Gas chromatography-mass spectrometry
Gas chromatography–mass spectrometry (GC-MS) is a method that combines the features of gas-liquid chromatography
Gas-liquid chromatography
Gas chromatography , is a common type of chromatography used in analytical chemistry for separating and analysing compounds that can be vaporized without decomposition. Typical uses of GC include testing the purity of a particular substance, or separating the different components of a mixture...

 and mass spectrometry
Mass spectrometry
Mass spectrometry is an analytical technique that measures the mass-to-charge ratio of charged particles.It is used for determining masses of particles, for determining the elemental composition of a sample or molecule, and for elucidating the chemical structures of molecules, such as peptides and...

 to identify different substances within a test sample. Applications of GC-MS include drug
Drug abuse
Substance abuse, also known as drug abuse, refers to a maladaptive pattern of use of a substance that is not considered dependent. The term "drug abuse" does not exclude dependency, but is otherwise used in a similar manner in nonmedical contexts...

 detection, fire
Fire is the rapid oxidation of a material in the chemical process of combustion, releasing heat, light, and various reaction products. Slower oxidative processes like rusting or digestion are not included by this definition....

 investigation, environmental analysis, explosives investigation, and identification of unknown samples. GC-MS can also be used in airport security to detect substances in luggage or on human beings. Additionally, it can identify trace element
Trace element
In analytical chemistry, a trace element is an element in a sample that has an average concentration of less than 100 parts per million measured in atomic count, or less than 100 micrograms per gram....

s in materials that were previously thought to have disintegrated beyond identification.

GC-MS has been widely heralded as a "gold standard
Gold standard (test)
In medicine and statistics, gold standard test refers to a diagnostic test or benchmark that is the best available under reasonable conditions. It does not have to be necessarily the best possible test for the condition in absolute terms...

" for forensic
Forensic science is the application of a broad spectrum of sciences to answer questions of interest to a legal system. This may be in relation to a crime or a civil action...

 substance identification because it is used to perform a specific test. A specific test positively identifies the actual presence of a particular substance in a given sample. A non-specific test merely indicates that a substance falls into a category of substances. Although a non-specific test could statistically suggest the identity of the substance, this could lead to false positive identification.


The use of a mass spectrometer as the detector in gas chromatography was developed during the 1950s by Roland Gohlke and Fred McLafferty
Fred McLafferty
Fred Warren McLafferty is an American chemist known for his work in mass spectrometry. He is best known for the McLafferty rearrangement reaction that was observed with mass spectrometry. WIth Roland Gohlke, he pioneered the technique of gas chromatography-mass spectrometry...

. These sensitive devices were bulky, fragile, and originally limited to laboratory settings.

The development of affordable and miniaturized computer
A computer is a programmable machine designed to sequentially and automatically carry out a sequence of arithmetic or logical operations. The particular sequence of operations can be changed readily, allowing the computer to solve more than one kind of problem...

s has helped in the simplification of the use of this instrument, as well as allowed great improvements in the amount of time it takes to analyze a sample. In 1964, Electronic Associates, Inc. (EAI), a leading U.S. supplier of analog computers, began development of a computer controlled quadruple mass spectrometerunder the direction of Robert E. Finnigan. By 1966 Finnigan and collaborator Mike Uthe's EAI division had sold over 500 quadrupole residual gas-analyzer instruments. In 1967, the Finnigan Instrument Corporation was formed and in early 1968, delivered the first prototype quadrapole GC/MS instruments to Stanford and Purdue University. FIC was eventually renamed Finnigan Corporation and went on to establish itself as the worldwide leader in GC/MS systems.

In 1996 the top-of-the-line high-speed GC-MS units completed analysis of fire accelerants in less than 90 seconds, whereas first-generation GC-MS would have required at least 16 minutes. By the 2000s computerized GC/MS instruments using quadrupole technology had become both essential to chemical research and one of the foremost instruments used for organic analysis. Today computerized GC/MS instruments are widely used in environmental monitoring of water, air, and soil; in the regulation of agriculture and food safety; and in the discovery and production of medicine.


