(1)University of Groningen

Hele tekst

(1)University of Groningen. Photoionization and excitation processes in proteins and peptides Egorov, Dmitrii. IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below.. Document Version Publisher's PDF, also known as Version of record. Publication date: 2018 Link to publication in University of Groningen/UMCG research database. Citation for published version (APA): Egorov, D. (2018). Photoionization and excitation processes in proteins and peptides. Rijksuniversiteit Groningen.. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum.. Download date: 17-07-2021.

(2) EXPERIMENT. Chapter 2 Experiment Most experiments presented in this thesis were performed with the tandem mass spectrometer PAULTJE. For a few experiments the nanocluster trap mass spectrometer [1] installed at the BESSY II synchrotron was used. PAULTJE was described in detail previously in the PhD theses of Sadia Bari [2] and Olmo Gonzalez-Magaña [3]. I will focus on the changes and improvements of the setup made during my PhD project which mainly concern the improvement of the biomolecular ion beam current. A high current which defines the target density is a stringent requirement for being able to perform experiments on gas phase molecules. Key aspects of a high-fluence source are variable frequency and amplitude RF supplies for ion funnel and octupole, allowing for maximum control over ion transmission, as well as large diameter inlet capillaries. In order to understand the dependency of ion transmission on RF-amplitude, frequency and pressure, SIMION 8.0.4 simulations of the ion transmission through the ion funnel and octupole were performed and compared with experimental data. Based on the performance tests, the entire design of the existing ion funnel chamber was improved. The photoabsorption experiments were performed at VUV and soft X-rays beamlines of the 3rd generation synchrotron BESSY II. Therefore, also a short description of the BESSY II facility and in particular the beamlines used by us is given.. 15. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 21.

(3) EXPERIMENT. 2.1. PAULTJE. The PAULTJE apparatus is a mobile tandem mass-spectrometry setup able to perform a wide range of experiments with gas-phase molecular ions. Examples are soft X-ray and VUV photoabsorption studies on peptides and proteins [4-7], nucleotides [8] and polyaromatic hydrocarbons (PAH) [9, 10], keV ion collision experiments [11, 12], femtosecond laser experiments [13, 14] and hydrogenation and abstraction reactions involving PAHs [15, 16]. The interaction of target molecular ions with synchrotron radiation, keV ion beams or atomic hydrogen takes place in the heart of the setup – the 3D RF Paul Trap, for which’s invention, Wolfgang Paul was awarded the Nobel Prize [17]. In order to gently transfer biomolecular ions into the gas-phase electrospray ionization (ESI), another Nobel Prize invention [18], is employed. Molecular ions which are produced by the electrospray ionization source are generated at atmospheric pressure. However, typical pressures in the Paul trap are as low as 10-6-10-7 mbar in order to prevent photon or keV ion interactions with residual gas in the trap. The transfer of ions from atmospheric pressure to high vacuum is a sophisticated multistage process, whose efficiency defines the transmission of ions from the source to the trap. The process starts with the ions being transferred from the atmospheric pressure region through a heated capillary (T=350 K) into a RF ion funnel (3-7x10-1 mbar) where the ions are phase space compressed. Subsequently, the ions enter a RF-octupole (3-5x10-4 mbar), in which they are accumulated for hundreds of ms up to several seconds by controlling the bias voltage on the exit diaphragm of the octupole. The ions are extracted from the octupole by lowering the exit diaphragm bias voltage for a duration of about 50 ms. The ions then enter the RF quadrupole mass-filter, which is used to mass-select the molecule with the m/z of interest. Eventually, the ions enter the Paul trap, where they are subjected to a 50 ms pulse of helium buffer gas which facilitates trapping by collisionally cooling of excess ion kinetic energy. The cooled and trapped ions are then exposed to the photon or keV ion beam for a well-defined period, before a second helium buffer gas pulse is injected in order to cool down the kinetic energy of fragments formed in dissociation processes of the precursor molecular ions. Finally the ions are extracted into the time of flight analyzer (p=5x10-8-2x10-7 mbar) and detected by a microchannel plate detector. Due to the limited ion capacity of the Paul trap (104-105), a large number of cycles, typically 500-2000, is required in order to obtain a good signal-to-noise ratio.. 16. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 22.

