Mass Spectrometry : Introduction

Mass spectrometry (MS) provides the molecular weight and valuable information about the molecular formula, using a very small sample.

Introduction to Mass Spectrometry

Infrared spectroscopy gives information about the functional groups in a molecule, but it tells little about the size of the molecule or what heteroatoms are present.

– To determine a structure, we need a molecular weight and a molecular formula.

– Molecular formulas were once obtained by careful analysis of the elemental composition and molecular weight was determined by freezing-point depression or some other difficult technique.

– These are long and tedious processes, and they require a large amount of pure material. Many important compounds are available only in small quantities, and they may be impure.

– Mass spectrometry (MS) provides the molecular weight and valuable information about the molecular formula, using a very small sample.

– High-resolution mass spectrometry (HRMS) can provide an accurate molecular formula, even for an impure sample.

– The mass spectrum also provides structural information that can confirm a structure derived from NMR and IR spectroscopy.

– Mass spectrometry is fundamentally different from spectroscopy. Spectroscopy involves the absorption (or emission) of light over a range of wavelengths.

– Mass spectrometry does not use light at all. In the mass spectrometer, a sample is struck by high-energy electrons, breaking the molecules apart.

– The masses of the fragments are measured, and this information is used to reconstruct the molecule.

– The process is similar to analyzing a vase by shooting it with a rifle and then weighing all the pieces.

(1) The Mass Spectrometer

– A mass spectrometer ionizes molecules in a high vacuum, sorts the ions according to their masses, and records the abundance of ions of each mass.

– A mass spectrum is a graph plotted by the mass spectrometer, with the masses plotted as the x-axis and the relative number of ions of each mass on the y-axis.

– Several methods are used to ionize samples and then to separate ions according to their masses.

– We will emphasize the most common techniques, electron impact ionization for forming the ions, and magnetic deflection for separating the ions.

Electron Impact Ionization

– In the ion source, the sample is bombarded by a beam of electrons.

– When an electron strikes a neutral molecule, it may ionize that molecule by knocking out an additional electron.

– When a molecule loses one electron, it then has a positive charge and one unpaired electron. The ion is therefore a radical cation.

– The electron impact ionization of methane is shown next.

– Most carbocations have a three-bonded carbon atom with six paired electrons in its
valence shell.

– The radical cation just shown is not a normal carbocation. The carbon atom has seven electrons around it, and they bond it to four other atoms.

– This unusual cation is represented by the formula , with + indicating the positive charge and the . indicating the unpaired electron.

– In addition to ionizing a molecule, the impact of an energetic electron may break it apart.

– This fragmentation process gives a characteristic mixture of ions.

– The radical cation corresponding to the mass of the original molecule is called the molecular ion, abbreviated M+.

– The ions of smaller molecular weights are called fragments.

– Bombardment of ethane molecules by energetic electrons, for example, produces the molecular ion and several fragments.

-Both charged and uncharged fragments are formed, but only the positively charged fragments are detected by the mass spectrometer.

– We will often use green type for the (invisible) uncharged fragments.

Separation of Ions of Different Masses

– Once ionization and fragmentation have formed a mixture of ions, these ions are separated and detected.

– The most common type of mass spectrometer shown in the next Figure, separates ions by magnetic deflection.

Mass Spectrometry : Introduction
A double-focusing mass spectrometer. This one is combined with a gas chromatograph to use as a GC–MS. The gas chromatograph separates a mixture into its components and injects the purified components into the ion source of the mass spectrometer
Mass Spectrometry : Introduction
Diagram of a mass spectrometer. A beam of electrons causes molecules to ionize and fragment. The mixture of ions is accelerated and passes through a magnetic field, where the paths of lighter ions are bent more than those of heavier ions. By varying the magnetic field, the spectrometer plots the abundance of ions of each mass


– After ionization, the positively charged ions are attracted to a negatively charged accelerator plate, which has a narrow slit to allow some of the ions to pass through.

– The ion beam enters an evacuated flight tube, with a curved portion positioned between the poles of a large magnet.

– When a charged particle passes through a magnetic field, a transverse force bends its path.

– The path of a heavier ion bends less than the path of a lighter ion.

– The exact radius of curvature of an ion’s path depends on its mass-to-charge ratio, symbolized by m/z (or by m/e in the older literature).

– In this expression, m is the mass of the ion (in amu) and z is its charge in units of the electronic charge.

– The vast majority of ions have a charge of +1, so we consider their path to be curved by an amount that depends only on their mass.

– At the end of the flight tube is another slit, followed by an ion detector connected to an amplifier.

– At any given magnetic field, only ions of one particular mass are bent exactly the right amount to pass through the slit and enter the detector.

– The detector signal is proportional to the number of ions striking it.

– By varying the magnetic field, the spectrometer scans through all the possible ion masses and produces a graph of the number of ions of each mass.

(2) The Mass Spectrum

– The mass spectrometer usually plots the spectrum as a graph on a computer screen.

– This information is tabulated, and the spectrum is printed as a bar graph or as a table of relative abundances (see Figure):

Mass Spectrometry : Introduction

– In the printed mass spectrum, all the masses are rounded to the nearest whole-number mass unit.

– The peaks are assigned abundances as percentages of the strongest peak, called the base peak.

– Notice that the base peak does not necessarily correspond to the mass of the molecular ion.

– It is simply the strongest peak, making it easy for other peaks to be expressed as percentages.

– A molecular ion peak (also called the parent peak) is observed in most mass spectra, meaning that a detectable number of molecular ions (M+) reach the detector without fragmenting.

– These molecular ions are usually the particles of the highest mass in the spectrum and (for compounds not containing nitrogen) the molecular ion usually has an even-numbered mass.

– The value of m/z for the molecular ion immediately gives the molecular weight of the compound.

– If no molecular ion peak is observed in the standard mass spectrum, the operator can use a gentler ionization.

– The energy of the electron beam can be decreased from the typical 70 electron volts (eV) to 20–25 eV, where much less fragmentation occurs.

(3)  Mass Spectrometry of Mixtures: The GC–MS

– Mass spectrometry is combined with gas chromatography for routine analysis of mixtures of compounds, such as reaction mixtures or environmental samples.

– The following Figure shows a simplified diagram of a common type of GC–MS.

Block diagram of a gas chromatograph–mass spectrometer (GC–MS). The gas chromatograph column separates the mixture into its components. The quadrupole mass spectrometer scans the mass spectra of the components as they leave the column.


– The gas chromatograph uses a heated capillary column coated on the inside with silicone rubber (or other stationary phase) to separate the components of the mixture.

– A small amount of sample (about 10-6 grams is enough) is injected into a heated injector, where a gentle flow of helium sweeps it into the column.

– As the sample passes through the column, the more volatile components (that interact less with the stationary phase) move through the column faster than the less volatile components.

– The separated components leave the column at different times, passing through a transfer line into the ion source of the mass spectrometer, where the molecules are ionized and allowed to fragment.

– Most gas chromatograph-mass spectrometer systems use a quadrupole mass filter to separate the ions.

– In a high vacuum, the ions pass down the length of four rods, which have varying voltages applied to them. (The figure above shows two of the four rods.)

– The varying electric fields cause the ions to follow complex orbits, and only one mass reaches the detector at any instant.

– By scanning the voltages, a wide range of masses can be measured in less than 1 second.

– In this way, many mass spectra are taken and stored on a computer disk as the components of the sample pass from the chromatograph column into the mass spectrometer.

– This powerful GC–MS combination allows many components of a mixture to be separated by the gas chromatograph and later identified by their mass spectra.

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