5.1.1 Short Course of Mass Spectra Interpretation
and GC/MS Based Identification
Key aspect of mass spectra interpretation is related to the fragmentation processes
occurring in the ion sources but that are mainly forced by the molecular properties of
the analytes. Interpretation of mass spectra uses various approaches.
A first one is the interpretation of the molecular ion. As a very simple fact, the
mass of organic molecules is commonly an even value (with one exception,
described later as the nitrogen rule). Consequently, fragments derived from one
bond linkage exhibit even mass values. The resulting mass spectra exhibit an even
molecular ion and are dominated by even fragment signals. Therefore, the molecular
ion can be characterized as highest even m/z value. The intensity of the molecular
characterizes the stability of the molecule or, with other words, the potential to resist
fragmentation from electron bombardment in the ion source. As a simple rule, the
higher the molecular peak intensity the higher the thermodynamic stability of the
molecule. Noteworthy, for very unstable molecules the molecular peak can disappear and is not visible in the mass spectrum. In that cases, only even fragment ions
occur in the spectra. Examples are given in Fig. 5.1.
A second approach tries to distinguish specific patterns. This can be well illustrated by examine mass spectra of aliphatic and aromatic hydrocarbons.
In Fig. 5.2a the mass spectra of n-tetradecane is given. A distinct pattern is
obvious that is typical for n-alkanes in general. A higher number of fragments, all
with the same m/z differences, appear with an abundance maximum at lower masses
(m/z 43 and 57 corresponding to C 3 H 7 and C 4 H 9 ions) followed by an exponential
but uniform decrease of abundance to higher masses. Only a slight increase towards
the molecular ion is visible. The relative low abundance of the molecular ion points
to a low thermodynamic stability of molecule or a high intrinsic potential for
fragmentation. The pattern of peak intensities also provides information on the
stability of the fragmented moieties: the higher the abundance the higher the
thermodynamic stability. Hence, propyl and butyl ions seem to be the most stable
ones. The systematic differences between the main peaks of m/z 14 clearly reflect the
homologues units of methylene groups –CH 2 –. Interestingly, the insertion of a
double bond does not change the principal pattern, but shifts the homologues mass
series by two units, reflecting the two missing hydrogen atoms (see Fig. 5.2b).
Noteworthy, the position of the double bond cannot be determined by mass spectrometry due to a dislocation of the unsaturation along the carbon chain during
ionization.
A first glance on the quality of MS based identification can be obtained by
comparing the mass spectra of the n-alkane (Fig. 5.2) with those of branched
alkanes, so-called iso-alkanes as given in Fig. 5.3. Variety of fragment peaks as
well as the systematic mass differences are obviously identical, but the abundance
pattern varies slightly. A few peaks in the higher mass range exceed a little bit the
uniform exponential decrease. These shifts point to the branched moieties, in
particular to their positions within the carbon chain. As basic aspect, the bond
98
5 GC/MS Data Evaluation
and GC/MS Based Identification
Key aspect of mass spectra interpretation is related to the fragmentation processes
occurring in the ion sources but that are mainly forced by the molecular properties of
the analytes. Interpretation of mass spectra uses various approaches.
A first one is the interpretation of the molecular ion. As a very simple fact, the
mass of organic molecules is commonly an even value (with one exception,
described later as the nitrogen rule). Consequently, fragments derived from one
bond linkage exhibit even mass values. The resulting mass spectra exhibit an even
molecular ion and are dominated by even fragment signals. Therefore, the molecular
ion can be characterized as highest even m/z value. The intensity of the molecular
characterizes the stability of the molecule or, with other words, the potential to resist
fragmentation from electron bombardment in the ion source. As a simple rule, the
higher the molecular peak intensity the higher the thermodynamic stability of the
molecule. Noteworthy, for very unstable molecules the molecular peak can disappear and is not visible in the mass spectrum. In that cases, only even fragment ions
occur in the spectra. Examples are given in Fig. 5.1.
A second approach tries to distinguish specific patterns. This can be well illustrated by examine mass spectra of aliphatic and aromatic hydrocarbons.
In Fig. 5.2a the mass spectra of n-tetradecane is given. A distinct pattern is
obvious that is typical for n-alkanes in general. A higher number of fragments, all
with the same m/z differences, appear with an abundance maximum at lower masses
(m/z 43 and 57 corresponding to C 3 H 7 and C 4 H 9 ions) followed by an exponential
but uniform decrease of abundance to higher masses. Only a slight increase towards
the molecular ion is visible. The relative low abundance of the molecular ion points
to a low thermodynamic stability of molecule or a high intrinsic potential for
fragmentation. The pattern of peak intensities also provides information on the
stability of the fragmented moieties: the higher the abundance the higher the
thermodynamic stability. Hence, propyl and butyl ions seem to be the most stable
ones. The systematic differences between the main peaks of m/z 14 clearly reflect the
homologues units of methylene groups –CH 2 –. Interestingly, the insertion of a
double bond does not change the principal pattern, but shifts the homologues mass
series by two units, reflecting the two missing hydrogen atoms (see Fig. 5.2b).
Noteworthy, the position of the double bond cannot be determined by mass spectrometry due to a dislocation of the unsaturation along the carbon chain during
ionization.
A first glance on the quality of MS based identification can be obtained by
comparing the mass spectra of the n-alkane (Fig. 5.2) with those of branched
alkanes, so-called iso-alkanes as given in Fig. 5.3. Variety of fragment peaks as
well as the systematic mass differences are obviously identical, but the abundance
pattern varies slightly. A few peaks in the higher mass range exceed a little bit the
uniform exponential decrease. These shifts point to the branched moieties, in
particular to their positions within the carbon chain. As basic aspect, the bond
98
5 GC/MS Data Evaluation