(4) EXPERIMENT. Figure 2.1 Sketch of the experimental setup. The length of the time of flight (TOF) system between the 3D RF trap and the MCP detector at the end of the TOF tube is not to scale.. 17. 517030-L-sub01-bw-Egorov. PDF page: 23. Processed on: 8-2-2018.

(5) EXPERIMENT. Figure 2.2 Sketch of the Nanocluster trap interfaced with the UE52-PGM beamline at BESSY II [1]. For our experiment the cluster source is replaced by our ESI+funnel combination.. 2.2. NANOCLUSTER TRAP SETUP. Most experiments presented in chapter 5 of this thesis were performed with the Nanocluster trap operated by the research group of T. Lau [1]. The Nanocluster trap, see Figure 2.2, is a stationary tandem mass-spectrometry setup permanently interfaced to the BESSY II UE52_PGM beamline. The apparatus is equipped with a superconducting solenoid magnet for magnetization of metal clusters and is mostly used for soft X-ray magnetic circular dichroism experiments [19, 20]. For our experiments we interfaced our ESI and RF ion funnel with the Nanocluster Trap. Due to the much larger ion capacity of the linear RF trap, it can accommodate mass selected ion currents of 100 pA or more. Typical ion currents of conventional combined ESI and RF funnel devices are of the order of 5 pA. The improvements made to our system to fully exploit the trapping capacity of the Nanocluster trap will be highlighted in the following subsection. Ions transferred into the gas-phase are guided by the RF hexapole ion guide (Figure 2.2, 1. ion guide) into the RF mass filter, where ions with the required m/z can be selected. Afterwards mass-selected ions are focused by electrostatic lenses and deflected by a static quadrupole bender into the liquid helium cooled linear RF-quadrupole ion trap. In contrast to the PAULTJE setup, in the Nanocluster trap, helium buffer gas is present during the entire operation cycle. Ions can be cooled to liquid helium temperature (4K, this corresponds to final internal temperatures of the ions between 10K and 15K due to RF heating in the trap). Ions fill the trap up to the space charge limit and are then subjected to polarized soft X-ray radiation with typical photon fluxes of 1012 18. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 24.

(6) EXPERIMENT. Figure 2.3 Timing scheme of the Nanocluster Trap experiment [1].. photons/s yielding about 105 daughter ions per second. Afterwards the ions are extracted from the ion trap into the reflectron time-of-flight mass spectrometer. The timing scheme for extraction is depicted in Figure 2.3. A fraction of the ions contained in the trap is extracted into the TOF spectrometer with every voltage pulse to the ion trap exit aperture. After a delay, tuned for detection of specific daughter ions, the first acceleration stage of the TOF spectrometer is pulsed and the daughter ion’s m/z and intensity is detected. At the end of the cycle, the obtained mass spectra are averaged and the ion trap is emptied by switching off the RF voltage. Subsequently, a new photon energy is set and a new measurement cycle starts. ȱȱȱȱȱȱȱȱȱȱȦ̇ǅŗŝŖŖǯȱ ȱȱȱȱ reach the MCP detector which detects the signal induced by 103-104 ions. About 110 % of the extracted ions is detected due to the efficiency of the detector. In addition to that, the extraction efficiency is not the same for ions with different m/z which affects the direct comparison of mass spectra.. 19. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 25.

(7) EXPERIMENT. Figure 2.4 Sketch of the ion funnel with capillary and octupole ion guide.. 2.3 OPTIMIZATION OF FLUENCE ESI SOURCE 2.3.1. THE. HIGH-. Ion funnel basics. The invention of electrospray ionization has provided a powerful tool for transfer of biomolecular ions from the liquid phase into the gas phase. Initially, the most common method for transfer from atmospheric pressure into vacuum was the application of a skimmer. However the ion transmission in this case is usually only around 0.01% [21]. Initially, our group was using a skimmer for the ion transfer, which was subsequently replaced by an ion funnel allowing for more efficient ion transmission. One of my first tasks was the optimization of the ion funnel performance. The key problem in the ion transfer is that according to the Liouville theorem it is not possible to slow down and focus ions at the same time, due to phase space volume conservation. However, the necessary ion transmission cannot be achieved without the slowing down and compression of the ion beam. The phase space can 20. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 26.