The GC-MS is composed of two major building blocks: the gas chromatograph and the mass spectrometer. The gas chromatograph utilizes a capillary column which depends on the column's dimensions (length, diameter, film thickness) as well as the phase properties (e.g. 5% phenyl polysiloxane). The difference in the chemical properties between different molecule
A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...

s in a mixture will separate the molecules as the sample travels the length of the column. The molecules are retained by the column and then elute (come off of) from the column at different times (called the retention time), and this allows the mass spectrometer downstream to capture, ionize, accelerate, deflect, and detect the ionized molecules separately. The mass spectrometer does this by breaking each molecule into ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...

ized fragments and detecting these fragments using their mass to charge ratio.

These two components, used together, allow a much finer degree of substance identification than either unit used separately. It is not possible to make an accurate identification of a particular molecule by gas chromatography or mass spectrometry alone. The mass spectrometry process normally requires a very pure sample while gas chromatography using a traditional detector (e.g. Flame Ionization Detector) detects multiple molecules that happen to take the same amount of time to travel through the column (i.e. have the same retention time) which results in two or more molecules to co-elute. Sometimes two different molecules can also have a similar pattern of ionized fragments in a mass spectrometer (mass spectrum). Combining the two processes reduces the possibility of error, as it is extremely unlikely that two different molecules will behave in the same way in both a gas chromatograph and a mass spectrometer. Therefore, when an identifying mass spectrum appears at a characteristic retention time in a GC-MS analysis, it typically lends to increased certainty that the analyte of interest is in the sample.

Purge and trap GC-MS

For the analysis of volatile
Volatility (chemistry)
In chemistry and physics, volatility is the tendency of a substance to vaporize. Volatility is directly related to a substance's vapor pressure. At a given temperature, a substance with higher vapor pressure vaporizes more readily than a substance with a lower vapor pressure.The term is primarily...

 compounds a Purge and Trap (P&T) concentrator system may be used to introduce samples. The target analytes are extracted and mixed with water and introduced into an airtight chamber. An inert gas such as Nitrogen
Nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...

 (N2) is bubbled through the water; this is known as purging. The volatile compounds move into the headspace above the water and are drawn along a pressure gradient
Pressure gradient
In atmospheric sciences , the pressure gradient is a physical quantity that describes in which direction and at what rate the pressure changes the most rapidly around a particular location. The pressure gradient is a dimensional quantity expressed in units of pressure per unit length...

 (caused by the introduction of the purge gas) out of the chamber. The volatile compounds are drawn along a heated line onto a 'trap'. The trap is a column of adsorbent material at ambient temperature that holds the compounds by returning them to the liquid phase. The trap is then heated and the sample compounds are introduced to the GC-MS column via a volatiles interface, which is a split inlet system. P&T GC-MS is particularly suited to volatile organic compounds (VOCs) and BTEX
BTEX is an acronym that stands for benzene, toluene, ethylbenzene, and xylenes. These compounds are some of the volatile organic compounds found in petroleum derivatives such as petrol . Toluene, ethylbenzene, and xylenes have harmful effects on the central nervous system.BTEX compounds are...

 compounds (aromatic compounds associated with petroleum).f

Types of mass spectrometer detectors

The most common type of mass spectrometer (MS) associated with a gas chromatograph (GC) is the quadrupole mass spectrometer, sometimes referred to by the Hewlett-Packard
Hewlett-Packard Company or HP is an American multinational information technology corporation headquartered in Palo Alto, California, USA that provides products, technologies, softwares, solutions and services to consumers, small- and medium-sized businesses and large enterprises, including...

 (now Agilent) trade name "Mass Selective Detector" (MSD). Another relatively common detector is the ion trap mass spectrometer. Additionally one may find a magnetic sector mass spectrometer, however these particular instruments are expensive and bulky and not typically found in high-throughput service laboratories. Other detectors may be encountered such as time of flight (TOF), tandem quadrupoles (MS-MS) (see below), or in the case of an ion trap MSn where n indicates the number mass spectrometry stages.


A mass spectrometer is typically utilized in one of two ways: Full Scan or Selective Ion Monitoring (SIM). The typical GC-MS instrument is capable of performing both functions either individually or concomitantly, depending on the setup of the particular instrument.

