What is GC-MS?

GC-MS can be used to study liquid, gaseous or solid samples. Analysis begins with the gas chromatograph, where the sample is effectively vaporized into the gas phase and separated into its various components using a capillary column coated with a stationary (liquid or solid) phase. The compounds are propelled by an inert carrier gas such as helium, hydrogen or nitrogen. As components of the mixture are separated, each compound elutes from the column at a different time based on its boiling point and polarity. The time of elution is referred to as a compound's retention time. GC has the capacity to resolve complex mixtures or sample extracts containing hundreds of compounds.

Once the components leave the GC column, they are ionized and fragmented by the mass spectrometer using electron or chemical ionization sources. Ionized molecules and fragments are then accelerated through the instrument’s mass analyzer, which quite often is a quadrupole or ion trap. It is here that ions are separated based on their different mass-to-charge (m/z) ratios. GC-MS data acquisition can be performed in either full scan mode, to cover either a wide range of m/z ratios, or selected ion monitoring (SIM) mode, to gather data for specific masses of interest.

The final steps of the process involve ion detection and analysis, with fragmented ions appearing as a function of their m/z ratios. Peak areas, meanwhile, are proportional to the quantity of the corresponding compound. When a complex sample is separated by GC-MS, it will produce many different peaks in the gas chromatogram and each peak generates a unique mass spectrum used for compound identification. Using extensive commercially available libraries of mass spectra, unknown compounds and target analytes can be identified and quantified.

Types of GC-MS and when to use them

Different analytical tasks require different detection abilities. While the gas chromatography system may remain the same, different types of mass spectrometers may be required for different types of analyses depending on the level of selectivity and sensitivity required.

Single quadrupole GC-MS

When gas chromatography is combined with a mass spectrometer that includes just one quadrupole, it is often referred to simply as GC-MS. GC-MS is well suited to the everyday analysis of samples where either targeted or untargeted analysis is required as these systems can be operated using either targeted selected ion monitoring (SIM) or untargeted full scan acquisition. Typical applications include pesticide analysis in food and environmental samples, analysis of biological samples for drugs of abuse and analysis of volatile organic compounds in water samples.

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Triple quadrupole GC-MS/MS

Gas chromatography combined with a triple quadrupole mass spectrometry system is referred to as GC-MS/MS. The triple quadrupole MS provides a higher level of selectivity and is best suited to analyses where the highest sensitivity is required. This is often the case when quantitating pesticides in food or environmental contaminants. GC-MS/MS systems are typically operated in selective reaction monitoring (SRM) mode. The high selectivity of the SRM helps reduce interferences from background ions and produce a high signal-to-noise for excellent detection capability.

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For comprehensive characterization of samples in a single analysis with high-confidence compound discovery, identification and quantitation, a GC system can be combined with a high resolution accurate mass (HRAM) mass spectrometer. These GC-MS/MS systems offer the quantitative power of a triple quadrupole GC-MS/MS combined with high-precision, full-scan HRAM capabilities available only from the most sensitive and accurate mass spectrometers. These systems are ideally suited for applications that require both accurate targeted analysis and confident unknown compound identification.

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Sample preparation

Sample Preparation

Samples for GC-MS analyses often need to be separated from complex and dirty matrices before being introduced into the gas chromatograph. Different manual and automated sample extraction processes are often used prior to gas chromatography. These processes differ depending on the sample matrix, the degree of selectivity required and the initial cleanliness of the samples. Automated on-line sample preparation with sample injection into a GC-MS is possible through robotic autosamplers, which can replace many basic and more complex manual sample handling operations.

For more information about sample preparation prior to GC-MS analysis, visit our GC-MS Sample Preparation Learning Center.

You can also check out the sample preparation products offered by Thermo Fisher Scientific when you download our Chromatography Consumables Catalog – Sample preparation products.

Gas chromatography columns

Gas chromatography columns

GC columns represent the stationary phase and separation tool of a gas chromatography analysis. The stationary phase ensures that different compounds are adequately separated and eluted from the column at different times. Different types of columns with different stationary phases can be used for different applications, such as determining volatile organic compounds (VOCs) or dioxins. They can be designed to separate polar or non-polar compounds or process samples at different speeds. It is important that columns do not release stationary phase compounds, thus providing minimal background signal in the resulting chromatogram, sometimes referred to as being “low bleed”. Inertness of GC column material is also a critical factor to considering in order to prevent unwanted chemical interactions with the sample.

To learn more about the different types of GC columns Thermo Fisher Scientific offers, visit our Gas Chromatography Columns page or download our Chromatography Consumables Catalog – GC Columns and accessories.

GC-MS Applications

From detection of potential toxic chemicals in foods to quantitation of organic contaminants in water or analysis of petroleum products during oil processing, GC-MS can be used for a variety of applications. Explore the sections below to learn about some of the most common analyses performed using these systems.

Food & beverage analysis

GC-MS analysis is integral to ensuring the safety and authenticity of the foods we eat and beverages we drink. From determination of pesticide residues to characterization of ingredients, GC-MS systems provide manufacturers and regulatory agencies with valuable information about the safety of our food supply.

Environmental analysis

GC-MS is a powerful tool for monitoring contaminants in air, water and soil. It is particularly useful for quantitation of volatile organic compounds (VOCs) and semi-volatile organic compounds (SVOCs), polychlorinated biphenyls (PCBs), organochlorinated pesticides, brominated flame retardants and polycyclic aromatic hydrocarbons (PAHs).


GC-MS offers some of the sophisticated analytical technologies required for complex metabolomic analyses. It allows researchers to explore deeper into the metabolome and gain complete coverage of metabolites to support research into primary and secondary metabolites in plants, animals, and microbes. As the applications below demonstrate, HRAM GC-MS is especially well-suited to the challenge of untargeted metabolite identification.

Oil and gas analysis

GC-MS can be used during many stages of petroleum and natural gas testing workflows to determine energy content, CHA, SIMDIS, H2S/organic sulfur content of natural gas and natural gas condensates. Additionally, GC-MS analysis can be used in refinery gas analysis (RGA) and detailed hydrocarbon analysis (DHA) to detect oxygenates, aromatics, BTEX compounds and PAHs in crude oil.

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Want to learn more about GC-MS products?

Thermo Fisher Scientific offers a full range of GC-MS systems, columns and consumables. To learn more about our robust, reliable GC-MS products, visit our Gas Chromatography-Mass Spectrometry page.

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