Gas chromatography-mass spectrometry
Gas chromatography-mass spectrometry (GC-MS) is a method that combines the features of gas-liquid chromatography and mass spectrometry to identify different substances within a test sample. Applications of GC-MS include drug detection, fire 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 elements in materials that were previously thought to have disintegrated beyond identification.
The GC-MS has been widely heralded as a "gold standard" for forensic 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, however, 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.

# History
The use of a mass spectrometer as the detector in gas chromatography was developed during the 1950s by Roland Gohlke and Fred McLafferty. These sensitive devices were bulky, fragile, and originally limited to laboratory settings. The development of affordable and miniaturized computers 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 analyse a sample. 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. This has led to their widespread adoption in a number of fields.

# Instrumentation
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 molecules in a mixture will separate the molecules as the sample travels the length of the column. The molecules take different amounts of time (called the retention time) to come out of (elute from) the gas chromatograph, 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 ionized 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 makes it 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.

## Split/Splitless GC-MS inlets
Samples are introduced to the column via an inlet.  This inlet is typically injection through a septum.  Once in the inlet, the heated chamber acts to volatilise (vapourise) the sample.  In a split system, a constant flow of carrier gas moves through the inlet.  A portion of the carrier gas flow acts to transport the sample into the column.  Another portion of the carrier gas flow gets directed to purge the inlet of any sample following injection (septum purge).  Yet another portion of the flow is directed through the split vent in a set ratio known as the split ratio.  In a splitless system, the advantage is that a larger amount of sample is introduced to the column.  However, a split system is preferred when the detector is sensitive to trace amounts of analyte and there is concern about overloading the column.

## Purge and Trap GC-MS
For the analysis of volatile 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 (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 (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 compounds (aromatic compounds associated with petroleum).

## 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 as a Mass Selective Detector.  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 throughput 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.

# Analysis
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 inputed 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 in 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 very 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.

## Selective Ion Monitoring
In Selective 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 as 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 (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 a hard ionization that fragments the molecule, and the way in which a molecule fragment is usually typical for all EI techniques.

### Chemical Ionization
In chemical ionization a reagent gas, typically methane or ammonia 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.
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.
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 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 containing the various elements which are believed to be in the compound. The isotope 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 ions 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-MS/MS
When a second phase of mass fragmentation is added, for example using a second quadrupole in a quadrupole instrument, it is called MS/MS or Tandem MS. Tandem mass spectrometry (MS/MS) is a more powerful technique 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, Single Reaction Monitoring (SRM) and 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 (MRM if more than one transition is chosen for the precursor ion). MRM is highly specific and virtually eliminates matrix background. Manufacturers of GC-MS/MS systems include Waters Corp. ; Chromtech/Chromsys (upgrade of Agilent Technologies standard GC-MS systems); Varian Inc. ; Thermo-Fisher Scientific

# Applications

## Environmental Monitoring and Cleanup
GC-MS is becoming the tool of choice for tracking organic pollutants in the environment. The cost of GC-MS equipment has fallen significantly, and the reliability has increased at the same time, which has contributed to its increased adoption in environmental studies as cost is always a major consideration in this kind of work. 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.
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## Criminal Forensics
GC-MS can analyze the particles from a human body in order to help link a criminal to a crime. The analysis of fire 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 narcotic, and may eventually supplant drug-sniffing dogs. It is also commonly used in forensic toxicology to find drugs and/or poisons in biological specimens of suspects, victims, or the deceased.

## Security
A post-September 11 development, explosive detection systems have become a part of all US airports. These systems run on a host of technologies, many of them based on GC-MS. There are only three manufacturers certified by the FAA 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
Foods and beverages contain numerous aroma 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.

## Astrochemistry
Several GC-MS have left earth. Two were brought to Mars by the Viking program. Venera 11 and 12 and Pioneer Venus analysed the atmosphere of Venus with GC-MS. The Huygens probe of the Cassini-Huygens mission landed one GC-MS on Saturn's largest moon, Titan. The material in the comet 67P/Churyumov-Gerasimenko will be analysed by the Rosetta mission with a chiral GC-MS in 2014. 

## Medicine
In combination with isotopic labeling of metabolic compounds, the GC-MS is used for determining metabolic activity. Most applications are based on the use of 13C 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.