Full scan MS

When collecting data in the full scan mode, a target range of mass fragments is determined and put into the instrument's method. An example of a typical broad range of mass fragments to monitor would be m/z 50 to m/z 400. The determination of what range to use is largely dictated by what one anticipates being in the sample while being cognizant of the solvent and other possible interferences. A MS should not be set to look for mass fragments too low or else one may detect air (found as m/z 28 due to nitrogen), carbon dioxide (m/z 44) or other possible interferences. Additionally if one is to use a large scan range then sensitivity of the instrument is decreased due to performing fewer scans per second since each scan will have to detect a wide range of mass fragments.

Full scan is useful in determining unknown compounds in a sample. It provides more information than SIM when it comes to confirming or resolving compounds in a sample. During instrument method development it may be common to first analyze test solutions in full scan mode to determine the retention time and the mass fragment fingerprint before moving to a SIM instrument method.

Selected ion monitoring

In selected ion monitoring (SIM) certain ion fragments are entered into the instrument method and only those mass fragments are detected by the mass spectrometer. The advantages of SIM are that the detection limit is lower since the instrument is only looking at a small number of fragments (e.g. three fragments) during each scan. More scans can take place each second. Since only a few mass fragments of interest are being monitored, matrix interferences are typically lower. To additionally confirm the likelihood of a potentially positive result, it is relatively important to be sure that the ion ratios of the various mass fragments are comparable to a known reference standard.

Types of ionization

After the molecules travel the length of the column, pass through the transfer line and enter into the mass spectrometer they are ionized by various methods with typically only one method being used at any given time. Once the sample is fragmented it will then be detected, usually by an electron multiplier diode, which essentially turns the ionized mass fragment into an electrical signal that is then detected.

The ionization technique chosen is independent of using Full Scan or SIM.

Electron ionization

By far the most common and perhaps standard form of ionization is electron ionization
Electron ionization
Electron ionization is an ionization method in which energetic electrons interact with gas phase atoms or molecules to produce ions...

 (EI). The molecules enter into the MS (the source is a quadrupole or the ion trap itself in an ion trap MS) where they are bombarded with free electrons emitted from a filament, not much unlike the filament one would find in a standard light bulb. The electrons bombard the molecules, causing the molecule to fragment in a characteristic and reproducible way. This "hard ionization" technique results in the creation of more fragments of low mass to charge ratio (m/z) and few, if any, molecules approaching the molecular mass unit. Hard ionization is considered by mass spectrometrists as the employ of molecular electron bombardment, whereas "soft ionization" is charge by molecular collision with an introduced gas. The molecular fragmentation pattern is dependant upon the electron energy applied to the system, typically 70 eV (electron Volts). The use of 70 eV facilitates comparison of generated spectra with library spectra using manufacturer-supplied software or software developed by the National Institute of Standards (NIST-USA). Spectral library searches employ matching algorithms such as Probability Based Matching and dot-product matching that are used with methods of analysis written by many method standardization agencies. Sources of libraries include NIST, Wiley, the AAFS, and instrument manufacturers. Library coverage can be checked at Compound Search.

Chemical ionization

In chemical ionization
Chemical ionization
Chemical ionization is an ionization technique used in mass spectrometry. Chemical ionization is a lower energy process than electron ionization. The lower energy yields less fragmentation, and usually a simpler spectrum...

 a reagent gas, typically methane
Methane is a chemical compound with the chemical formula . It is the simplest alkane, the principal component of natural gas, and probably the most abundant organic compound on earth. The relative abundance of methane makes it an attractive fuel...

 or ammonia
Ammonia is a compound of nitrogen and hydrogen with the formula . It is a colourless gas with a characteristic pungent odour. Ammonia contributes significantly to the nutritional needs of terrestrial organisms by serving as a precursor to food and fertilizers. Ammonia, either directly or...

 is introduced into the mass spectrometer. Depending on the technique (positive CI or negative CI) chosen, this reagent gas will interact with the electrons and analyte and cause a 'soft' ionization of the molecule of interest. A softer ionization fragments the molecule to a lower degree than the hard ionization of EI. One of the main benefits of using chemical ionization is that a mass fragment closely corresponding to the molecular weight of the analyte of interest is produced.

