Interpreting spectra in Mass Spetrometry

A simple spectrum, that of methanol, is shown here. CH3OH+. (the molecular ion) and fragment ions appear in this spectrum. Major peaks are shown in the table next to the spectrum. The x-axis of this bar graph is the increasing m/z ratio. The y-axis is the relative abundance of each ion, which is related to the number of times an ion of that m/z ratio strikes the detector. Assignment of relative abundance begins by assigning the most abundant ion a relative abundance of 100% (CH2OH+ in this spectrum). All other ions are shown as a percentage of that most abundant ion. For example, there is approximately 64% of the ion CHO+ compared with the ion CH2OH+ in this spectrum. The y-axis may also be shown as abundance (not relative). Relative abundance is a way to directly compare spectra produced at different times or using different instruments.

EI ionization introduces a great deal of energy into molecules. It is known as a "hard" ionization method. This is very good for producing fragments which generate information about the structure of the compound, but quite often the molecular ion does not appear or is a smaller peak in the spectrum.

Of course, real analyses are performed on compounds far more complicated than methanol. Spectra interpretation can become complicated as initial fragments undergo further fragmentation, and as rearrangements occur. However, a wealth of information is contained in a mass spectrum and much can be determined using basic organic chemistry "common sense".

Following is some general information which will aid EI mass spectra interpretation:

Molecular ion (M .+):If the molecular ion appears, it will be the highest mass in an EI spectrum (except for isotope peaks discussed below). This peak will represent the molecular weight of the compound. Its appearance depends on the stability of the compound. Double bonds, cyclic structures and aromatic rings stabilize the molecular ion and increase the probability of its appearance.

Reference Spectra: Mass spectral patterns are reproducible. The mass spectra of many compounds have been published and may be used to identify unknowns. Instrument computers generally contain spectral libraries which can be searched for matches.

Fragmentation:General rules of fragmentation exist and are helpful to predict or interpret the fragmentation pattern produced by a compound. Functional groups and overall structure determine how some portions of molecules will resist fragmenting, while other portions will fragment easily. A detailed discussion of those rules is beyond the scope of this introduction, and further information may be found in your organic textbook or in mass spectrometry reference books. A few brief examples by functional group are described (see examples).

Isotopes:Isotopes occur in compounds analyzed by mass spectrometry in the same abundances that they occur in nature. A few of the isotopes commonly encountered in the analyses of organic compounds are below along with an example of how they can aid in peak identification.

Relative Isotope Abundance of Common Elements: