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The CHROMacademy Essential Guide Tutorial to Understanding GC-MS Analysis (Part 1)
When to use GC-MS jump to section »
The GC-MS Process - GC Considerations jump to section »
Interfacing GC with MS detection
jump to section »
Analyte Ionisation in the Mass Spectrometer jump to section »
Mass Analysers for GC-MS jump to section »
Detectors jump to section »
Vacuum System Considerations jump to section »
Introduction to GC-MS Data jump to section »
Tony Taylor (Crawford Scientific Technical Director), presents the fundamentals of using gas chromatography with mass spectrometric detectors all supported by Interactive Multi-Media from The CHROMacademy.  The session will consider key topics such as controlling and optimizing the vacuum system, ensuring good analyte transfer from the GC column, the theory and instrumentation of electron impact ionization and a detailed introduction to the quadrupole mass analyser.  A must see for everyone using or developing methods for GC-MS.
When to use GC-MS

GC-MS is a hyphenated technique, which combines the separating power of Gas Chromatography (GC), with the detection power of mass spectrometry.

Most users turn to GC-MS for two main reasons:

  1. They wish to identify or characterize the analytes within their sample
  2. They want to increase analytical sensitivity and cannot use a compound or element specific detector such as ECD, NPD, FPD or chemiluminesence

The mass spectrometric detector can be used to fragment analytes and produce a mass spectrum which can serve as a ‘fingerprint’ of the molecule and which can be identified from one of the many commercial or in-house GC-MS libraries. Further, if the compound is new or cannot be found within a library, then the spectrum itself may used to propose analyte molecular weight and elemental composition, identify major features and elucidate the structure of the molecule.

As the mass spectrometer can be used to essentially ‘filter’ the gas-phase column effluent for a specific mass, it is possible to achieve higher detection sensitivity by filtering out background noise and concentrating on the signal of interest only.

Fairly recently, GC has been coupled to triple quadrupole mass spectrometric detectors which allow even greater sensitivity through the use of multiple reaction monitoring type spectral experiments. GC-MS analysis with Time of Flight (ToF) detection is now also possible and ToF instruments give the added advantage of high resolution (and high accuracy) mass measurement which can result in empirical formulae and less ambiguous compound identification as well as high sensitivity


Overview of a Typical GC-MS System

Mass Spectrometry is a wide-ranging analytical technique, which involves the production and subsequent separation and identification of charged species according to their mass to charge (m/z) ratio.
Schematic Diagram of a typical GC-MS system

Figure 1: Schematic Diagram of a typical GC-MS system.    

1. Gas Supply: Gas is fed from cylinders through regulators and tubing to the instrument. It is usual to filter gases to ensure high gas purity and to regulate the gas supply pressure. Required gases might include:

  • Carrier - (H2, He, N2 - helium is most usual with MS detection)
  • Make-up gas– (H2, He, N2  - if using an FID detector in parallel to the MS detector)
  • Detector fuel gas – (H2 & Air - if using an FID detector in parallel to the MS detector)

2. Pneumatic controls: The gas supply is regulated to the correct pressure (or flow) and then fed to the required part of the instrument. Modern GC instruments have Electronic Pneumatic pressure controllers – older instruments may have manual pressure control via regulators.

3. Injector: Here, typically, the sample is volatilised and the resulting gas entrained into the carrier stream entering the GC column. Many inlet types exist including:

  • Split/Splitless – a broadly applicable vapourising inlet
  • Programmed Thermal Vaporising (PTV) – used to introduce thermally labile samples or for large volume injection for low concentration analytes.
  • Cool-on-column (COC) - introduces the sample into the column as a liquid to avoid thermal decomposition or improve quantitative accuracy.
  • Headspace injection – to introduce gas phase analytes volatilized from the sample.
  • Thermal desorption – used to desorb analyte from adsorbent tubes onto which volatile analytes have been trapped, typically used for environmental monitoring.

4. Oven: A column oven that is temperature programmable, typically between 5oC and 400oC but may go as low as -25oC with cryogenic cooling.

5. Column: Gas Chromatography uses a gaseous mobile phase to transport sample components through hollow capillary columns containing the stationary phase coated onto the inner wall. Capillary GC columns are usually several meters long (10 – 120m is typical) with an internal diameter of 0.10 – 0.50mm.