Positive Chemical Ionization
In Positive Chemical Ionization (PCI) the reagent gas interacts with the target molecule, most often with a proton exchange. This produces the species in relatively high amounts.

Negative Chemical Ionization
In Negative Chemical Ionization (NCI) the reagent gas decreases the impact of the free electrons on the target analyte. This decreased energy typically leaves the fragment in great supply.
The primary goal of instrument analysis is to quantify an amount of substance. This is done by comparing the relative concentrations among the atomic masses in the generated spectrum. Two kinds of analysis are possible, comparative and original. Comparative analysis essentially compares the given spectrum to a spectrum library to see if its characteristics are present for some sample in the library. This is best performed by a computer
A computer is a programmable machine designed to sequentially and automatically carry out a sequence of arithmetic or logical operations. The particular sequence of operations can be changed readily, allowing the computer to solve more than one kind of problem...

 because there are a myriad of visual distortions that can take place due to variations in scale. Computers can also simultaneously correlate more data (such as the retention times identified by GC), to more accurately relate certain data.

Another method of analysis measures the peaks in relation to one another. In this method, the tallest peak is assigned 100% of the value, and the other peaks being assigned proportionate values. All values above 3% are assigned. The total mass of the unknown compound is normally indicated by the parent peak. The value of this parent peak can be used to fit with a chemical formula
In mathematics, a formula is an entity constructed using the symbols and formation rules of a given logical language....

 containing the various elements
Chemical element
A chemical element is a pure chemical substance consisting of one type of atom distinguished by its atomic number, which is the number of protons in its nucleus. Familiar examples of elements include carbon, oxygen, aluminum, iron, copper, gold, mercury, and lead.As of November 2011, 118 elements...

 which are believed to be in the compound. The isotope
Isotopes are variants of atoms of a particular chemical element, which have differing numbers of neutrons. Atoms of a particular element by definition must contain the same number of protons but may have a distinct number of neutrons which differs from atom to atom, without changing the designation...

 pattern in the spectrum, which is unique for elements that have many isotopes, can also be used to identify the various elements present. Once a chemical formula has been matched to the spectrum, the molecular structure and bonding can be identified, and must be consistent with the characteristics recorded by GC-MS. Typically, this identification done automatically by programs which come with the instrument, given a list of the elements which could be present in the sample.

A “full spectrum” analysis considers all the “peaks” within a spectrum. Conversely, selective ion monitoring (SIM) only monitors selected peaks associated with a specific substance. This is done on the assumption that at a given retention time, a set of ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...

s is characteristic of a certain compound. This is a fast and efficient analysis, especially if the analyst has previous information about a sample or is only looking for a few specific substances. When the amount of information collected about the ions in a given gas chromatographic peak decreases, the sensitivity of the analysis increases. So, SIM analysis allows for a smaller quantity of a compound to be detected and measured, but the degree of certainty about the identity of that compound is reduced.

GC-tandem MS

When a second phase of mass fragmentation is added, for example using a second quadrupole in a quadrupole instrument, it is called tandem MS (MS/MS). MS/MS can sometimes be used to quantitate low levels of target compounds in the presence of a high sample matrix background.

The first quadrupole (Q1) is connected with a collision cell (q2) and another quadrupole (Q3). Both quadrupoles can be used in scanning or static mode, depending on the type of MS/MS analysis being performed. Types of analysis include product ion scan, precursor ion scan, Selected Reaction Monitoring (SRM) (sometimes referred to as Multiple Reaction Monitoring (MRM)) and Neutral Loss Scan. For example: When Q1 is in static mode (looking at one mass only as in SIM), and Q3 is in scanning mode, one obtains a so-called product ion spectrum (also called "daughter spectrum"). From this spectrum, one can select a prominent product ion which can be the product ion for the chosen precursor ion. The pair is called a "transition" and forms the basis for SRM. SRM is highly specific and virtually eliminates matrix background.