(8) EXPERIMENT Table 2.1 Tabulation overview of the standard settings of the ESI, ion funnel (IF) and octupole (8-pole), see Figure 2.4 , for the ion transmission experiments. Vpp indicates the peak-to-peak voltages of a specific RF field.. ESI (kV) Capillary (V) Elect1 (V) 4.53. 100. 8-pole bias (V). 8-pole RF (kHz). 8. 700. 110. Elect26 (V) Diaph (V) IF RF (kHz) IF RF Vpp (V) 13. 11. 8-pole RF 8-pole exit 8-pole Vpp (V) (V) pulse (V) 190. 5. 50. 500. 240. Einzel lens (V). IF pressure (mbar). 7.7. 0.3. be compressed by means of collisional damping, which takes place in low vacuum RF devices such as the ion funnel. The funnel was first implemented in 1997 by [22] in order to optimize the transmission efficiency. Subsequently, a large number of ion funnel designs was developed, while key features of the ion funnel remained the same. Typical funnels consist of a stack of rings, whose internal diameters gradually decrease towards the funnel exit, see Figure 2.4. An RF field is applied to the ring electrodes in a way that the phase difference between adjacent electrodes is 180 degrees. As in a conventional ring electrode trap [23] ions are confined radially. At the same time ions are pushed forward by the application of a continuous DC gradient between the first and the last ring. Due to collisional damping the ions are eventually focused near the exit of the ion funnel and transferred to the octupole. The funnel we are using is sketched in Figure 2.4 together with the entrance capillary and the octupole. The funnel is based on the design described in [24].. 2.3.2. Ion inlet system improvement. One of the most obvious possible improvements of the initial stage of the ion guiding system is the increase of the capillary diameter. An increase of the capillary diameter from 0.508 to 0.762 mm (standard commercial capillary inner diameters) increases the capillary cross section by more than a factor of two and as a consequence the biomolecular ion flow into the funnel increases by a similar factor. The implementation of such a large diameter capillary however has implications on the required pumping speed. We use an IGX6/100l Edwards root pump with a booster. It has a pumping speed of 600 m3/h, and allows for a minimum pressure in the ion funnel chamber of 0.3 mbar.. 2.3.3. Ion funnel and octupole ion transmission experiments. In order to quantify and optimize the high fluence ESI source it was necessary to perform ion transmission experiments. We investigated the transmission 21. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 27.

(9) EXPERIMENT. Figure 2.5 Ion transmission as a function of the ion funnel’s RF frequency for two pressures inside the ion funnel of p=0.3 mbar and p=0.7 mbar. System settings are listed in the Table 2.1.. dependency on ion funnel and octupole settings by using a beam of [leucine enkephalin+H]+, a model peptide for mass-spectrometry with m=555.6 Da. In conventional mass spectrometric systems, ion funnels are operated with RF voltage generators with fixed frequency. We use a much more versatile approach, where sine signals of variable frequency and amplitude are generated by a function generator and amplified by RF power amplifiers. Full control over frequency and amplitude allows for much better optimization of the ESI output. We have systematically investigated the influence of the diaphragm voltage, capillary voltage, first electrode voltage, octupole RF voltage and frequency, ion funnel RF amplitude and frequency. The basic experimental settings used in the optimization are summarized in Table 2.1. Throughout the following sections, these settings are used, unless stated otherwise. Additionally, we have varied the pressure in the ion funnel chamber from 0.3 to 0.7 mbar by modifying the pumping speed to investigate the pressure effect on ion transmission. On the respective graphs, ion transmission is normalized to the maximal ion transmission in the measurement series and labeled as relative transmission. It was established during the experiments that the ion transmission depends strongly on the ion funnel. 22. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 28.

