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Fundamentals

Mass spectrometry is a sensitive analytical technique which is able to quantify known analytes and to identify unknown molecules at the picomoles or femto-moles level. A fundamental requirement is that atoms or molecules are ionized and analyzed as gas phase ions which are characterized by their mass (m) and charge (z). A mass spectrometer is an instrument which measures precisely the abundance of molecules which have been converted to ions. In a mass spectrum m/z is used as the dimensionless quantity that is an independent variable. There is still some ambiguity how the x-axis of the mass spectrum should be defined. Mass to charge ratio should not lo longer be used because the quantity measured is not the quotient of the ion's mass to its electric charge. Also, the use of the Thomson unit (Th) is considered obsolete [15, 16]. Typically, a mass spectrometer is formed by the following components: (i) a sample introduction device (direct probe inlet, liquid interface), (ii) a source to produce ions, (iii) one or several mass analyzers, (iv) a detector to measure the abundance of ions, (v) a computerized system for data treatment (Fig. 1.1).

Most mass analyzers operate under high vacuum or at low pressure, so that the charged particles do not deviate from their trajectories due to collision with resid-

Fig. 1.1 Principle of a mass spectrometer, the outcome of an analysis is a mass spectrum with m/z in the x-axis and ion intensities in the y-axis. The ion intensities can be given in percentages (relative intensity) or in counts or in counts per second (absolute intensity). The most abundant peak at m/z 578.6 is called the base peak.

Fig. 1.1 Principle of a mass spectrometer, the outcome of an analysis is a mass spectrum with m/z in the x-axis and ion intensities in the y-axis. The ion intensities can be given in percentages (relative intensity) or in counts or in counts per second (absolute intensity). The most abundant peak at m/z 578.6 is called the base peak.

ual gas and thus never reach the detector. Mass spectrometers can be grouped into different types of operation mode: continuous mode (magnetic sector, quad-rupole), pulsed mode (time of flight), and ion trapping mode (quadrupole traps, Fourier transform ion cyclotron, orbitrap). In the source, positive or negative ions are produced either under vacuum or at atmospheric pressure. Depending on the ionization technique either molecular ions (M+ ) with an odd electron number or protonated ions ([M+H]+) with an even electron number are formed. In the mass spectrum when no fragmentation occurs, in general the most intense peak represents the molecular ion, the protonated molecule or a molecule with an ad-duct ion followed by ions containing the heavier isotopes. Mr is the mass of one molecule of a compound, with a specified isotopic composition, relative to one-twelfth of the mass of one atom of 12C. An important aspect is that many atoms have naturally occurring isotopes which can be differentiated by mass spectrome-try. Molecules analyzed by organic mass spectrometry contain in general carbon, hydrogen, nitrogen, oxygen and sulfur. These elements have stable isotopes (Table 1.1) which have different atomic mass. Therefore, under certain conditions and for a given molecule, the isotopic contribution can be measured by mass spectrometry.

For example, carbon is composed of two naturally occurring isotopes: 12C for 98.9% and 13C for 1.1% abundance, respectively. For cyclohexane (C6H12) the M+' ion composed exclusively of 12 C and 1H atoms is observed at a nominal mass of m/z 84. The nominal mass is the integer of the sum of the masses calculated from the most abundant naturally occurring isotopes. The monoisotopic

Table 1.1 Isotopic abundance of common elements. Interesting to note is that chlorine and bromine have two naturally intense isotopes.

Element

Atomic mass

Symbol

Isotopic mass

Abundance (%)

Carbon

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