6. Interface: After separation in the GC system, analyte species have to be transported to the mass spectrometer to be ionised, mass filtered and detected. The interface in modern instruments is heated to prevent analyte condensation and in some instruments will contain a device to remove carrier gas molecules to allow analyte pre-concentration.

7. Ion Source: In the ion source, the products are ionized prior to analysis in the mass spectrometer.

Ionization is the process in which the analyte molecule is charged, typically via the creation of a radical cation (Electron Impact, EI) or via association or charge transfer (Chemical ionization, CI) whereby electrons are either removed or added to atoms or molecules to produce ions.

8. Mass Analyser: There are several very popular types of mass analyser associated with routine GC–MS analysis and all differ in the fundamental way in which they operate. However, all separate species on the basis of their mass-to-charge ratio.

9. Detector: The ion beam that emerges from the mass analyzer, has to be detected and transformed into a usable signal.

The detector generates a signal from incident ions by either generating secondary electrons, which are further amplified, or by inducing a current (generated by moving charges).

10. Vacuum System: Mass analysers require high levels of vacuum in order to operate in a predictable and efficient way.

Modern GC-MS vacuum systems consist of a differentially pumped system, usually with a foreline pump establishing a ‘rough’ vacuum and a high vacuum pump or pumps attached to the analyser body to establish the high levels of vacuum required for effective mass to charge ratio measurement.

11. Control Electronics: The MS parameters can be selected and controlled from this panel. Modern instruments will allow control of MS parameters from a computer by using specially designed software.

The GC-MS Process – GC Considerations   back to top »

There are several discrete stages in GC/MS analysis, typically these include:

  • Sample Introduction
  • Sample components separation
  • Transfer from the GC Column into the high vacuum of the mass analyser
  • Ionisation of sample components
  • Separation and detection of gas phase ions

There are several special GC considerations when mass spectrometric detectors which may not apply when using other detector types.

Gas Purity – The recommended carrier gas purity is 99.999%. Gas of lower purity may result in a contaminated mass analyser, interfering ions within the mass spectrum and a reduction in instrument sensitivity. Gas purification is required to ensure optimum gas cleanliness; typically hydrocarbons, moisture and oxygen are removed from the carrier using activated charcoal, molecular sieve and alumina respectively.

Carrier Gas Flow Rate - The carrier gas flow-rate is very important in GC–MS. It also has a major impact on the vacuum level of the MS system. Higher carrier flows will result in lower mass analyser vacuum levels that can, in turn, effect the filament lifetime — filaments will have shorter lifetimes at higher carrier gas flow-rates. Further, the vacuum level can have an effect on the efficiency of the electron impact ionization process and so may change the appearance of the spectrum or the effectiveness of ion transport through the analyser — lowering the sensitivity of the device. One should operate in ‘constant carrier gas flow’ mode to avoid unwanted changes in the response of the mass spectrometric detector.

Capillary column dimensions are usually chosen so that they will operate optimally below around 2 mL/min, which is the maximum carrier flow that can be tolerated using typical modern systems — although some will tolerate up to 4 mL/min with special high performance pump systems.

Carrier gas Column length (m) Flow rate (mL/min)
0.20 mm column I.D. 0.25 mm column I.D. 0.32 mm column I.D. 0.53 mm column I.D.
Hydrogen 15 0.77 1.1 1.73 4.34
30 0.98 1.29 1.9 4.5
60 1.43 1.72 2.27 4.93
Nitrogen 15 0.21 0.31 0.49 1.24
30 0.24 0.34 0.51 1.38
60 0.31 0.41 0.58 1.38
Helium 15 0.66 0.91 1.35 3.35
30 1.01 1.14 1.56 3.54
60 1.47 1.66 2.04 3.97

Table 1:  Schematic Typical Column Flow Rates for a number of Carrier Gas  / Column Geometry Combinations.


Some systems may be capable of using columns that require higher carrier gas flow-rates, however, some form of carrier gas ‘separator’ or ‘pre-concentrator’ will be required — see section on interfacing GC with MS below.

The choice of carrier gas is also important as the various common gases used for GC have different densities (compressibility) and will, therefore, produce different levels of vaccum. Some manufacturers warn against the use of hydrogen due to safety concerns.

