Gas Chromatography Mass Spectroscopy (GC-MS)

Gas Chromatography-Mass Spectroscopy combines two instrumental systems: a gas chromatograph component where the sample is volatized, followed by a mass spectrometer, which filters the incoming gaseous particles by their mass. This system outputs a quantitative representation of the chemicals present in a sample.

In the GC component, the sample is vaporized and accelerated with a carrier gas (typically He or Ar) into a chromatographic column, where the sample particles begin to separate based on their variable interactions with the column walls. They are carried onward to pass through an ionizing domain, which imbues the incoming particles with charge.

Finally, the sample ions continue to travel through an electrostatic field, which filters them according to their mass / charge (m/z) ratio. They arrive at a detector which reads out the number of incident particles associated with each mass increment, to produce a spectrum of peaks at the characteristic m/z ratios of all chemical constituents of the sample.

GC-MS is distinct from ICP-MS in that it captures more molecular structure information for organic samples, and can be used to separate and quantify compounds in chemical mixtures.

Experimental modes for GC-MS

Mode How it Works Why it’s used
Standard GC-MS Heat induced vaporization of the sample produces particle analytes that are carried through a chromatograph column, ionized, and then separated by mass to generate a final spectrum. Industry standard for validating purity and chemical content of organic solvents Biochemistry and pharmaceutical analysis Volatile compound analysis
Headspace GC-MS Liquid samples stored in airtight environment are transferred to container with headspace above the fluid. The sample is heated, and vapor phase particles are allowed to equilibrate. Over time, this concentrates volatile analytes in the headspace which are extracted and analyzed using standard GC-MS. Accurately isolates volatile organic compounds from liquid / aqueous samples
Pyrolysis GC-MS The sample is subjected to very-high temperatures in a deoxygenated environment, stimulating pyrolysis. Large, complex molecules are fractured into smaller fragments and then analyzed using standard GC-MS. Identifies additives and low-concentration contaminants Evaluates thermal degradation of the sample under differential chemical environments
Thermal Desorption GC-MS Adsorbent compounds within the sample surface are captured by an applied flow of gaseous sorbent molecules. The mixture travels through a specialized chamber before entering the GC-MS, which filters the sorbents to leave only the adsorbed species. Selectively characterizes adsorbed compounds Accurately determines vapor chemical composition Improves detection threshold for GC-MS

Measurements from GC-MS

  • Molecular composition (solid / liquid / gas)
  • Identification of chemicals in a mixture
  • Quantification of compounds and molecular fragments


  • What it is great for:
    • Identification of impurities and contamination in organic compounds / solutions
    • Quality assurance of chemical purity
    • Characterization of small molecules and volatiles
    • Biomolecule analysis
  • Limitations:
    • Requires time-intensive data analysis / interpretation
    • Destructive
    • Cannot directly analyze nonvolatile, polar, or combustible samples


Agilent Technologies 7890A GC
The 7890A model gas chromatograph employs improved electro pneumatics to achieve industry leading retention time locking precision. Upgraded microfluidics controls and robust backflush components allow for rapid oven cool down and accelerated GC thermal maps. This GC includes its own internal detection systems to deploy even more advanced analysis in GC-MS measurements, and accepts a broader array of sample types and analyses within even the GC alone

Agilent Technologies 59758 XLMSD
This high performance mass spectrometer has expanded qualitative characterization capabilities: intelligent auto-sequencing, intrinsic semi-quantitative concentration determination for non-calibrated analytes, and fully automated control of reagent gas and ionization source tuning. This system can accommodate up to four simultaneous signal acquisitions, with two distinct mass spectrometer detectors integrated for improved accuracy by parallel detection. A hyperbolic gold-coated quadrupole analyzer facilitates analysis of molecules up to 1050 u, with precision mass sensitivity and stability even at scan speeds up to 10,000 u / sec.