Environmental monitoring and cleanup

GC-MS is becoming the tool of choice for tracking organic pollutants
Persistent organic pollutant
thumb|right|275px|State parties to the Stockholm Convention on Persistent Organic PollutantsPersistent organic pollutants are organic compounds that are resistant to environmental degradation through chemical, biological, and photolytic processes...

 in the environment. The cost of GC-MS equipment has decreased significantly, and the reliability has increased at the same time, which has contributed to its increased adoption in environmental studies
Environmental monitoring
Environmental monitoring describes the processes and activities that need to take place to characterise and monitor the quality of the environment...

. There are some compounds for which GC-MS is not sufficiently sensitive, including certain pesticides and herbicides, but for most organic analysis of environmental samples, including many major classes of pesticides, it is very sensitive and effective.

Criminal forensics

GC-MS can analyze the particles from a human body in order to help link a criminal to a crime
Crime is the breach of rules or laws for which some governing authority can ultimately prescribe a conviction...

. The analysis of fire
Fire is the rapid oxidation of a material in the chemical process of combustion, releasing heat, light, and various reaction products. Slower oxidative processes like rusting or digestion are not included by this definition....

 debris using GC-MS is well established, and there is even an established American Society for Testing Materials (ASTM) standard for fire debris analysis. GCMS/MS is especially useful here as samples often contain very complex matrices and results, used in court, need to be highly accurate.

Law enforcement

GC-MS is increasingly used for detection of illegal narcotics, and may eventually supplant drug-sniffing dogs.[1] It is also commonly used in forensic toxicology to find drugs and/or poisons in biological specimens of suspects, victims, or the deceased.

Sports anti-doping analysis

GC-MS is the main tool used in sports anti-doping laboratories to test athletes' urine samples for prohibited performance-enhancing drugs, for example anabolic steroids.


A post–September 11 development, explosive detection
Explosive detection
Explosive detection is a non-destructive inspection process to determine whether a container contains explosive material. Explosive detection is commonly used at airports, ports and for border control.-Dogs:...

 systems have become a part of all US airport
An airport is a location where aircraft such as fixed-wing aircraft, helicopters, and blimps take off and land. Aircraft may be stored or maintained at an airport...

s. These systems run on a host of technologies, many of them based on GC-MS. There are only three manufacturers certified by the FAA
Federal Aviation Administration
The Federal Aviation Administration is the national aviation authority of the United States. An agency of the United States Department of Transportation, it has authority to regulate and oversee all aspects of civil aviation in the U.S...

 to provide these systems, one of which is Thermo Detection (formerly Thermedics), which produces the EGIS, a GC-MS-based line of explosives detectors. The other two manufacturers are Barringer Technologies, now owned by Smith's Detection Systems, and Ion Track Instruments, part of General Electric Infrastructure Security Systems.

Food, beverage and perfume analysis

Food is any substance consumed to provide nutritional support for the body. It is usually of plant or animal origin, and contains essential nutrients, such as carbohydrates, fats, proteins, vitamins, or minerals...

s and beverages contain numerous aromatic compounds, some naturally present in the raw materials and some forming during processing. GC-MS is extensively used for the analysis of these compounds which include esters, fatty acids, alcohols, aldehydes, terpenes etc. It is also used to detect and measure contaminants from spoilage or adulteration which may be harmful and which is often controlled by governmental agencies, for example pesticides.


Several GC-MS have left earth. Two were brought to Mars
Mars is the fourth planet from the Sun in the Solar System. The planet is named after the Roman god of war, Mars. It is often described as the "Red Planet", as the iron oxide prevalent on its surface gives it a reddish appearance...

 by the Viking program
Viking program
The Viking program consisted of a pair of American space probes sent to Mars, Viking 1 and Viking 2. Each spacecraft was composed of two main parts, an orbiter designed to photograph the surface of Mars from orbit, and a lander designed to study the planet from the surface...

. Venera
The Venera series probes were developed by the Soviet Union between 1961 and 1984 to gather data from Venus, Venera being the Russian name for Venus...