Choice of Septa & Ferrules - Ferrules are often used in GC to help form a seal between the column and the inlet and detector connections. For GC–MS applications there is a special requirement that the ferrules used do not allow air/oxygen to permeate. This will result in an increased air background signal in the mass spectrometer. The preferred ferrule materials for GC–MS are graphite/vespel composites or special metal ferrules

Septa ‘bleed’ into the sample inlet, which can result in these bleed products appearing in the background of the mass spectrum, adding complexity, confounding elucidation and lowering instrument sensitivity. Special low-bleed septa that are manufactured using materials that can stand higher temperatures or are PTFE faced should be used for GC–MS applications.


Septum Material

Compatible with

Incompatible with

Max. Temp.

Rubber (Natural/Butyl)

ACN, acetone, DMF, alcohols, diethylamine, DMSO, phenols

Chlorinated solvents, aromatics, hydrocarbons, carbon disulfide


PTFE/Natural or Butyl Rubber

PTFE resistance until punctured, then septa or liner will have compatibility of rubber



Silicone/Silicone Rubber

Alcohol, acetone, ether, DMF, DMSO

ACN, THF, benzene chloroform, pyridine, toluene, hexane, heptane


PTFE/Silicone, PTFE/Silicone/PTFE

PTFE resistance until punctured, then septa will have compatibility of silicone




Chlorinated solvents, benzene, toluene, alcohols, hexane, heptane

DMF, DMSO, ACN, THF, pyridine, dioxane, methanol, acetone


Table 2:  Some common types of septum currently used in GC-MS applications.

Stationary Phase Selection for GC-MS - Most stationary phases can be used with GC–MS systems, however, it is a good idea to choose a phase for your application that has the lowest amount of column bleed possible to avoid spurious ions within the mass spectrometer that will confound elucidation and reduce detector sensitivity. Column bleed results from the breakdown of the siloxane backbone of the stationary phase polymer and is promoted by higher temperatures and the presence of oxygen within the carrier gas.

Figure 2:  An arylene stationary phase shows low bled characteristics  

Many manufacturers produce stationary phases that are chemically modified to reduce the amount of ‘bleed’ suffered by the column. A typical example is shown below where a 5% phenyl polydimethylsiloaxne column can be produced in two forms; one which has the phenyl groups pendant to the polymer backbone; the other (a so called ‘arylene’ phase), incorporates the phenyl moieties into the backbone of the polymer, so reducing column bleed.
A further advantage of these phases, therefore, is their upper temperature limit.


Note that whilst bleed is reduced, the selectivity of these two phases will differ and one should take care when choosing a low-bleed ‘equivalent’ phase for an existing method. The following rules of thumb are useful when selecting a stationary phase for GC–MS analysis:

  • Polar stationary phases (see manufacturer or previous Essential Guide to Column Selection in Gas Chromatography) bleed more than their less polar counterparts.
  • Columns with thicker stationary phase films bleed more.
  • Longer columns bleed more.
  • Be aware of both the gradient and isothermal maximum temperature limits for the stationary phase you are using and do not exceed these limits.

Some of the typical ‘fingerprint’ ions from column bleed products are shown in Table 3.

Ions (m/z) Compound Possible Source
13,14,15,16 Methane CI gas
18, 28, 32, 44 or 14, 16 H2O, N2, O2, CO2 or N, O Residual air and water, air leaks
31, 51, 69, 100, 119, 131, 169, 181, 214, 219, 264, 376, 414, 426, 464, 502, 576, 614 PFTBA and related ions PFTBA (tuning compound)
31 Methanol Cleaning solvent
43, 58 Acetone Cleaning solvent
78 Benzene Cleaning solvent
91, 92 Toluene or xylene Cleaning solvent
105, 106 Xylene Cleaning solvent
151, 153 Trichloroethane Cleaning solvent
69 Foreline pump fluid or PFTBA Foreline pump oil vapor or calibration valve leak
73, 147, 207, 221, 281, 295, 355, 429 Dimethylpolysiloxane Septum bleed or methyl silicone column coating
77, 94, 115, 141, 168, 170, 262, 354, 446 Diffusion pump fluid Diffusion pump fluid and related ions
149 Plasticizer (phthalates) Vacuum seals (O-rings) damaged by high temperatures, use of vinyl or plastic gloves
Peaks spaced 14 Da apart Hydrocarbons Fingerprints, foreline pump oil
Table 3:  Some common contaminant ion masses in GC-MS analysis.
Interfacing GC with MS detection   back to top »

After separation in the GC column, analyte species have to be transported to the mass spectrometer to be ionized, mass filtered and detected.

