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Guide to Mass Spectrometers

By: John Buie Published: September 28 2012

Mass spectrometry (MS) involves the ionization of chemical samples to generate charged molecules or molecular fragments and measuring their mass-to-charge ratio. MS is used for determining the elemental composition of a sample and the chemical structures of molecules, such as peptides and other compounds. The first stage in selecting a mass spectrometer is to decide whether you need a standalone instrument or an integrated system that combines mass spectrometry with other analytical techniques, such as GC or LC.

Standalone Systems

A number of techniques are available to ionize the sample as it is introduced into the mass spectrometer. Different ionization techniques are available, and the appropriate method should be selected based on the properties of the sample.

A. Inductively Coupled Plasma Mass Spectrometry (ICP-MS)

ICP-MS is a highly sensitive type of mass spectrometry widely used for the determination of a range of metals and nonmetals at concentrations below one part in 10.

B. Matrix-Assisted Laser Desorption/Ionization (MALDI)

MALDI is a gentle ionization technique that allows the analysis of biomolecules, such as proteins and peptides, and large organic molecules, such as polymers and dendrimes. Molecules of this type tend to be too fragile to be analyzed by conventional ionization methods, fragmenting when ionized.

C. Fourier Transform Ion Cyclotron Resonance (FTICR) Mass Spectrometry

FTICR is a very high resolution technique in that mass can be determined with very high accuracy. Many applications of FTICR-MS use this mass accuracy to help determine the composition of molecules based on accurate mass. This is possible due to the mass defect of the elements.

D. Thermal Ionization Mass Spectrometry (TIMS)

TIMS relies on the thermal ionization of samples prior to detection and is widely used in radiometric dating, geochemistry, geochronology, and cosmochemistry. the sample is ionized under vacuum. The relative abundance of different isotopes can then be measured, yielding isotope ratios.

Integrated Systems

Mass spectrometry is frequently combined with separation techniques to form powerful and widely used integrated systems such as GC-MS, lC-MS or MS-MS-GC. The appropriate choice of a system depends on the properties of the sample.

A. GC-MS

GC-MS is considered the gold standard for many analytical processes, including forensic substance identification. Other applications include drug detection, fire investigation, environmental analysis, explosives investigation, and identification of unknown samples. In addition, it can identify trace elements in disintegrated materials. GC-MS instruments are available with a number of different mass analyzers, of which time-of-flight (TOF) and quadrupole are the most common.

1. GC-MS –Time-of-Flight
GC-MS-TOF delivers faster results and a greater sensitivity compared with quadrupole systems. GC-TOF instruments are found in environmentally focused and material analysis labs for organic analysis and large molecule screening applications. They are also used in advanced life science research.

  • High Resolution TOF GC-MS: High resolution mass spectrometry techniques allow molecular fragments that are close together in m/z to be successfully separated.

2. GC-MS (Quadrupole)
The quadrupole GC-MS is a particularly popular instrument due to its reliability, cost advantage, ease-of-use, versatility, and high sensitivity. However, this technique is not typically used for unknown or new compound identification due to its nominally unit mass resolution and lack of tandem MS capabilities.

  • GC-MS (Quadrupole) – Portable: Portable gC-ms are ideal for use in the field or where space in a laboratory is limited. These instruments can be highly accurate and versatile.
  • GC-MS - Quadrupole Standard: GC-MS instruments offer a range of ionization techniques.
  • Electron Ionization (EI): EI is by far the most common and perhaps standard form of ionization. Molecules are bombarded with free electrons emitted from a filament, causing the molecule to fragment in a characteristic and reproducible way.
  • Electron Ionization (EI) or Chemical Ionization (CI): Some mass spectrometers offer a choice of EI or CI. In CI, a reagent gas is introduced into the mass spectrometer to interact with the analyte and cause a 'soft' ionization of the molecule of interest. 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.
  • Electron Ionization (EI) or Chemical Ionization (CI) (PCI or NCI): 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.

3. GC-MS (Ion Trap)
The ion-trap mass spectrometer uses three electrodes to trap ions in a small volume. The advantages of the ion-trap mass spectrometer include compact size and the ability to trap and accumulate ions to increase the signal-to-noise ratio of a measurement.

  • Electron Ionization (EI): EI is by far the most common and perhaps standard form of ionization. Molecules are bombarded with free electrons emitted from a filament, causing the molecule to fragment in a characteristic and reproducible way.
  • Electron Ionization (EI) or Chemical Ionization (CI): Some mass spectrometers offer a choice of EI or CI. In CI, a reagent gas is introduced into the mass spectrometer to interact with the analyte and cause a 'soft' ionization of the molecule of interest. 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.
  • Electron Ionization (EI) or Chemical Ionization (CI) (PCI or NCI): 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.
  • External Ionization Source

B. LC-MS

LC-MS is a powerful technique used for many applications that has very high sensitivity and selectivity. Generally, its application is oriented towards the specific detection and potential identification of chemicals in the presence of other chemicals (in a complex mixture).

1. Quadrupole
Quadrupole mass spectrometers use oscillating electrical fields to selectively stabilize or destabilize the paths of ions passing through a radiofrequency field created between 4 parallel rods.

2. Ion Trap
The quadrupole LC-MS is a particularly popular instrument due to its reliability, cost advantage, ease-of-use, versatility, and high sensitivity. However, this technique is not typically used for unknown or new compound identification, due to its nominally unit mass resolution and lack of tandem MS capabilities.

3. Time-of-Flight (TOF)
TOF analyzers use an electric field to accelerate the ions through the same potential, and then measure the time they take to reach the detector. Lighter ions will reach the detector first.

4. Quadrupole Time-of-Flight (Q-TOF)
Q-TOF mass spectrometers are a hybrid quadrupole and time-of-flight (TOF) mass spectrometer that also include MS-MS capability. In MS mode the ion guide is operated by the quadrupole, in MS-MS mode the quadrupole functions as the mass selection device. In both MS and MS-MS mode the TOF analyzer acts as the mass resolving device. During MS-MS usage a collision cell placed between the quadrupole and TOF analyzer induces fragmentation, while final detection is achieved with a mirochannel plate.

5. Orbitrap
Orbitrap LC-MS technology routinely delivers high resolution and mass accuracy through an extended dynamic range and high sensitivity. Orbitrap mass spectrometers are often used in protein and metabolite identification, characterization and quantitation, among many other applications.

6. Quadrupole Orbitrap
The Quadrupole orbitrap mass spectrometer combines both quadrupole precursor selection and high-resolution accurate mass (HR-AM) orbitrap mass analysis in one system.

C. GC-MS-MS

MS-MS, also known as tandem MS, is achieved by adding a second MS to the output of the first system. This technique reduces sample prep, shortens analysis cycles, eliminates false results, and simplifies data review for improved productivity.

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