GC-MS is used to analyze samples that are thermally stable, below 850 u molecular weight, and have a boiling point below 270 degrees C.

The approximate minimum sample quantity for a GC-MS run may be compared to that of methyl stearate which needs is 50 pg per run (this applies only to the Chemical and Biological Sciences Mass Spectrometry Facility. This value varies according to instrument).

The solution in which the sample may be dissolved can vary depending on the GC column used. Generally, chloroform is the best solvent. Another solvent commonly used is methanol. Before using other solvents please check with facility personnel. Remember to use clean solvents or the contaminates will show up in your mass spectra.

The sample is injected into the GC where it is separated by a column. As the GC gas elutes from the column it is constantly monitored by the mass spectrometer. By the end of the analysis hundreds if not thousands of mass spectra are recorded.

The ion intensities in each mass spectrum is summed and this sum is plotted against time to produce a total ion chromatogram (TIC), below.

The above TIC is from 500 pg of a methyl stearate sample. The TIC is similar to a GC trace obtained using an FID detector. Notice in this sample there are three other major peaks in the TIC trace along with many minor peaks indicating the sample is impure. If the TIC trace were actually a trace from a FID detector, one would have to run a purer standard in order to identify which peak is methyl stearate.

But unlike a FID detector, when a mass spectrometer is used as a detector, mass spectral information is available for each peak. The mass spectrum for the peak labeled "methyl stearate" in the TIC trace is show below.

The mass spectrum was identified as methyl stearate by computer comparison against a mass spectral library containing over 300,000 mass spectra. This is a very powerful tool for identifying unknowns.