The column outlet needs to be connected to the ion source of the mass spectrometer and different strategies have been implemented to achieve this; all of which need to fulfill the following conditions:

  • Analyte must not condense in the interface
  • Analyte must not decompose before entering the mass spectrometer ion source
  • The gas load (dictated by the mobile phase gas flow rate) entering the ion source must be within the pumping capacity of the mass spectrometer

Perhaps the most widely used design for modern capillary GC is the ‘capillary direct’ interface. The advent of capillary columns brought about a significant reduction in the volumetric gas flow exiting the column (typically 1 mL/min or below for columns of 0.32 mm i.d. and less), and the need to split the analyte away from the carrier gas to reduce gas load into the ion source was eliminated.

In a direct interface, the column is inserted directly into the mass spectrometer ionization chamber. This interface gives the highest sensitivity, however, changing the GC column may be a time-consuming process unless curtain gas devices are fitted.

Figure 3:  Schematic Diagram of a GC-MS Direct Interface Device  

Figure 3: Schematic Diagram of a GC-MS Direct Interface Device.


Figure 4:  GC-MS Direct interface in operation.


It should be noted that ALL interface designs contain a heat source or are lagged with a heating jacket in order to prevent analyte condensation within the transfer line. The heat applied to the interface must prevent condensation but must also avoid thermal decomposition of labile analytes. In general, the temperature applied to the successive instrument regions in the GC–MS system will increase as analytes transition from the column through the interface to the ion source and mass analyser.

Different ionization modes [electron impact (EI) and chemical ionization (CI)] require different interface, ion source and mass analyser temperatures for optimum operation.

The physical method of connecting the GC column to the MS device is important, especially in terms of providing an air-tight seal and there are various designs available to achieve this including:

  • Traditional nut and ferrule
  • Curtain gas connectors
  • Couplings with restrictors
  • Couplings using deactivated silica tubing ‘pig-tails’

The last of these devices can be used for ‘vent-free’ column change, which negates the requirement to vent the mass spectrometer to facilitate a column change without catastrophic loss of vacuum within the detector.

Analyte Ionisation in the Mass Spectrometer   back to top »

Mass spectrometry involves the separation of charged species that are produced by a variety of ionization methods in GC–MS . These include:

  • Electron impact Ionisation (EI) - where analyte molecules are directly ionised through collision with a bombarding electron stream resulting in the removal of an electron to form a radical cation species.
  • Chemical Ionisation (CI) - where analyte molecules are charged through reaction processes with a charged reagent gas plasma producing either anion or cation species depending upon the analyte and analyser polarity.

Some representative reactions for electron impact and chemical ionization are presented next. In electron impact molecules are ionised by the interaction with electrons.

(where M is the analyte molecule)

In a chemical ionization experiment, ions are produced through the collision of the analyte with ions of a reagent gas that are present in the ion source. Some common reagent gases include methane, ammonia and isobutane. Some typical reactions schemes for ammonia chemical ionization might include:

(Production of the reagent gas ion)

Electron Impact (EI) Ionisation - In the electron impact (EI) process, electrons are emitted from a heated filament (usually made of tungsten, rhenium or an alloy) and are accelerated across the source by using an appropriate potential (5–100 V) to achieve the required electron energy. The industry standard for the energy of the impacting electron energy is standardized at 70 eV (electron volts) which, depending upon the analyte structure and 1st ionization potential, will result in more or less fragmentation of the in-tact gas phase analyte.

Figure 5:  Typical Ion Source Schematic representing Electron Impact Ionisation.


The analyte is introduced into the mass spectrometer ion source, where it is impacted by the beam of ionizing electrons, leading to the formation of an analyte radical cation. The process can be described as follows:

The process is a relatively harsh form of ionization and as a consequence, the parent molecule often breaks apart producing a variety of fragments with a relatively small amount of the parent ion remaining. In some circumstances, if the molecule is sufficiently labile, no parent ion may be seen within the resulting spectrum. The degree of fragmentation depends upon the magnitude of the first ionisation potential of the analyte molecule and the energy of the impacting electrons.

