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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 themonoisotopic 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.

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Q: What is the difference between base peak and molecular ion peak in mass spectra?
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