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. Typically only one ionization method being used at any given time. Once the sample is fragmented it will then be detected, usually by an electron multiplier diode. The diode treats the ionized mass fragment like an electrical signal that is then detected.
Chemists select an ionization technique separately from choosing Full Scan or SIM monitoring.
The most common type 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 hit with free electrons emitted from a filament. This is like the filament one would find in a standard incandescent light bulb. The electrons hit the molecules, causing the molecule to fragment in a characteristic way that can be repeated. This "hard ionization" technique results in the creation of more fragments of low mass to charge ratio (m/z). EI has few, if any, fragments having a mass that is near the mass of the original molecule. Chemists consider hard ionization to be shooting electrons into the sample molecules. In contrast, "soft ionization" is placing a charge on the sample molecule by hitting it with an introduced gas. The molecular fragmentation pattern depends on the electron energy applied to the system, typically 70 eV (electron Volts). The use of 70 eV helps to compare the spectra generated from the test sample against known library spectra. (The library spectra can come from manufacturer-supplied software or software developed by the National Institute of Standards (NIST-USA)). The software searches the library spectra using a matching algorithm such as Probability Based Matching or dot-product matching. Many method standardization agencies now control these algorithms and methods to assure their objectivity.
In chemical ionization (CI), a reagent gas, typically methane or ammonia is put into the mass spectrometer. There are two types of CI: positive CI or negative CI. Either way, the 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. Chemists prefer CI over EI. This is because CI produces at least one mass fragment with a weight, that is nearly the same as the molecular weight of the analyte of interest.
In Positive Chemical Ionization (PCI) the reagent gas interacts with the target molecule, most often with a proton exchange. This produces the ion 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 fragments do not break up further.)
The primary goal of instrument analysis is to measure an amount of substance. This is done by comparing the relative concentrations among the atomic masses in the generated mass 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 known sample in the library. This is best performed by a computer because there are many visual distortions that can take place due to variations in scale. Computers can also correlate more data (such as the retention times identified by the 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 set at 100%. The other peaks given a value equal to the ratio of the peak height to the tallest peak height. 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 is unique for elements that have many isotopes. So, it can also be used to identify the various elements present. This tells the overall chemical formula of the unknown molecule. Because a molecule's structure and bonds break apart in characteristic ways, they can be identified from the difference in peak masses. The identified molecule structure must be consistent with the characteristics recorded by GC-MS. Typically, this identification is done automatically by computer programs which come with the instrument. Those programs match the spectra against a library of known compounds that have same list of elements which could be present in the sample.
A “full spectrum” analysis considers all the “peaks” within a spectrum. But, selective ion monitoring (SIM) only monitors selected peaks associated with a specific substance. Chemists assume that at a given retention time, a set of ions is characteristic of a certain compound. SIM is a fast and efficient analysis. SIM works best when 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.
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 are good at measuring low levels of target compounds in a sample with a matrix of background compounds that are not of interest.
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 used. Types of analysis include product ion scan, precursor ion scan, Selected Reaction Monitoring (SRM) 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 almost completely eliminates matrix background.
Many chemists believe that GC-MS is the best tool for monitoring organic pollutants in the environment. The cost of GC-MS equipment has decreased a lot. The reliability of GC-MS has increased at the same time. Both improvements have increased use in environmental studies. Some compounds, such as certain pesticides and herbicides, cannot be identified by GS-MS. They are too similar to other related compounds. But for most organic analysis of environmental samples, including many major classes of pesticides, GC-MS is very sensitive and effective.
GC-MS can analyze the particles from a human body in order to help link a criminal to a crime. The law accepts using GC-MS to analyze fire debris. In fact, the American Society for Testing Materials (ASTM) has a 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.
GC-MS is used for detection of illegal narcotics, and may eventually replace drug-sniffing dogs. It is also commonly used in forensic toxicology. It helps to find drugs and/or poisons in biological specimens taken from suspects, victims, or a dead body.