All charged species produced are then accelerated using a positive voltage applied to the ion source and are then accelerated through a voltage potential and the ‘beam’ of ions focused through a series of electrostatic lenses. More details of this process will be given in part two of this series on GC–MS

The subsequently mass filtered radical cation pseudomolecular ions (i.e. the radical cation version of the in-tact analyte) and all charged fragments (which can also include fragments that have undergone intermolecular re-arrangements), when detected, form the mass spectrum of the analyte. Typically these are plotted as mass spectra of abundance against mass to charge ration as shown in Figure 5. This mass spectrum can be searched against commercial or in-house libraries to produce tentative identification or may be elucidated using ab initio techniques to elucidate the molecular structure.

Figure 6:  Typical Electron Impact Ionisation Spectrum of the Cocaine molecule

Figure 6:  Typical Electron Impact Ionisation Spectrum of the Cocaine molecule.


Chemical Ionisation (CI) - Chemical ionization involves the ionization of a reagent gas, such as methane or ammonia at relatively high pressure (~1 mbar) in an electron impact source. Once produced, the reagent gas ions collide with the analyte molecules producing ions through gas phase reaction processes such as proton transfer and adduction as shown below:

(Production of the reagent gas ion)
(Analyte ionised by Proton Transfer)
(Analyte ionised by Adduct Formation)

Chemical ionization is a relatively soft process because the energy of the reagent ions, in general, does not exceed 5eV and as a consequence the spectrum produced by this technique usually shows much less fragmentation than EI spectra. This technique is particularly useful when a molecular weight of the analyte is required or when used (in negative ion mode) as a very sensitive technique for the quantitative determination of analytes that are capable of electron capture (typically halogenated molecules).


Figure 7:  Typical Ion Source Schematic representing Chemical Ionisation.


Under chemical ionization conditions, the registered spectra will strongly depend upon the nature of the reagent used, and because of that, different structural information can be obtained by choosing different reagent gases.

Commonly-used reagent gases are methane, iso-butane, ammonia or combinations of these gases.

Figure 8:  Typical Negative Ion Chemical Ionisation spectrum of Afalatoxin B1
Figure 8:  Typical Negative Ion Chemical Ionisation spectrum of Afalatoxin B1.

Suitable samples for GC/MS: Electron impact is the most commonly used method of ionization and a great number of organic compounds are amenable to EI. To give an EI spectrum, the sample must be volatile enough to undergo GC analysis and may be solid, liquid or gas. Since samples must usually be heated, thermally labile samples may be unsuitable or may require derivatization. Unfortunately, some compounds will fragment completely and won’t give molecular ions, however, this does not preclude these analyte types. Ionic samples generally do not work well by EI.

Figure 9: Common ionisation techniques  / application range
Figure 9: Common ionisation techniques  / application.

For compounds that do not work by EI, alternate methods of ionization have been developed and among them chemical ionization is the most widely used.

CI can produce molecular ions for some volatile compounds that do not give molecular ions in EI. CI is also particularly useful for highly sensitive quantitative analysis of halogenated compounds.

Mass Analysers for GC-MS   back to top »

In its simplest form the process of mass analysis in GC–MS involves the separation or filtration of analyte ions or fragments of analyte ions created in the ion source.

There are several very popular types of mass analyser associated with routine gas chromatography mass-spectrometric analysis and all differ in the fundamental way in which they separate species on a mass-to-charge basis.

Quadrupole and Ion Trap Mass analysers: Ions are filtered using electrostatic potentials applied to the elements of the mass analysers that are used to ‘select’ ions according to their mass to charge ratio; non-selected ions are ejected from the mass analysing device and are not detected.

Time of Flight (TOF) mass analysers: Use differences in flight times of accelerated ions through an extended flight path to separate ions.

Magnetic Sector Mass Analysers: Use magnetic fields to select ions by directing the beam of ions of interest towards the detector.

Quadrupole Mass Analysers: In quadrupole mass analysing devices, electric fields are used to separate ions according to their mass-to-charge ratio (m/z) as they pass along the central axis of four parallel equidistant rods (or poles). Ion separation is performed by using controlled voltages applied to the mass analyser rods, which impart an electrostatic field inside the analysing device.

Figure 10: Schematic representation of a Quadrupole Mass Analyser – note that the internal radius has been extended for clarity
Figure 10: Schematic representation of a Quadrupole Mass Analyser – note that the internal radius has been extended for clarity.

