Mass spectrum analysis
Mass-spectrum analysis is an integral part of mass spectrometry. Organic chemists obtain mass spectra of chemical compounds as part of structure elucidation and the analysis is part of every organic chemistry curriculum.
Basic peaks 
Electron ionization mass spectra have several distinct sets of peaks: the molecular ion, isotope peaks, fragmentation peaks,metastable peaks.
In the mass spectra the molecular ion peak is often most intense, but can be weak or missing. The molecular ion is a radical cation (M+.) as a result of removing one electron from the molecule. Identification of the molecular ion can be difficult. Examining organic compounds, the relative intensity of the molecular ion peak diminishes with branching and with increasing mass in a homologous series. In the spectrum for toluene for example, the molecular ion peak is located at 92 m/z corresponding to its molecular mass. Molecular ion peaks are also often preceded by a M-1 or M-2 peak resulting from loss of a hydrogen radical or dihydrogen.
The peak with the highest intensity is called the base peak which is not necessarily the molecular ion.
More peaks may be visible with m/z ratios larger than the molecular ion peak due to isotope distributions, called isotope peaks. The value of 92 in the toluene example corresponds to the monoisotopic mass of a molecule of toluene entirely composed of the most abundant isotopes (1H and 12C). The so-called M+1 peak corresponds to a fraction of the molecules with one higher isotope incorporated (2H or 13C) and the M+2 peak has two higher isotopes. The natural abundance of the higher isotopes is low for frequently encountered elements such as hydrogen, carbon and nitrogen and the intensity of isotope peaks subsequently low. In halogens on the other hand, higher isotopes have a large abundance which results in a specific mass signature in the mass spectrum of halogen containing compounds.
Peaks with mass less than the molecular ion are the result of fragmentation of the molecule. Many reaction pathways exist for fragmentation, but only newly formed cations will show up in the mass spectrum, not radical fragments or neutral fragments.
Metastable peaks are broad peaks with low intensity at non-integer mass values. These peaks result from ions with lifetimes shorter than the time needed to traverse the distance between ionization chamber and the detector.
The fragmentation pattern of the spectra beside the determination of the molar weight of an unknown compound also suitable to give structural information, especially in combination with the calculation of the degree of unsaturation from the molecular formula (when available). Neutral fragments frequently lost are carbon monoxide, ethylene, water, ammonia, and hydrogen sulfide.
fragmentations arise from:
- In this depiction single-electron movements are indicated by a single-headed arrow.
- or the McLafferty rearrangement. As it is not always obvious where a lone electron resides in a radical cation a square bracket notation is often used.
- Ion-neutal complex formation. This pathway involves bond homolysis or bond heterolysis, in which the fragments do not have enough kinetic energy to separate and, instead, reaction with one another like an ion-molecule reaction.
Some general rules:
- A useful aid is the nitrogen rule: if the m/z ratio is an even number, the compound contains no nitrogen or an even number of nitrogens.
- Cleavage occurs at alkyl substituted carbons reflecting the order generally observed in carbocations.
- Double bonds and arene fragments tend to resist fragmentation.
- Allylic cations are stable and resist fragmentation.
- the even-electron rule stipulates that even-electron species (cations but not radical ions) will not fragment into two odd-electron species but rather to another cation and a neutral molecule.
Toluene example 
The mass spectrum for toluene has around 30 signals. Several peaks can be rationalized in this fragmentation pattern.
Isotope effects 
Isotope peaks within a spectra can help in structure elucidation. Compounds containing halogens (especially chlorine and bromine) can produce very distinct isotope peaks. The mass spectrum of methylbromide has two prominent peaks of equal intensity at m/z 94 (M) and 96 (M+2) and then two more at 79 and 81 belonging to the bromine fragment.
Even when compounds only contain elements with less intense isotope peaks (carbon or oxygen), the distribution of these peaks can be used to assign the spectrum to the correct compound. For example, two compounds with identical mass of 150 Da, C8H12N3+ and C9H10O2+, will have two different M+2 intensities which makes it possible to distinguish between them.
Natural abundance of some elements 
|Isotope||% nat. abundance||atomic mass|
See also 
- COmponent Detection Algorithm (CODA), an algorithm used in mass spectrometry data analysis