Gas chromatography-mass spectrometry (GC-MS) is the fastestgrowing GC method. Mass detection, which can take a variety of forms based on the MS component, provides a dimension that conventional thermal conductivity or flame ionization detectors cannot, namely selectivity and absolute identification of both known and unknown compounds.

GC-MS is suited to every organic chemical discipline where GC is found, including the chemical, pharmaceutical, environmental, and forensics industries, as well as basic research. But the limitations of GC-MS are the same as for GC alone: compounds must be volatilized and relatively nonpolar; molecular weights are therefore limited to about 800 Dalton.

GC-MS identifies compounds based on matching a mass spectrum from a run with entries in a database or spectral library generated with the same MS technique (hardware, ionization, detection).

Whereas co-elution is common in GC, MS distinguishes closely related compounds, for example, structural isomers, on the basis of their fragmentation patterns. And while MS cannot tell mirror-image enantiomers and most diastereomers apart, GC columns can—in the case of enantiomers, with a chiral stationary phase. This is one reason why GC and MS are considered complementary techniques, and why their combination is so powerful.

Environmental Protection Agency and U.S. Pharmacopoeia GC methods are bedrock techniques used and referred to for environmental and pharmaceutical analysis, respectively. These methods have benefitted tremendously from the adoption of mass detection, notes Trisa Robarge, GC and GCMS product manager at Thermo Fisher Scientific (Austin, TX). “As regulations for both industries evolve toward lower detection limits and higher specificity, analysts have benefitted particularly from triple- quad MS, which facilitates analysis of low-level compounds from complex samples.”

Software and information technology supporting GC-MS have also greatly improved, Robarge says. Many systems today are supported by compound libraries and integrate with laboratory information management systems and/or electronic notebooks that allow archiving, managing, and sharing of analytical data.

A typical entry-level GC-MS system would likely incorporate a single-quadrupole (“quad”) detector or a more sophisticated ion trap, which allows extensive analysis of fragments and fragments of fragments—“MS/MS” experiments. Also popular are time-offlight (TOF) instruments.

These detectors suffice for most applications but their resolution is only about one atomic mass unit. To analyze isotope ratios, one would turn to either a triple-quad or magnetic-sector MS detector. “But as selectivity goes up so does your investment,” Robarge tells Lab Manager Magazine.

Despite the appeal of GC-MS and the broad range of cost and capability available, not every method demands its sensitivity and selectivity. Flame ionization is perfectly suited to quantifying blood-alcohol levels or analyzing low-molecular-weight hydrocarbons in the oil and gas industry, and electron capture is routinely used to screen pesticides in foods.

Mark Taylor, GC and GC-MS product manager at Shimadzu Scientific Instruments (Columbia, MD), notes that GC, particularly GC-MS, has been losing market share to liquid chromatographymass spectrometry (LC-MS). “GC-MS was the flagship analysis tool for organic compounds for many years. But when ionization issues were overcome with LC-MS, users realized that LC was easier to operate and required less sample preparation than GC-MS.”

Recently Released GC-MS SYSTEM GC-MS


  • Simple to use, incredibly sensitive, and deliver robust and reliable performance
  • Comes complete in a space-saving package that makes upgrading a simple and cost effective process
  • Come with an MRM Method Builder – designed by chromatographers
  • Include a factory-installed compound library that contains over 2500 MRM transitions


Clarus SQ 8

  • Delivers excellent throughput and productivity by minimizing requirements for calibration of instruments and reducing the need for sample preparation and concentration
  • Includes the patented GC oven, which has the fastest heat-up and cool-down times for shorter injection-to-injection and analytical cycle times
  • Has an 800:1 signal to noise specification and reduces background noise



  • Enhanced maximum column flow up to 4 mL/minute gives users the ability to select from a variety of columns so that productivity and sample throughput can be dramatically increased.
  • Optional direct injection probe lets users easily obtain a mass spectrum when analyzing materials that don’t lend themselves to chromatography
  • Front-opening chamber means maintenance can be performed with ease


TSQ Quantum XLS

  • Features proprietary DuraBrite IRIS ion source, for high sensitivity in the low femtogram range
  • Combines full scan MS analyses of metabolites and targeted analysis
  • Features the ability to change from EI to CI without venting the system
  • Includes a zero cross-talk angled collision cell to eliminate false positives

Thermo Fisher Scientific