(10) EXPERIMENT. Figure 2.6. The dependency of ion transmission on the voltage on the exit diaphragm of the funnel for funnel pressures of p=0.3 mbar and p=0.7 mbar. System settings are listed in the Table 2.1.. diaphragm voltage, pressure, RF frequency and peak-to-peak voltage (see Figure 2.5 - Figure 2.7). The influence of the voltages on the first electrode and capillary appears less significant (see Figure 2.8). Figure 2.5 shows the dependency of ion transmission on the ion funnel’s RF peakto-peak voltage and frequency for two pressures. It can be clearly seen that the ion transmission dramatically varies with the amplifier frequency. The ion transmission as a function of RF frequency exhibits a broad peak with a maximum ȱǅŚśŖȱ £ȱȱƽŖǯŝȱǰȱȱǅŝŖŖȱ £ȱȱƽŖǯřȱǯȱȱ¡ȱȱȱ transmission notably shifts to lower frequencies with increasing pressure. Figure 2.6 shows the ion transmission as a function of the voltage on the exit diaphragm of the funnel for gas pressures inside the funnel of p=0.3 mbar and p=0.7 mbar. For both pressures the transmission dependency on the diaphragm voltage maximizes over a range of voltages, i.e 9-13 V. The distribution is somewhat broader for the lower pressure of p=0.3 mbar. This can be explained by the higher energy of the ions in the end of the ion funnel. This happens due to less collisional damping events at a lower pressure. 23. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 29.

(11) EXPERIMENT. Figure 2.7 Relative ion transmission through the ion funnel as a function of the RF peak-to-peak voltage (Vpp) for various frequencies. System settings are listed in the Table 2.1.. 24. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 30.

(12) EXPERIMENT. Vcap = 120 V Vcap = 60 V Vcap = 0 V. Relative transmission. 1.0. 0.8. 0.6. 0.4. 0.2. 0.0. 0. 50. 100. 150. 200. 250. Electrode 1 (V). 0. 50. 100. 150. 200. Capillary (V). Figure 2.8 Left panel: relative ion transmission as a function of the voltage on electrode 1 for 3 different capillary voltages (Vcap). Right panel: relative ion transmission as a function of capillary voltage for a fixed electrode 1 voltage of 110 V. System settings are listed in the Table 2.1.. Figure 2.7 depicts the ion transmission as a function of the RF peak-to-peak voltage for 6 different frequencies. It can be clearly seen that the working range is extremely narrow for low frequencies (100, 200 kHz) and tends to broaden and shift to higher voltages with increasing frequency. Figure 2.8 shows the ion transmission as a function of capillary voltage and electrode 1 voltage. The measurements indicate that the operating region for these parameters is very broad. The lower relevance of the electrode1 and capillary voltage to the ion transmission can be explained by the notable gas flow near the exit of the capillary which is additionally pushing ions towards the exit of the ion funnel, thus making the values of the voltages near the entrance area less important for the ion transmission. Figure 2.9 shows the ion transmission as a function of octupole RF frequency. It can be clearly seen that similar to the case of the ion funnel’s RF frequency, the operation range shifts to higher peak-to-peak voltages when the frequency increases. However, there is no observable operation range broadening as found for the ion funnel. Having mapped the ion transmission as a function of the relevant parameters, it is now possible to choose optimum settings for ESI operation. It is also clear that using a wide band RF power amplifier is key to optimizing the transmission, as the transmission is very sensitive to experimental settings, as can be seen from Figure 2.5. 25. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 31.

(13) EXPERIMENT. 1.0. f=500 kHz. f=700 kHz. f=900 kHz. f=1200 kHz. 0.8. Relative transmission. 0.6. 0.4. 0.2 1.0. 0.8. 0.6. 0.4. 0.2. 0. 50. 100. 150. 200. 250. 50. 100. 150. 200. 250. Octupole RF Vpp (V) Figure 2.9 Ion transmission as a function of octupole RF peak-to-peak amplitude for various frequencies. System settings are listed in Table 2.1.. 2.3.4. RF ion funnel SIMION simulation. In order to develop an ion funnel design for maximum ion transmission and to define precision limits for the maximum allowed misalignment between e.g. funnel and octupole it was necessary to model ion trajectories through the ion funnel and the octupole. To this end, the ion optics simulation package SIMION 8.0.4 was used [25]. Initially, SIMION calculates the electric field at every point of a userdefined potential array by solving the Laplace equation. Subsequently, ion trajectories can be calculated in a three dimensional space using a 4th-order RungeKutta method. Collisions of the electrosprayed ions with residual gas molecules in the ion funnel chamber were taken into account by the application of a hard sphere 26. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 32.

