Nano Research Facility School of Engineering & Applied Science



Gas Chromatograph - Mass Spectrometer


Agilent 5975C Series GC/MSD 




Mass Spectrometry - The Basics


Mass spectrometry is used to identify unknown compounds and quantify known compounds. It is sensitive and selective and is commonly used in combination with a separation technique, such as gas or liquid chromatography, to analyze complex mixtures.


 Mass Spectrometer

After a molecule is introduced into the mass spectrometer, the molecule is first ionized, then fragmented. Following this, the ions can be selected and counted.  A plot of the ion abundance versus the mass-to-charge ratio is a mass spectrum.

 Vacuum System

 For proper operation, the interior of the mass spectrometer must be evacuated. The ion source, mass filter, and detector all are under vacuum.  The vacuum system makes it possible  for ions to move from the ion source  to the detector without colliding with other ions and molecules.

 Sample Inlet

The first step to producing a mass spectrum is directing molecules into the mass spectrometer through the sample inlet.  Typically, the molecules go from atmospheric pressure to a lower pressure as they move through the inlet.  Gas, liquid, and solid compounds can be introduced into the ion source through specially designed inlets. In all cases, the sample must be in the vapor state when it enters the ion source.

Ion Source

Before the mass spectrometer can analyze a sample, the sample molecule must be ionized. In the ion source, the molecules go through an ionization and fragmentation process. The ions are then directed into the mass filter.

 Mass Filter

The mass filter allows selected ions to move from the ion source to the detector. In the mass filter, the ions are separated based on their mass-to-charge ratio (m/z). Only the ions that match the mass filter parameters are passed through the mass filter at a given time.


 A detector is used to collect and count ions. The detector counts the ions and a signal is generated that is proportional to the total number of ions. Once an ionized sample has been filtered by mass-to-charge ratio in the mass filter,  the ions are detected and reported to the data system.          

Use the following links for more information:




GC-MS Reference Guide