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How are the molecular and fragment ions produced in the ion source?

In the commonly used electron ionization (EI) source, (sometimes referred to as "electron impact" in older literature), ions are generated by bombarding the gaseous sample molecules with a beam of energetic electrons as illustrated in Figure 3. (Other methods of ionization will be discussed in a later section.) In the EI technique, a mixture of positive and negative ions, as well as neutral species, is generated. The energy of the bombarding electrons is generally much greater than that of the bonds which hold the molecule together. Thus when high energy electrons interact with the molecule not only does ionization occurs, but bonds are broken and fragments are formed , giving rise to the ions other than the intact molecular ion that appear in a mass spectrum.

Although both positive and negative ions are generated in the ion source at the same time, only one polarity is recorded at a time; hence any given mass spectrum consists of either positve or negative ions. Molecules that are not ionized and neutral fragments are pumped away.

Positive-ion EI mass spectra are most commonly recorded, because many fewer negative ions are formed by this particular ionization technique than positive ions. Positive ions are propelled into the analyzer by maintaining the ion source at an electrical potential positive relative to the analyzer and by focusing with voltages applied to a lens system located between the source and the analyzer. The repeller electrode assists in focusing the ions into the analyzer. Negative ions and electrons are attracted to the positively charged electron trap.