(14) EXPERIMENT. Figure 2.10 Ion funnel simulation result sample for [leucine-enkephalin+H]+. Simulation settings are based on the Table 2.1. Starting ion energy is 1-3 eV.. collision model. This model is based on the following approximations: x. Ion collisions are treated as collisions between two hard spheres. Energy transfer occurs solely via these collisions.. x. The collisions are elastic.. x. Background gas is assumed to be neutral.. x. The background gas velocity follows a Maxwell-Boltzmann distribution.. x. The mean velocity of the background gas may be non-zero.. x. Kinetically cooling and heating collisions are considered, i.e, both positive and negative energy transfer from the buffer gas to the ions is possible.. x. Background gas as a whole is unaffected by ion collisions: no heating, ionization or fragmentation processes are taken into account.. Knowing the approximate current of ions from experiments it was possible to calculate the ion repulsion effect on ion trajectories. The method employed only takes into account the Coulomb repulsion between ions. However, it assumes that the ion beam propagates evenly in the ion funnel, while in reality some biomolecular ions can be trapped between ion funnel electrodes for a time longer than average ion flight time, leading to an extra space-charge. The ion trajectories 27. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 33.

(15) EXPERIMENT. Relative transmission. 1.0 0.8 0.6 0.4 0.2 0.0 200. 400. 600. 800 1000 1200 1400. Ion funnel RF frequency (kHz). 4. 6. 8. 10. 12. 14. 16. 18. 20. Diaphragm voltage (V). Figure 2.11 Comparison of measured and simulated ion transmission: 1) left panel: Ion funnel frequency scan 2) right panel: diaphragm scan. White squares are the simulation results, black squares are the experiment results. The parameter settings are given in Table 2.1.. Figure 2.12 ȱȱȱȱȱǻΗǼȱ ȱȱȱȱȱȱȱȱȱ exit diaphragm. SIMION simulations were performed for gap distances of 1.5 mm, 2.5 mm and 5 mm.. obtained by means of the simulation method just described can be seen on Figure 2.10. The area in the vicinity of the capillary exit is known to be a region where supersonic expansion of the incoming biomolecular ion beam occurs [26]. 28. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 34.

(16) EXPERIMENT. However, the model applied is unable to simulate such gas flow dynamics which may play a significant role in the area near the exit of the capillary. This results in considerable uncertainties in the ion trajectories near their natural starting points adjacent to the capillary exit. Therefore, simulations for different capillary voltages are inconsistent with ion transmission measurements as a function of capillary voltage and not presented here. Because of these uncertainties and the aforementioned ones concerning charge repulsion effects, it was necessary to verify the reliability of the simulation. We started out by performing ion transmission (see Figure 2.11) tests as a function of the RF frequency and the voltage on the diaphragm. Similar trends are found when comparing the ion transmission efficiency experiments performed with the real setup in the region of the maximal transmission (ion funnel RF frequency=400-800 kHz, diaphragm voltage=8-14 V) to the simulations. Simulations with the diaphragm voltages above 14 V indicate severe ion trapping in the area between the last electrode and diaphragm, hampering ion transport. On the simulation side this results in very long computational times and therefore further simulations with diaphragm voltages above 14 V were not conducted. One of the most important design features of the ion funnel is the distance between the last electrode and diaphragm, the shorter it is the more efficient the transmission is between the ion funnel and octupole. It cannot be made infinitesimally small, so it is important to define the value below which a further decrease will not result in appreciable improved ion transmission. In order to establish this, simulations were run for gaps of 5 mm, 2.5 mm and 1.5 mm, see Figure 2.12. We obtained the following transmission values for different distances: 5 mm: 57%, 2.5 mm: 71%, 1.5 mm: 73%. It can be clearly seen that the transmission increase between 2.5 mm and 1.5 mm is not too large. For larger gaps the ion current decreases strongly. Therefore it was decided to take a distance of 2 mm. The aforementioned improvements in the ion funnel and capillary inlet system have resulted in a high-fluence electrospray source able to produce more than 2 nA of non-mass selected current and more than 150 pA of mass-selected current, what has made the experiments with the Nanocluster Trap feasible. Additionally, we performed a test to determine the maximal allowed misalignment of octupole and quadrupole. Allowing for an acceptable decrease in ion transmission due to misalignment of 10 %, misalignments up to 0.2 mm are acceptable.. 29. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 35.

