Hi I'm Gerard Sharp. Welcome to the November 2011 issue of the monthly newsletter. This month the Tech Tip is on How a GC-MS Ion Source Works. This is the last Newsletter for 2011 so I'd like to wish everyone a Merry and safe Christmas. The next newsletter will be in February 2012.

Dr Gerard Sharp...

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Tech Tip - How a GC-MS Ion Source Works


The ion source is a critical component of a GC-MS and the part which requires constant monitoring and eventual maintenance. In this article, the function of the ion source will be described and related to performance and maintenance. The purpose of the ion source in GC-MS is to:

  • remove an electron from the molecules eluting from the GC column thereby producing a charged molecule
  • break apart this charged molecule into smaller fragments
  • direct these fragments to the mass analyze
By far the most common type of ionization is Electron Ionization (EI) which was once known as electron impact ionization. This type of ionization produces consistent spectra thereby ideal for creating libraries of spectra which can be searched and compared.

 Ion Source Components

Broadly speaking, the ion source components can be categorized into three groups. The first is the source of the electrons which both cause ionization and fragmentation – the filament. Secondly, the repeller which drives the ions toward the mass analyzer. And thirdly, the ion source lenses (ion focus etc.) which focuses the resultant ions into the mass analyzer.

The filament consists of a thin wire which is resistively heated. Upon heating, this metal wire emits electrons of a certain energy. The emitted electrons then collide with molecules which are eluting from the end of the capillary column. The column in this slide is shown as a circle and is protruding perpendicular to the page. The energy associated with these electrons is measured in electron volts (eV) and is typically 70eV. This value is chosen because it is higher than the energy required to remove the first electron from an organic molecule – the first ionization potential. There is ample energy available to also fragment the molecule.

The two magnets shown here are used to collimate the electron beam into a tighter path. This results in more ionization and thus more sensitivity. Cleaning these magnets is not recommended as this may change the magnetic field strength and therefore the degree of collimation.

The ions formed have to be directed towards the mass analyzer. The main component responsible for this is the repeller. A positive potential is applied to the repeller and this potential then repels all positive ions towards the analyzer. The neutral and negative ions are lost at this stage.

Up to the end of the capillary column, the direction of movement of molecules has been due to the carrier gas flow. The movement of ions now through the mass spectrometer is based on electrostatic forces. In fact the flow direction is down away from the mass analyzer towards the vacuum system.

The formed ions, after repulsion by the repeller, need to be focused to direct as many as possible towards the mass analyzer. Also the ratio of the ions across the mass range is important to ensure consistent spectra for interpretation and library searching. The ion source lenses are responsible for these two functions. Dirty lenses can result in not only a loss in senstivity but also a change in ion ratios i.e. comparing the abundance of the low mass ions to the abundance of the high mass ions.

Ionization and Fragmentation

The energy associated with electrons emitted from the filament is 70eV. This is higher than the ionization potential of organic compounds analyzed by GC-MS and this value also results in substantial fragmentation. Changing this value will change the mass spectrum ion ratios. There is only one requirement for a chemical to be found in a commercial library of mass spectra and that is the mass spectrum must have been obtained using 70eV energy. There are usually two filaments present in the ion source, one is used and the other is a spare.

As the filament electrons ‘collide’ with the molecules eluting from the capillary column, an electron is removed from the molecule creating a positive charge. Because only one electron is removed from a pair of electrons in the original molecule, this leaves an unpaired electron which is referred to as a radical. The electron which is removed will can either be involved in a covalent bond or a lone pair (unbonded) of electrons e.g. those on a nitrogen or oxygen atom. The molecular ion is known as a radical cation and the notion used is M.+.

This diagram shows the removal of a lone (unbonded) electron from an oxygen molecule involved in a ketone group. The ‘R’ group refers to any other group bonded to the carbonyl carbon e.g. for R = CH3, the molecule is acetone

Fragmentation involves the breaking of at least one covalent bond and the creation of smaller molecules. The smaller molecules may or may not be charged. Only the positively charged molecules are detected. In this example, the single-headed arrow represents the movement of one electron. The covalent bond between the ‘R’ group (R = methyl for acetone) and the carbonyl carbon is broken by one electron of the paired electrons in the bond moving to the double bond of the carbonyl group and the other electron moving to the ‘R’ group. This creates a radical on the ‘R’ group which is not detected because the molecule is not charged. The charge is retained on the other group which is detected. For acetone this would account for the loss of a methyl (15 amu) group from the molecular ion. The 43 m/z (= 58 – 15) ion is the base (most abundant) peak in the acetone mass spectrum.

Source Cleaning

The source components become dirty from column bleed, GC inlet contamination (e.g. septum) and sample contamination. As the surface of the components become contaminated, they are not as effective in their function and the voltages across the components need to be changed to maintain performance. For example, in a standard tune, the voltage of the repeller determines how many ions get repelled toward the mass analyzser. This voltage is coupled with the electron multiplier voltage to meet the required sensitivity. As the repeller surface becomes contaminated, the repeller needs to 'work' harder to drive the ions forward to the mass analyzer and the voltage increases. This is an excellent diagnostic to the cleaniness of the source.

Source cleaning nvolves removing the source from the MS and abrasively cleaning all dirty surfaces with either an alumina paste or glass paper. The components are then rinsed with a series of solvents, ultra-sonicated between each rinse, and re-installed in the MS. it is important to ensure the magnet is not cleaned as this will weaken the magnet strength and decrease sensitivity. Also, any ceramic insulators should not be cleaned with solvents as ceramic will absorb the solvent and outgas under vacuum producing contaminant ions in the spectrum. The insulators can be cleaned in a muffle furnace.

Source Cleaning Summary:

  • Clean lens surfaces 
  • Remove organic contamination and ion burn
  • Do not scratch
  • Remove organic contamination from ceramic parts
  • Sonicate to remove abrasive



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