The sample flows through the column experiencing the normal separation processes. As the various sample components emerge from the column opening, they flow into the capillary column interface.
Some interfaces are separators and concentrate the sample via removal of the helium carrier.
The sample then enters the ionization chamber. Two potential methods exist for ion production. For electron impact ionization a collimated beam of electrons impact the sample molecules causing the loss of an electron from the molecule. When the resulting peak from this ion is seen in a mass spectrum, it gives the molecular weight of the compound. Some of the molecular ions fragment into smaller daughter ions and neutral fragments.