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Mass Spectrometry

Published on Nov 30, 2023


Mass Spectrometry is a powerful technique for identifying unknowns, studying molecular structure, and probing the fundamental principles of chemistry. Applications of mass spectrometry include identifying and quantitating pesticides in water samples, it identifying steroids in athletes, determining metals at ppq (Parts Per Quadrillion) levels in water samples, carbon-14 dating the Shroud of Turin using only 40 mg of sample (1), looking for life on Mars, determining the mass of an 28Si atom with an accuracy of 70 ppt(2), and studying the effect of molecular collision angle on reaction mechanisms.

Mass spectrometry is essentially a technique for "weighing" molecules.* Obviously, this is not done with a conventional balance or scale. Instead, mass spectrometry is based upon the motion of a charged particle, called an ion, in an electric or magnetic field. The mass to charge ratio (m/z)** of the ion effects this motion. Since the charge of an electron is known, the mass to charge ratio a measurement of an ion's mass. Typical mass spectrometry research focuses on the formation of gas phase ions, the chemistry of ions, and applications of mass spectrometry.

A variety of ionization techniques are used for mass spectrometry. Most ionization techniques excite the neutral analyte molecule which then ejects an electron to form a radical cation (M+)*. Other ionization techniques involve ion molecule reactions that produce adduct ions (MH+).** The most important considerations are the physical state of the analyte and the ionization energy. Electron ionization and chemical ionization are only suitable for gas phase ionization. Fast atom bombardment, secondary ion mass spectrometry, electrospray, and matrix assisted laser desorption are used to ionize condensed phase samples. The ionization energy issignificant because it controls the amount of fragmentation observed in the mass spectrum. .

Although this fragmentation complicates the mass spectrum, it provides structural information for the identification of unknown compounds. Some ionization techniques are very soft and only produce molecular ions,* other techniques are very energetic and cause ions to undergo extensive fragmentation. Although this fragmentation complicates the mass spectrum, it provides structural information for the identification of unknown compounds. Electron Ionization. Electron Ionization (EI) is the most common ionization technique used for mass spectrometry.** EI works well for many gas phase molecules, but it does have some limitations. Although the mass spectra are very reproducible and are widely used for spectral libraries, EI causes extensive fragmentation so that the molecular ion is not observed for
many compounds. Fragmentation is useful because it provides structural information for interpreting unknown spectra.

The electrons used for ionization are produced by passing a current through a wire filament (Figure 2). The amount of current controls the number of electrons emitted by the filament. An electric field accelerates these electrons across the source region to prodce a beam of high energy electrons. When an analyte molecule passes through this electron beam, a valence shell electron can be removed from the molecule to produce an ion.

Measurement principles

In the following figure the essential parts of an analytical mass-spectrometer are depicted. Its procedure is as follows:

Mass Spectrometry

1. A little amount of a compound, typically one micromole or less is evaporated. The vapor is leaking into the ionization chamber where a pressure is maintained of about 10-7 mbar.

2. The vapor molecules are now ionized by an electron-beam. A heated cathode, the filament, produces this beam. Ionization is achieved by inductive effects rather then strict collision. By loss of valence electrons, mainly positive ions are produced.

3. The positive ions are forced out of the ionization chamber by a small positive charge (several Volts) applied to the repeller opposing the exit-slit (A). After the ions have left the ionization chamber, they are accelerated by an electrostatic field (A>B) of several hundreds to thousands of volts before they enter the analyzer.

4. The separation of ions takes place in the analyzer at a pressure of about 10-8 mbar. This is achieved by applying a strong magnetic field perpendicular to the motional direction of the ions. The fast moving ions then will follow a circular trajectory, due to the Lorenz acceleration, whose radius is determined by the mass/charge ratio of the ion and the strength of the magnetic field. Ions with different mass/charge ratios are forced through the exit-slit by variation of the accelerating voltage (A>B) or by changing the magnetic-field force.

5. After the ions have passed the exit-slit, they collide on a collector-electrode.

The resulting current is amplified and registered as a function of the magnetic-field force or the accelerating voltage. The applicability of mass-spectrometry to the identification of compounds comes from the fact that after the interaction of electrons with a given molecule an excess of energy results in the formation of a wide range of positive ions. The resulting mass distribution is characteristic (a fingerprint) for that given molecule. Here there are certain parallels with IR and NMR. Massspectrograms in some ways are easier to interpret because information is presented in terms of masses of structure-components.


As already indicated a compound normally is supplied to a mass-spectrometer as a vapor from a reservoir. In that reservoir, the prevailing pressure is about 10 to 20 times as high as in the ionization chamber. In this way, a regular flow of vapor-molecules from the reservoir into the mass-spectrometer is achieved. For fluids that boil below about 150oC the necessary amount evaporates at room temperature. For less volatile compounds, if they are thermally stabile, the reservoir can be heated. If in this way sampling can't be achieved one passes onto to direct insertion of the sample.

The quality of the sample, volatility and needed amount are about the same for massspectrometry and capillary gas chromatography. Therefore, the effluent of a GC often can be brought directly into the ionization chamber. Use is then made of the excellent separating power of a GC in combination with the power to identify of the mass-spectrometer. When packed GC is used, with a much higher supply of carrier-gas, it is necessary to separate the carrier gas prior to the introduction in the mass-spectrometer (jet-separator).

The separation of ions.

There are several ways to separate ions with different mass/charge ratios, e.g. magnetic sector analyzers, quadrupole mass filters, quadrupole ion traps, time-of-flight analyzers and ion cyclotron-resonance instruments. The first two types presently account for the great majority of instruments used in organic chemistry. Ideally, when separating, it is possible to distinguish between ions with very little difference in mass/charge ratio while maintaining a high flow of ions. These conditions are not in agreement and a compromise should be reached. For some applications a nominal mass discrimination will do, for other applications a much higher resolving power is needed. For example when one needs to distinguish between ions C2H4 +, CH2N+, N2 + and CO+ (with respective masses of 28.031, 28.019, 28.006 and 27.995 amu) a resolving power of 0.01 mass units is needed. The main differences in mass-spectrometers are encountered in the way ions are separated.

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