GC-MS? What is that???

In a few of my previous posts, and a few yet to come, I mention Gas Chromatography- Mass Spectrometry (GC-MS). It is used when we want to be able to separate and identify the different chemicals which may make up a particular aroma, food, blood sample, soil, and the list goes on! This means that it can be used to identify many things, including drugs in urine samples, poisons in blood, explosive chemicals in soil, and as you would have picked up already in my blog (see Sniff Your Soy and Making wine smell like whiskey), the different chemical components which make up a particular smell. Now is as good a time as any to explain exactly what a GC-MS is, and how it works. It is quite a complex instrument, but I will try to explain it as simply as I can, so that you get the gist of why I will talk about it so much!


Here’s the picture of the GC-MS that I use!

The name Gas Chromatography- Mass Spectrometry gives you a hint that the instrument is made up of two separate parts. The GC part of GC-MS is used to separate different chemical compounds. A gas is set up to flow through a column, which is lined on the inside with particular chemical groups (for example, OH or NH or waxes). By injecting a chemical mixture (for example, the volatiles from soy sauce) down the column, the chemicals can be separated. They separate based on how big they are (larger chemicals may take longer to travel from one end of the column to the other), or how sticky they are to the groups lining the column (certain groups on the chemicals to be separated will try to hold on to the lining of the column, and take longer to travel through the column).


A schematic of a GC.

Once the chemical components are separated, they leave the column and are sent on to the detector.  The detector is the part of the instrument that helps us to work out what the compounds are, and even how much of each compound there is. There are many possible detectors, but in this case, we will just talk about a Mass Spectrometer (MS).

The word ‘mass’ gives you a hint that we are able to identify the different chemical components by looking at their mass. The MS is able to determine the identity of the compound coming off the column by looking at the mass of the compound, as well as the way that the structure can break apart. You see, we hit the chemicals with really strong, energetic hammers known as electrons. These electrons breaks the chemicals apart in very distinct ways, which give very distinct patterns depending on the chemical. So it is as though each chemical has it’s own ‘fingerprint’ map that we can identify it by (known as a mass spectrum).


The ‘fingerprint’ of dodecane, a chemical that is made up of 12 carbons bonded to hydrogens.

Using the MS, we can not only identify the chemical by its ‘fingerprint’, but we can also work out how much of each of these chemicals there are. This is because, on the readout produced by the GCMS (known as a gas chromatogram), it shows a series of peaks. Each peak is representative of one chemical that has been separated by the GC (if the separation is a good one), and therefore each peak would have its own mass spectrum. The area under these peaks tells us how much of the chemical there is, so the larger the peak, the more of the chemical.


A gas chromatogram: The larger the peak, the more there is of that particular chemical.

We can also use what we call ‘standards’. These standards are chemicals for which we know the chemical footprint, concentration, and how long it will take to travel through the column. So if we send the standard through the GCMS, we have an accurate description of not only how long it will take to appear in the MS detector, and how big the peak would be for a certain concentration.

Wow, that was a lot of information! If it helps, here is a five minute video which may explain GC-MS to you in a different way: http://www.youtube.com/watch?v=08YWhLTjlfo



Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )


Connecting to %s