(17) EXPERIMENT. Figure 2.13 Schematic representation of the operating principle of a microchannel plate (MCP) detector.. 2.4. MICROCHANNEL PLATE SENSITIVITY. A Microchannel plate (MCP) detector is a device commonly used in various fields of science and technology and capable of detection of incoming ions, electrons, neutrons and photons. Its operation is based on electron multiplication. A MCP consists of a regular array of tubes (microchannels) with a diameter of 2-50 μm (12 μm for our case). Each of the channels is an electronic multiplier (see Figure 2.13). The channels are inclined with respect to the surface normal (typically 5°-10°), therefore particles entering the channel are guaranteed to hit its wall. This triggers a cascade of electrons propagating through the tube. The amplification of a single MCP is around 104. Stacking two or more MCPs will yield an amplification of 108 or more. An issue playing a significant role in the detection of molecules with high m/z is the MCP sensitivity. Earlier, using C60 ions the dependency of a MCP detector sensitivity versus ion speed was measured [27]. It was shown that the detector efficiency can be approximated with the following equation: ܲ=. 1 + tanh ቀ. ‫ ݒ‬െ 28500 ቁ 11000 2. where v is the ion’s speed in m/s. From Figure 2.14 it can be clearly seen that for large molecules, P does not depend on the charge state of the molecule. The detection efficiency being independent of the molecule’s charge state was also ୰ା established in experiments of C଺଴ with gold surfaces [28, 29]. For light ions such as Ar ୯ା [30] electron emission and thus detection efficiency strongly depends on the charge state. This can be explained by the fact that the number of electrons emitted in an ion collision with a surface depends on the kinetic energy of the projectile 30. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 36.

(18) EXPERIMENT. Figure 2.14 MCP sensitivity with speed of singly, doubly, triply and quadruply charged C60 ions, taken from [27].. and on its potential energy, i.e. the projectile charge state. However, for larger molecules the potential energy is redistributed into vibrational excitations, which leads to fragmentation instead of electron emission. Kinetic-energy related electron emission dominates for the case of big molecules. All further experiments concern large biomolecular ions, so the MCP sensitivity is assumed to be independent of the charge state of the ion and to be described by the expression given above.. 2.5. BESSY II SYNCHROTRON FACILITY. All experiments mentioned in this thesis were performed at the third-generation synchrotron facility HZB-BESSY II (Berlin, Germany). A linear accelerator injects electrons into the storage ring up to a maximal operational value of the current of 300 mA at a kinectic energy of 1.7 GeV. Passing through periodic magnetic structures, the so called undulators, electrons are forced to oscillate and emit radiation with an energy distribution defined by the undulator periodicity and gap. The photon energy can be selected and controlled by the application of a monochromator behind the undulator. In total 11 undulators and more than 50 31. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 37.

(19) EXPERIMENT. Figure 2.15 PAULTJE interfaced with a BESSY II beamline at the HZB (Berlin, Germany). working stations operate at BESSY II. The Paultje setup interfaced with a beamline can be seen on Figure 2.15 Soft X-ray experiments were performed on the U49/2-PGM1 beamline [31] which produces photons with energy of 85-1600 eV with a flux of 5x1012 - 1.5x1013 photons/s. Undulator U49-2 is a periodic structure of magnets which consists of 84 periods each 49.4 mm long with a minimal gap of 15.64 mm. The monochromator is a plane grating monochromator (PGM). Usually, there is a significant photon flux drop around the carbon K-edge, due to photoabsorption by carbon-containing compounds on gratings. This has led to a significant irradiation time required to achieve a significant photoabsorption for YG10F and leucine– enkephalin: 1-3 seconds per cycle. Photoabsorption scales with the molecular size, so for the larger molecules we studied the irradiation time was less than 1 second per cycle. VUV experiments were performed using the U125-2 10m-NIM beamline [32] which consists of a quasi-periodic undulator and a normal incidence monochromator. This system provides the user with 6-40 eV photons with a flux of 5x1011-5x1012 32. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 38.

