³CH₄, with a mass of 17. The mass spectrum of methane thus shows a peak at m/z = 16 and a peak at m/z = 17 with 1% of the peak height.

In every organic molecule, the M⁺ ion peak will be accompanied by a second peak at 1 extra mass unit with much lower height. The extra peak is called the M+1 peak as it always occurs 1 mass unit higher.

The mass spectrum below is that of methane. Notice the small peak at m/z = 17 corresponding to the M+1 peak.
In ethane, the chance of a molecule containing one ¹³C atom is roughly twice as large as that for methane as either of the C atoms could be ¹³C. The peak height for the M+1 ion of ethane is roughly 2% of the parent ion peak.

The relative heights of the M⁺ and M+1 peaks can be used to work out the number of carbon atoms in the molecule.

Note that as ¹³C has only 1% relative abundance, the chance of a molecule containing two ¹³C atoms is very, very small and so M+2 peaks (and higher ones) can usually be ignored.