GCMS: How Does It Work?

How does the GCMS work?

The GCMS instrument is made up of two parts. The gas chromatography (GC) portion separates the chemical mixture into pulses of pure chemicals and the mass spectrometer (MS) identifies and quantifies the chemicals.

The GC separates chemicals based on their volatility, or ease with which they evaporate into a gas. It is similar to a running race where a group of people begin at the starting line, but as the race proceeds, the runners separate based on their speed. The chemicals in the mixture separate based on their volatility. In general, small molecules travel more quickly than larger molecules.

The MS is used to identify chemicals based on their structure. Let’s say after completing a puzzle, you accidentally drop it on the floor. Some parts of the puzzle remain attached together and some individual pieces break off completely. By looking at these various pieces, you are still able to get an idea of what the original puzzle looked like. This is very similar to the way that the mass spectrometer works.

1. Gas chromatography (GC)

   1. Injection port – One microliter (1 µl, or 0.000001 L) of solvent containing the mixture of molecules is injected into the GC and the sample is carried by inert (non-reactive) gas through the instrument, usually helium. The inject port is heated to 300° C to cause the chemicals to become gases.
   2. Oven –The outer part of the GC is a very specialized oven. The column is heated to move the molecules through the column. Typical oven temperatures range from 40° C to 320° C.
   3. Column - Inside the oven is the column which is a 30 meter thin tube with a special polymer coating on the inside. Chemical mixtures are separated based on their votality and are carried through the column by helium. Chemicals with high volatility travel through the column more quickly than chemicals with low votality.
      
      
      

2. Mass Spectrometer (MS)

   1. Ion Source: After passing through the GC, the chemical pulses continue to the MS. The molecules are blasted with electrons, which cause them to break into pieces and turn into positively charged particles called ions. This is important because the particles must be charged to pass through the filter.
   2. Filter– As the ions continue through the MS, they travel through an electromagnetic field that filters the ions based on mass. The scientist using the instrument chooses what range of masses should be allowed through the filter. The filter continuously scans through the range of masses as the stream of ions come from the ion source.
   3. Detector – A detector counts the number of ions with a specific mass. This information is sent to a computer and a mass spectrum is created. The mass spectrum is a graph of the number of ions with different masses that traveled through the filter.
      
      
      

3. Computer

   1. The data from the mass spectometer is sent to a computer and plotted on a graph called a mass spectrum.

Data Analysis