(20) EXPERIMENT. photons/s. The undulator consists of 32 periods each 125 mm long with a minimal gap of 15.7 mm. The 10m-NIM monochromator is an off-Rowland Circle normal incidence monochromator (NIM) and contains a spherical grating with a 10 m focus. The exit slit width can be varied from 0 to 2000 μm. The larger width of the ¡ȱȱȱȱȱ̇ȱȱȱ¢ȱȱȱȱȱ¡ǯȱ ȱȱ ȱ ȱ ̇ȱ ȱ ȱ ȱ ȱ ǰȱ ¢ȱ ȱ ȱ ȱ ȱ for low (14 eV) and high (35 eV) photon energies photoflux is generally low. In addition to that, photoabsorption by peptides at these energies is low [5]. For this reason the slit width was kept to its maximum value of 2 mms in order to obtain the maximal photoflux. Another important issue to be mentioned here is contamination by higher harmonics photons. Higher order contamination of the photon beam is partly suppressed by the dislocations in the periodic pattern of the undulator making it quasiperiodic. The quasiperiodic structure of the undulator leads to slight red shift of the harmonics what results in their efficient filtering out by the monochromator. Experiments with the Nanocluster Trap were performed at the U52_PGM beamline for polarized soft X-ray radiation of 85-1600 eV energy and typical photon fluxes of 1012 photon/s [33]. The elliptical undulator U52 can produce polarized soft X-rays which can be either polarized linearly (any orientation) or circularly. It consists of 77 periods each 52 mm long and has a minimal gap of 16 mm.. 33. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 39.

(21) BIBLIOGRAPHY. BIBLIOGRAPHY [1] K. Hirsch, J.T. Lau, P. Klar, A. Langenberg, J. Probst, J. Rittmann, M. Vogel, V. Zamudio-Bayer, T. Moeller and B. von Issendorff, Journal of Physics B-Atomic Molecular and Optical Physics, 42, 154029 (2009). [2] S. Bari, "The influence of peptide structure on fragmentation pathways", PhD Thesis, University of Groningen (2010). [3] O. Gonzalez-Magaña, "Ionization-induced fragmentation dynamics of isolated complex molecules", PhD Thesis, University of Groningen (2013). [4] D. Egorov, L. Schwob, M. Lalande, R. Hoekstra and T. Schlathölter, Physical Chemistry Chemical Physics, 18, 26213 (2016). [5] S. Bari, O. Gonzalez-Magaña, G. Reitsma, J. Werner, S. Schippers, R. Hoekstra and T. Schlathölter, J.Chem.Phys., 134, 024314 (2011). [6] O. Gonzalez-Magaña, G. Reitsma, S. Bari, R. Hoekstra and T. Schlathölter, Phys.Chem.Chem.Phys., 14, 4351 (2012). [7] O. Gonzalez-Magaña, G. Reitsma, M. Tiemens, L. Boschman, R. Hoekstra and T. Schlathölter, J Phys Chem A, 116, 10745 (2012). [8] O. Gonzalez-Magaña, M. Tiemens, G. Reitsma, L. Boschman, M. Door, S. Bari, P.O. Lahaie, J.R. Wagner, M.A. Huels, R. Hoekstra and T. Schlathölter, Physical Review A, 87, 032702 (2013). [9] G. Reitsma, L. Boschman, M.J. Deuzeman, O. Gonzalez-Magaña, S. Hoekstra, S. Cazaux, R. Hoekstra and T. Schlathölter, Phys.Rev.Lett., 113, 053002 (2014). [10] G. Reitsma, L. Boschman, M.J. Deuzeman, S. Hoekstra, R. Hoekstra and T. Schlathölter, J.Chem.Phys., 142, 024308 (2015). [11] S. Martin, C. Ortega, L. Chen, R. Bredy, A. Vernier, P. Dugourd, R. Antoine, J. Bernard, G. Reitsma, O. Gonzalez-Magaña, R. Hoekstra and T. Schlathölter, Physical Review A, 89, 012707 (2014). [12] S. Bari, R. Hoekstra and T. Schlathölter, Physical Chemistry Chemical Physics, 12, 3376 (2010). [13] G. Reitsma, O. Gonzalez-Magaña, O. Versolato, M. Door, R. Hoekstra, E. Suraud, B. Fischer, N. Camus, M. Kremer, R. Moshammer and T. Schlathölter, International Journal of Mass Spectrometry, 365, 365 (2014). [14] T. Schlathölter, G. Reitsma, D. Egorov, O. Gonzalez-Magaña, S. Bari, L. Boschman, E. Bodewits, K. Schnorr, G. Schmid, C.D. Schroeter, R. Moshammer and R. Hoekstra, Angewandte Chemie-International Edition, 55, 10741 (2016). 34. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 40.

