Gas Chromatography – Mass Spectrometry (GC-MS)

Gas Chromatography – Mass Spectrometry (GC-MS) is a combined instrumentation that allows for qualitative analysis of complex solutions. GC-MS is heralded as one of the primary methods available for qualitatively identifying the molecular makeup of a sample. Gas chromatography (GC) divides molecules based on their chemical properties with regards to an internal column gas affinity. Mass spectrometry (MS) fragments components, ionizing them and then separating these fragments based on their mass-to-charge ratio (M/Z). To generalize the process, GC separates elements of a complex sample and MS provides details of these individual components lending to their identification.

A chemist can take a sample and use this device to separate the solution into its individual components. Once the components are separated the chemist can determine the identity of the individual components and the concentration of each.
GC-MS can be used in:

  • Petrochemical industry
  • Pharmacology
  • Forensics
  • Manufacturing
  • Law enforcement
  • Litigation cases

To provide services such as:

  • Precise identification of complex mixtures of similar compounds
  • Prospecting
  • Refining
  • Compliance Testing
  • Determining purity of reagents
  • Identifying synthesis products
  • Identifying medicines and illicit drugs
  • Drug testing
  • Forensic analysis
  • Environmental contaminant identification
  • Manufacturing quality control

The GC’s reports reveal the spectral output of a solution’s components. The purpose of this report is to divide a complex mixture into discrete chromatographic peaks each containing only one substance. Additively an MS generates what is called a mass spectrum which represents the abundance of fragments with particular mass to charge ratios. This allows a researcher to piece together what is called a parent mass, thus identifying the precise elements comprising the solution. So while GC provides insight into how much of differing elements there are within a solution, MS provides the pieces necessary to identify the individual elements. Combined GC-MS provides conclusive qualitative data. The GC-MS process is outlined below.

The first thing to note is that in order to provide conclusive results a technician must run a control standard before running a specimen. This means a sample containing a verified composition identical to the presumed contents of the specimen for testing must be run through GC-MS under identical conditions of the specimen testing. The technician must also maintain record of the time at injection and time of elution (as described below).


1. The sample solution is injected into the GC injection inlet which is temperature controlled and set to the temperature necessary to immediately vaporize the sample upon dissemination. This is what is called the mobile phase as the vaporized sample travels into the chromatographic column by way of an inert carrier gas.

2. As the sample travels through the column the independent compounds of the sample separate as they interact in varying ways with the column’s coating and carrier gas. This is called the stationary phase as the compounds are interacting with a stationary material. As each compound interacts at a differing rate those that interact at the highest rate will elute from the column first. This separation process can be adjusted by altering the temperature of this stationary phase, or by adjusting the pressure of the mobile phase. A temperature increase affects the elution rate as compounds with low boiling points will escape the column sooner than those with higher boiling points. This reveals two distinct forces at work separating the compounds – temperature and stationary phase interactions. Note that these determining aspects must be controlled prior to the experiment and consistent throughout the testing.

3. As the unique compounds emerge from the column a detector measures the substance passing through at differing time intervals. The time elapsed between injection of the sample to elution is referred to as “retention time” (RT) and can assist in differentiating between some compounds. It is important to note that if two samples do not have equal RT those samples are conclusively not of the same substance. However, compounds with equal RT have only a possibility of being the same substance. In fact, thousands of chemicals may have the same RT and receive the same read out on the GC detector. At this stage it is possible to narrow the options as to the identity of the compounds, as a given compound will always elute from the column at a consistent RT if GC conditions are controlled. However, as previously noted, similar compounds often have the same RT and so these assumptions are inconclusive.

4. At this point mass spectrometry comes into play. The compounds, after exiting the column pass through a high voltage transfer line and are ionized into charged fragments. These particles are charged ions of defined mass. The mass of a fragment divided by its charge is referred to as the mass to charge ratio (M/Z). Most fragments have a charge of +1 and therefore the mass to charge ratio most often represents the molecular weight of the fragment. Each charged fragment travels independently to the accelerator.

5. Within the acceleration chamber an accelerating voltage causes the charged fragment to proceed with increased velocity. The voltage varies and with it particular fragments of specific mass accelerate and reach the detector. The voltage fluctuates until all fragments have reached the detector. The ions pass through this detector, called a mass analyzer, and are separated according to their mass to charge ratio.

6. When an independent ion meets the surface of the detector many electrons come out from the surface of the detector. These electrons accelerate towards a second surface where the process repeats and even more electrons are emitted and collide with yet another surface. After multiple collisions with various surfaces there are thousands of electrons generated emitting from a final surface. This results in the amplification of the original ion’s charge and is recorded as the fragment’s mass proportional to the detected charge. The charge is then sent to the computer to produce the mass spectrum.

7. The mass spectrum is a chart depicting the M/Z ratios on the x-axis, and the signal intensity (abundance) for each of the ions detected during the scan on the y-axis. Each peak represents a value for the total mass of an individual kind of ion. The height of the peak indicates the number of fragments detected of that particular mass. For any given chemical compound the mass spectrum should be the same every time it is generated. Therefore this technology allows us to accurately identify a compound. There are libraries of sample mass spectrum which allow for easy comparison and generate lists of likely identities with the associated probabilities. These sample analysis of known compounds are called references and are used to identify the particles within a given sample by matching retention time and the pattern of ion fragmentation.

The ability to correctly identify the compounds relies heavily on the technician’s understanding and capabilities. Though computers and libraries can provide valuable information, alone technology cannot determine molecular structure as well as a skilled analyst. GC is not a reliable source for identifying substances as multiple compounds are known to generate the same RT. MS will provide us with specific data. This is why the combination in GC-MS testing allows for the greatest analytical results, providing both retention times and mass spectral data. This data must then be weighed by a knowledgeable analyst in order to define the compounds in question and give conclusive proof for identification.


To see what services our scientists use GC-MS for click here.