phenylalanine (F) immonium ion, which we will refer to as a near edge X-ray
absorption mass spectrometry (NEXAMS) spectrum. Qualitatively, very similar
NEXAMS spectra are observed for all fragments. The spectrum in Fig. 11.8b is
dominated by two sharp peaks at 285.4 (A) and 288.4 eV (B) with full widths at
half-maximum (fwhm) of 0.6 and 0.7 eV, respectively. A broader structure (C)
starts approximately at 290 eV and extends far beyond 300 eV. Very recently,
photoionisation of the large protein cytochrome c was studied, and very similar
partial ion yields have been observed [20]. However, whereas for cytochrome c, the
structure C dominates the spectrum, here highest intensities are observed for A or B.
Transitions can be assigned to the NEXAMS peaks, by comparison to existing
near edge X-ray absorption data for the gas-phase amino acids tyrosine (Y),
phenylalanine (F) [7] and glycine (G) [9]. Peak A (285.4 eV) is solely due to C
1s excitations into the π*-orbitals of the Y and F aromatic rings. This transition
therefore is a good candidate for localised ionisation in future pump-probe studies.
Peak B (288.4 eV) is due to C 1s–π C¼O
* transitions in the amino group and thus
not site specific, regarding single amino acids. A small contribution on the low
energy side of B is due to C 1s !σ* excitations in the Y and F aromatic rings.
Structure C is partly due to C 1s ionisation of the peptide. The respective binding
energies have been determined experimentally for glycylglycine as 292.32 eV (C
bonded to amino groups), 293.85 eV (peptide bond C), and 295.37 eV (carboxyl
terminal C) [10]. The ionisation energies of the aromatic side chains are 290.2 eV
(Y) and 290.3 eV (F) [9] which is exactly at the onset of the broad structure C (see
Fig. 11.8). Structure C is thus partly due to K-shell ionisation, which, in light
elements such as C, rapidly decays nonradiatively by Auger de-excitation [37].
Here, a triply charged [YGGFL+H]
3+ is formed, whereas below threshold, resonant
Auger decay leads to the formation of [YGGFL+H]
2+ intermediates, which may
contribute to a peak at m ¼ 278. Peak C also includes contributions from various C
1s σ
* and Rydberg transitions. In the high energy tail of C, mainly shape resonances
contribute [9, 10].
In the context of the VUV results, it is of particular interest to have a closer look
into the NEXAMS spectra for the immonium ions of the aromatic amino acids and
their fragments, as well as into the spectra for the fragments related to the two-step
fragmentation mechanism.
Figure 11.9 displays the results for the immonium related ions. It is again
obvious that these fragments are formed for absorption along the backbone (B),
the aromatic sidechains (A) and in case of double ionisation and other transitions
(C). The Y immonium ion with m ¼ 136 has a relatively large cross section for
photoabsorption on the aromatic rings—peak A is high. For the F immonium ion
(m ¼ 120), A is relatively smaller, probably due to the fact that for a non-terminal
immonium ion, two rather than one bonds need to be disrupted. With decreasing
size of immonium fragments, A is getting relatively smaller and C increases, i.e.
ionisation becomes more dominant. This decrease of peak A is intuitively expected
as higher initial charge and/or excitation energy in the system usually shifts the
fragmentation pattern toward smaller masses.
222
T. Schlatho ¨ lter and R. Hoekstra
absorption mass spectrometry (NEXAMS) spectrum. Qualitatively, very similar
NEXAMS spectra are observed for all fragments. The spectrum in Fig. 11.8b is
dominated by two sharp peaks at 285.4 (A) and 288.4 eV (B) with full widths at
half-maximum (fwhm) of 0.6 and 0.7 eV, respectively. A broader structure (C)
starts approximately at 290 eV and extends far beyond 300 eV. Very recently,
photoionisation of the large protein cytochrome c was studied, and very similar
partial ion yields have been observed [20]. However, whereas for cytochrome c, the
structure C dominates the spectrum, here highest intensities are observed for A or B.
Transitions can be assigned to the NEXAMS peaks, by comparison to existing
near edge X-ray absorption data for the gas-phase amino acids tyrosine (Y),
phenylalanine (F) [7] and glycine (G) [9]. Peak A (285.4 eV) is solely due to C
1s excitations into the π*-orbitals of the Y and F aromatic rings. This transition
therefore is a good candidate for localised ionisation in future pump-probe studies.
Peak B (288.4 eV) is due to C 1s–π C¼O
* transitions in the amino group and thus
not site specific, regarding single amino acids. A small contribution on the low
energy side of B is due to C 1s !σ* excitations in the Y and F aromatic rings.
Structure C is partly due to C 1s ionisation of the peptide. The respective binding
energies have been determined experimentally for glycylglycine as 292.32 eV (C
bonded to amino groups), 293.85 eV (peptide bond C), and 295.37 eV (carboxyl
terminal C) [10]. The ionisation energies of the aromatic side chains are 290.2 eV
(Y) and 290.3 eV (F) [9] which is exactly at the onset of the broad structure C (see
Fig. 11.8). Structure C is thus partly due to K-shell ionisation, which, in light
elements such as C, rapidly decays nonradiatively by Auger de-excitation [37].
Here, a triply charged [YGGFL+H]
3+ is formed, whereas below threshold, resonant
Auger decay leads to the formation of [YGGFL+H]
2+ intermediates, which may
contribute to a peak at m ¼ 278. Peak C also includes contributions from various C
1s σ
* and Rydberg transitions. In the high energy tail of C, mainly shape resonances
contribute [9, 10].
In the context of the VUV results, it is of particular interest to have a closer look
into the NEXAMS spectra for the immonium ions of the aromatic amino acids and
their fragments, as well as into the spectra for the fragments related to the two-step
fragmentation mechanism.
Figure 11.9 displays the results for the immonium related ions. It is again
obvious that these fragments are formed for absorption along the backbone (B),
the aromatic sidechains (A) and in case of double ionisation and other transitions
(C). The Y immonium ion with m ¼ 136 has a relatively large cross section for
photoabsorption on the aromatic rings—peak A is high. For the F immonium ion
(m ¼ 120), A is relatively smaller, probably due to the fact that for a non-terminal
immonium ion, two rather than one bonds need to be disrupted. With decreasing
size of immonium fragments, A is getting relatively smaller and C increases, i.e.
ionisation becomes more dominant. This decrease of peak A is intuitively expected
as higher initial charge and/or excitation energy in the system usually shifts the
fragmentation pattern toward smaller masses.
222
T. Schlatho ¨ lter and R. Hoekstra