As long as x and y, which determine the position of an ion from the centre of the rods, remains less than r0, the ion will be able to pass through the quadrupole without touching the rods.  This is known as a non-collisional or stable trajectory.

Where the ion is caused to oscillate with a trajectory whose amplitude exceeds r0 it will collide with a rod and become discharged and subsequently pumped to waste. This is known as an unstable or collisional trajectory.

Figure 11: Typical working principle of a quadrupole mass analyzing.
Advantages Disadvantages
Reproducibility Low resolution
Low cost Mass discrimination. Peak height vs. mass response must be 'tuned'

Time-of-flight (TOF): The basic principles of mass analysis using time-of-flight mass analysers are relatively straightforward in comparison to many of the other typical mass analysing devices.

Ions are extracted (or produced) in short bursts or packets within the ion source and subjected to an accelerating voltage. The ions then ‘drift’ or ‘fly’ down an evacuated tube of a set length (‘d’). Once free from the region of accelerating voltage the speed at which the ions travel down the tube is dependant upon their mass (m) and charge (z). This mass analyser is useful as all ions are detected (almost) simultaneously. Scanning the mass range of all ions is very rapid and as such the inherent sensitivity of the instrument is increased.


Figure 12: Schematic of a Time of Flight Mass Analyser Flight Tube.


This analyser has the added advantage that it can produce high resolution and mass accuracy that will allow the position of one or a limited number of potential elemental formulae for the analyte molecule.

Figure 13: Schematic of a Modern Time of Flight Mass Analyser

Figure 13: Schematic of a Modern Time of Flight Mass Analyser.


Modern time of flight instruments often double the length of the flight tube of the instrument through the use of a ‘reflection’ ion mirror that increases the resolution of the instrument.

Advantages Disadvantages
  • High ion transmission
  • Fast digitizers used in TOF can have limited dynamic range
  • Highest practical mass range of all MS analyzers
  • Detection limit

    Ion Trap Mass Analyser

    Ion trap mass spectrometers work on the basis of storing ions in a “trap” and manipulating the ions by using applied DC and RF fields. The amplitude of the applied voltages enables the analyser to trap ions of specified mass to charge ratio within the analysing device. Non-selected ions are given a trajectory by the electrostatic field that causes them to exit the trap. By filling the trap with an inert gas fragmentation of selected ions is possible. This is useful when structural information is required.

    The system has some unique capabilities, including being able to perform multiple product ion scans with very good sensitivity (MSn). It should be noted that the spectra acquired with an ion trap mass analyser may be significantly different to those acquired from a triple quadrupole system due to the different collision regimes within the systems (collision energy/gas).


    Figure 14: Schematic of an Ion Trap Mass Analyser.

    Advantages Disadvantages
  • High sensitivity
  • Produces very unusual spectra if the ions are stored in the trap too long.
  • Multiple Product Ion scan capability (MS)n
  • Easily saturated
  • High resolution
  • Poor for low mass work (below 100 Da)
  • Good for DDA analyses
  • Poor dynamic range (except the most modern devices) and hence may have limited quantitative use

    Magnetic sector - Magnet/electric sector instruments are employed for mass analysis using the principle that charged species can be deflected in magnetic and electric fields. The degree of ion deflection in a magnetic field is proportional to the square root of their m/z ratio and the potential through which they are accelerated prior to mass analysis, making the measurements of mass-to-charge ratio very accurate when using this type of mass analyser.

    Electric fields are used in conjunction with magnetic fields to focus a fast moving beam of ions created in the source according to the kinetic energy of each ion, allowing each m/z value to be sharply focused prior to deflection in the magnetic field. This focusing action helps to improve the resolution of the magnetic sector mass analyser so that measurements can be made between ions whose mass to charge ratio differs by only a few parts per million.

    Figure 15: Schematic of a Magnetic Sector Mass Analyser.


    This analyser also has the added advantage that it can produce high resolution and mass accuracy that will allow the position of one, or a limited number, of potential elemental formulae for the analyte molecule.


    Tandem Mass Spectrometry (MS/MS) - MS–MS is the combination of two or more MS experiments. The aim is either to get structural information by fragmenting the ions isolated during the first experiment, and/or to achieve better selectivity and sensitivity for quantitative analysis by selecting representative ion transitions using both the first and second analysers.