 11 and 12 and Pioneer Venus analysed the atmosphere of Venus
Venus is the second planet from the Sun, orbiting it every 224.7 Earth days. The planet is named after Venus, the Roman goddess of love and beauty. After the Moon, it is the brightest natural object in the night sky, reaching an apparent magnitude of −4.6, bright enough to cast shadows...

 with GC-MS. The Huygens probe
Huygens probe
The Huygens probe was an atmospheric entry probe carried to Saturn's moon Titan as part of the Cassini–Huygens mission. The probe was supplied by the European Space Agency and named after the Dutch 17th century astronomer Christiaan Huygens....

 of the Cassini-Huygens
Cassini–Huygens is a joint NASA/ESA/ASI spacecraft mission studying the planet Saturn and its many natural satellites since 2004. Launched in 1997 after nearly two decades of gestation, it includes a Saturn orbiter and an atmospheric probe/lander for the moon Titan, although it has also returned...

 mission landed one GC-MS on Saturn's largest moon, Titan
Titan (moon)
Titan , or Saturn VI, is the largest moon of Saturn, the only natural satellite known to have a dense atmosphere, and the only object other than Earth for which clear evidence of stable bodies of surface liquid has been found....

. The material in the comet
A comet is an icy small Solar System body that, when close enough to the Sun, displays a visible coma and sometimes also a tail. These phenomena are both due to the effects of solar radiation and the solar wind upon the nucleus of the comet...

Comet Churyumov–Gerasimenko, officially designated 67P/Churyumov–Gerasimenko, is a comet with a current orbital period of 6.6 years. It is the destination of the European Space Agency's Rosetta spacecraft mission, launched on March 2, 2004....

 will be analysed by the Rosetta mission with a chiral GC-MS in 2014.


Dozens of congenital metabolic diseases also known as Inborn error of metabolism
Inborn error of metabolism
Inborn errors of metabolism comprise a large class of genetic diseases involving disorders of metabolism. The majority are due to defects of single genes that code for enzymes that facilitate conversion of various substances into others...

 are now detectable by newborn screening tests, especially the testing using gas chromatography–mass spectrometry. GC-MS can determine compounds in urine even in minor concentration. These compounds are normally not present but appear in individuals suffering with metabolic disorders. This is an increasingly becoming a common way to diagnose IEM for earlier diagnosis and institution of treatment eventually leading to a better outcome. It is now possible to test a newborn for over 100 genetic metabolic disorders by a urine test at birth based on GC-MS.

In combination with isotopic labeling
Isotopic labeling
Isotopic labeling is a technique for tracking the passage of a sample of substance through a system. The substance is 'labeled' by including unusual isotopes in its chemical composition...

 of metabolic compounds, the GC-MS is used for determining metabolic activity
Metabolism is the set of chemical reactions that happen in the cells of living organisms to sustain life. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories...

. Most applications are based on the use of 13C
Carbon-13 is a natural, stable isotope of carbon and one of the environmental isotopes. It makes up about 1.1% of all natural carbon on Earth.- Detection by mass spectrometry :...

 as the labeling and the measurement of 13C-12C ratios with an isotope ratio mass spectrometer (IRMS); an MS with a detector designed to measure a few select ions and return values as ratios.

See also

  • Liquid chromatography-mass spectrometry
    Liquid chromatography-mass spectrometry
    Liquid chromatography–mass spectrometry is an analytical chemistry technique that combines the physical separation capabilities of liquid chromatography with the mass analysis capabilities of mass spectrometry. LC-MS is a powerful technique used for many applications which has very high...

  • Ion mobility spectrometry-mass spectrometry
    Ion mobility spectrometry-mass spectrometry
    Ion-mobility spectrometry–mass spectrometry is a method that combines ion-mobility spectrometry and mass spectrometry to identify different substances within a test sample.-History:...

  • Prolate trochoidal mass spectrometer
    Prolate trochoidal mass spectrometer
    A prolate trochoidal mass spectrometer is an chemical analysis instrument in which the ions of different mass-to-charge ratio are separated by means of mutually perpendicular electric and magnetic fields so that the ions follow a prolate trochoidal path...

External links

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