(22) BIBLIOGRAPHY. [15] L. Boschman, G. Reitsma, S. Cazaux, T. Schlathölter, R. Hoekstra, M. Spaans and O. Gonzalez-Magaña, Astrophysical Journal Letters, 761, L33 (2012). [16] S. Cazaux, L. Boschman, N. Rougeau, G. Reitsma, R. Hoekstra, D. Teillet-Billy, S. Morisset, M. Spaans and T. Schlathölter, Scientific Reports, 6, 19835 (2016). [17] W. Paul, Rev.Mod.Phys., 62, 531 (1990). [18] J. Fenn, M. Mann, C. Meng, S. Wong and C. Whitehouse, Science, 246, 64 (1989). [19] S.T. Akin, V. Zamudio-Bayer, K. Duanmu, G. Leistner, K. Hirsch, C. Buelow, A. Lawicki, A. Terasaki, B. von Issendorff, D.G. Truhlar, J.T. Lau and M.A. Duncan, Journal of Physical Chemistry Letters, 7, 4568 (2016). [20] V. Zamudio-Bayer, K. Hirsch, A. Langenberg, A. Lawicki, A. Terasaki, B. van Issendorff and J.T. Lau, J.Chem.Phys., 143, 244318 (2015). [21] R. Smith, J. Loo, R. Loo, M. Busman and H. Udseth, Mass Spectrom.Rev., 10, 359 (1991). [22] S. Shaffer, K. Tang, G. Anderson, D. Prior, H. Udseth and R. Smith, Rapid Communications in Mass Spectrometry, 11, 1813 (1997). [23] K. Giles, S. Pringle, K. Worthington, D. Little, J. Wildgoose and R. Bateman, Rapid Communications in Mass Spectrometry, 18, 2401 (2004). [24] R. Julian, S. Mabbett and M. Jarrold, J.Am.Soc.Mass Spectrom., 16, 1708 (2005). [25] D. Dahl, International Journal of Mass Spectrometry, 200, 3 (2000). [26] A. Bruins, Mass Spectrom.Rev., 10, 53 (1991). [27] T. Schlathölter, R. Hoekstra and R. Morgenstern, J.Phys.B-At.Mol.Opt.Phys., 31, 1321 (1998). [28] K. Toglhofer, F. Aumayr, H. Kurz, H. Winter, P. Scheier and T. Mark, J.Chem.Phys., 99, 8254 (1993). [29] H. Winter, M. Vana, G. Betz, F. Aumayr, H. Drexel, P. Scheier and T. Mark, Physical Review A, 56, 3007 (1997). [30] H. Kurz, K. Toglhofer, H. Winter, F. Aumayr and R. Mann, Phys.Rev.Lett., 69, 1140 (1992). [31] Helmholtz-Zentrum Berlin für Materialien und Energie, Journal of large-scale research facilities, 2, A72 (2016). [32] Helmholtz-Zentrum Berlin für Materialien und Energie, Journal of large-scale research facilities, 2, A53 (2016). 35. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 41.

(23) BIBLIOGRAPHY. [33] Helmholtz-Zentrum Berlin für Materialien und Energie, Journal of large-scale research facilities, 2, A70 (2016).. 36. 517030-L-sub01-bw-Egorov Processed on: 8-2-2018. PDF page: 42.

(24)

No results found