    Product ion MS–MS analysis can be achieved either by coupling multiple analysers (of the same or different kind) or, with an ion trap and carrying out successive fragmentations of trapped ions.

    MSn (should read MS to the n) is an acronym that refers to multiple ion production and filtering within a single instrument. Most common instruments use a combination of quadrupoles (as shown below) with a collision cell (usually a multi-pole device) between the analysing devices in which the emergent ions from the first analyser are fragmented prior to secondary mass filtering. Other combinations of mass analysing devices such as quadrupoles and time of flight, or quadrupoles with magnetic sector instruments are possible.

    Figure 16: Schematic of a Triple Quadrupole Mass Analyser.

    1. Transfer Line: The column’s effluent is directed to the ion source
    2. Ion Source: In the ion source, the products are ionized prior to analysis in the mass spectrometer.
    3. Octapole: The ion beam that emerges from the source is focused prior to the first mass analyser.
    4. Quadrupole: In quadrople mass analysing devices, electric fields are used to separate ions according to their mass-to-charge ratio (m/z) as they pass along the central axis of four parallel equidistant rods (or poles).
    5. Collision Cell: The function of a collision cell is to modify ions by either colliding into fragments or to react them with other molecules.
    6. Detector: The ion beam that emerges from the mass analyser has to be detected and transformed into a usable signal.
    Detectors   back to top »

    Once the ions have passed the mass analyser they have to be detected and transformed into a usable signal. The detector is an important element of the mass spectrometer that generates a signal from incident ions by either generating secondary electrons, which are further amplified, or by inducing a current (generated by moving charges).

    Ion detector systems fall into two main classes:

    Point detectors: Ions are not spatially resolved and sequentially impinge upon a detector situated at a single point within the spectrometer geometry.

    Figure 17: Working principle of a point detector

    Figure 17: Working principle of a point detector

    Most quadrupole devices will operate using electron multiplier detectors (using either continuous or plate dynodes) which detect the ions exiting from the mass spectrometer and subsequently produce electrons from the ‘active’ surface coating which then are amplified in a cascade process.  An amplification factor of multiple million times for each ion is not untypical for this detector type.
    Array detectors: Ions are spatially resolved and all ions arrive simultaneously (or near simultaneously) and are recorded along a plane using a bank of detectors.
    Figure 18: Working principle of an array detector

    Figure 18: Working principle of an array detector

    Vacuum System Considerations   back to top »

    The entire MS process must be carried out at very low pressures (~10-8 atm) and in order to meet this requirement a vacuum system is required.

    The processes of ion isolation and separation on the basis of mass to charge ratio require the analyte ions under investigation to behave in a way that can be predictably managed and influenced by the instrument electrostatic components. Ions need to be guided on a specific pathway through the spectrometer, influenced only by the imposition of electric, magnetic and/or radio frequency fields, which can only be practically realized when vacuum technology is used to remove the majority of background (air) molecules, which might, for example, cause deviation of ions through collision.

    A high level of vacuum within the instrument prevents deviation of the analyte ions from the required path and assists the processes of ion movement and separation in the following ways:

    • By providing an adecuate mean free path for the analyte ions.
    • By providing collision free ion trajectories.
    • By reducing ion-molecular reactions.
    • By reducing background interference.

    The vacuum systems of most modern GC–MS systems consist of a differentially pumped system, usually with a foreline pump establishing a ‘rough’ vacuum and a high vacuum pump or pumps situated on the analyser body to establish the high levels of vacuum required for effective mass to charge ratio measurement.

    The quality of the vacuum established will have a direct bearing on the sensitivity of the detector and as such regular maintenance is required, especially for oil filled foreline pumps that should be regularly ballasted and have frequent oil changes according to the manufacturer’s specification.
    Introduction to GC-MS Data   back to top »

    Quadrupole GC–MS systems operate in two distinct modes: ‘Scanning’ and ‘Selected Ion Recording’. In the first mode of acquisition, the quadrupole settings are ramped through a range of values that allow successively lower mass to charge ratio ions to ‘scan’ the range of ions emerging from the quadrupole device.

    The scanning operation takes a finite time to complete (although scan rates of 5–20 Hz are typical) and each individual m/z value is measured for only a fraction of the time that they elute into the mass analyser.


