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The lines in the mass spectrum represent the mass-to-charge ratio (m/z) of the molecular ion and the fragment ions.
Mass spectral interpretation is the process of identifying a molecule by deducing information from its mass spectrum. Interpretation is done by an "expert" or by a program that mimics an "expert." Interpretation methods can identify molecules that are not in a database.
Mass Spectra of Singly-charged SpeciesThe abundance of the molecular ion and its fragment ions are plotted versus their mass-to-charge ratio (m/z) to produce a mass spectrum. Usually, the information that one hopes to gain is the unambiguous identity of the analyte.
Mass of a Water MoleculeThe mass of a water molecule is 18 Daltons. This mass is the sum of two hydrogen atoms and one oxygen atom. If you measured the mass of numerous water molecules and recorded the number of molecules as a function of mass, this graph would result. All the water molecules have a mass of 18 Daltons. The abundance information reflects the number of molecules of a given mass that are counted.
Simple Mass SpectrumIn the ion source, many of the water molecules are ionized. If none of the ions fragment, the resulting plot is a simple mass spectrum. The x-axis of a mass spectrum is labeled m/z. This is the mass-to-charge ratio.
For these water ions, m/z=18 because the mass or the original molecule was 18 and the charge is +1.
FragmentationMost of time, a water molecule does not fragment when it is ionized. However, about 20 percent of the time, the molecule loses one hydrogen. This results in a mass spectrum with lines at m/z=17 and m/z=18.
Molecular IonThe ion formed by the removal of one electron from a molecule, without fragmentation of the molecular structure, is called the molecular ion. Because the molecular ion is the molecule with one electron stripped off, it will have the same nominal mass as the neutral molecule. All other ions in the spectrum are derived from decomposition of the molecular ion.
IsotopesThere are two isotopes of chlorine: chlorine-35 and chlorine-37. When hydrogen chloride molecules are ionized in a mass spectrometer ion source, the presence of two different masses of hydrogen chloride ions will be detected. If all hydrogen chloride ions stayed intact, a mass spectrum of hydrogen chloride would contain two peaks, one at m/z 36 and another at m/z 38.
Relative AbundanceThe relative heights of these peaks are identical to the ratio of chlorine-35 to chlorine-37 in nature. The peak at m/z=38 has a relative abundance of 33 percent.
The abundance axis can be defined in absolute abundance or relative abundance. The highest peak in the mass spectrum is the base peak and that is defined as 100 percent relative abundance.
Isotopic SignatureIn the chlorine example, the pattern of two peaks, two units apart with a relative ratio of three-to-one, is a strong indication of the presence of a single chlorine atom in the original molecule. Such a pattern is termed an isotopic signature. There are certain elements in organic mass spectrometry that have very characteristic and very dominant isotopic peaks. Classic examples of this are chlorine and bromine. Isotopic signatures can be readily observed in mass spectra.
Determining the Carbon NumberOne ways to determine the number of carbons in a singly charged species is to use the relative abundances of the carbon-13 and carbon-12 peaks.
Logical LossesFor a given molecule, only certain losses are possible based on chemical principles. Such losses are termed logical losses.