    Figure 19: Data collection principle for a Quadrupole Device operating in ‘Scanning’ mode.

    The intensity of all peaks within a spectrum are summed to give an overall signal intensity and this may be plotted against time to give the TOTAL ION CURRENT, which has the appearance of a chromatogram obtained by GC with FID detection for example.

    The intensity of the TOTAL ION CURRENT (TIC) is governed by the scanning speed of the instrument. The faster the scan rate, the more data is collected and the intensity of ALL IONS within the spectrum increases. As all m/z values are recorded, background signal and ions at very low intensity are all summed to give instantaneous signal intensity.

    By choosing to set the quadrupole to certain voltage values, we are able to choose only certain masses for transmission through the mass analyser.

    This type of spectral experiment, known as selected or specific ion monitoring (SIM), or selected ion recording (SIR), has certain advantages over scanning wide mass ranges. Because not all m/z values are recorded the mass analyser can perform a SIM experiment very rapidly (102–104 increase over scanning experiment speeds) therefore acquiring more data points.

    Figure 20: TIC and SIC signals from a quadrupole mass analyser

    Figure 20: TIC and SIC signals from a quadrupole mass analyser


    Further, if only the ‘useful’ m/z values are recorded (i.e., those that are compound specific or most intense), the intensity of the SELECTED ION CURRENT (SIC) that is recorded will have a much higher signal to noise ratio (sensitivity) than a TIC of the same sample. In this way the sensitivity of the quadrupole mass analyser may be improved for quantitative purposes.

    In practice quadrupole instruments can be scanned over mass ranges in excess of 1000 Da in a few milliseconds, giving the advantage of real time spectral monitoring for tuning and diagnostic purposes. However, it is usual to slow the scanning speed (100 ms scans) or perform SIM experiments when analysing samples to increase instrument sensitivity by increasing the ion count at each mass.

    The following subjects are covered in

    The Theory Of HPLC
    Introduction (1.5hrs)
    Chromatographic Parameters (3hrs)
    Band Broadening (3hrs)
    Column chemistry (4hrs)
    Reverse phase (partition) chromatography (6hrs)
    Ion-Pair Chromatography (3hrs)
    Normal phase (absorption) chromatography (3hrs)
    Gradient HPLC (3hrs)
    Quantitative and Qualitative HPLC (3hrs)
    FAST HPLC (4.5hrs)
    HILIC (3hrs)
    SFC (3hrs)
    Ion Chromatography(3hrs)

    Theory and Instrumentation of GC
    Introduction (1.5hrs)
    Chromatographic Parameters (3hrs)
    Band Broadening (3hrs)
    Gas Supply and Pressure Control (2hrs)
    Sampling Techniques (4.5hrs)
    Sample Introduction (5hrs)
    GC Columns (5.5hrs)
    GC Temperature Programming (3hrs)
    GC Detectors (2.5hrs)
    SFC (3hrs)

    Instrumentation of HPLC
    Mobile Phase Considerations (3.5hrs)
    Solvent Pumping Systems (4hrs)
    Autosamplers (4.5hrs)
    Detectors (4.5hrs)

    Solid Phase Extraction
    Molecular Properties (4hrs)
    SPE Overview (3.5hrs)
    SPE Mechanisms (4.5hrs)
    Method Development (5.0hrs)
    Primary Sample Preparation Techniques (2hrs)
    Liquid / Liquid Extraction Techniques (1.5hrs) Approaches to Automation for SPE (1.5hrs)

    Fundamental GC-MS
    Introduction (1.5hrs)
    GC Considerations (4.5hrs)
    GC -MS Interfaces (2.5hrs)

    Fundamental LC-MS
    Introduction (1.5hrs)
    Electrospray Ionisation Theory (6hrs)
    Electrospray Ionisation Instrumentation (4hrs)
    Mass Analyzers (9.5hrs)
    Atmospheric Pressure Chemical Ionisation (3.5hrs)
    Atmospheric Pressure Photoionisation (3hrs)
    Solvents, Buffers and Additives (3.5hrs)
    Vacuum Systems (3hrs)
    Flow Rates and Flow Splitting (3hrs)
    Orbitrap Mass Analyzers (3hrs)

    MS Interpretation
    General Interpretation Strategies (11hrs)
    Intro to MS Proteomics Research (3.5hrs)

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