University of Groningen
Photoionization and excitation processes in proteins and peptides
Egorov, Dmitrii
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Publication date: 2018
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Egorov, D. (2018). Photoionization and excitation processes in proteins and peptides. Rijksuniversiteit Groningen.
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517030-L-sub01-bw-Egorov 517030-L-sub01-bw-Egorov 517030-L-sub01-bw-Egorov 517030-L-sub01-bw-Egorov Processed on: 8-2-2018 Processed on: 8-2-2018 Processed on: 8-2-2018
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Photoionization and excitation
processes in proteins and peptides
517030-L-sub01-bw-Egorov 517030-L-sub01-bw-Egorov 517030-L-sub01-bw-Egorov 517030-L-sub01-bw-Egorov Processed on: 8-2-2018 Processed on: 8-2-2018 Processed on: 8-2-2018
Processed on: 8-2-2018 PDF page: 2PDF page: 2PDF page: 2PDF page: 2 Zernike Institute PhD thesis number: 2018:10
ISSN: 1570-1530
ISBN (printed version): 978-94-034-0436-3 ISBN (electronic version): 978-94-034-0436-6
Cover: Liana Egorova reviewing chapter 5 of this thesis Printed by: Ipskamp Printing, Enshede, February 2018
The research presented in this PhD thesis was performed in the research group Quantum Interactions and Structural Dynamics (QISD) which is part of the Zernike Institute for Advanced Materials at the University of Groningen, the Netherlands.
The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement n.°312284. The authors would like to acknowledge the contribution of the COST Action CM1204 "XUV/X-ray light and fast ions for ultrafast chemistry" (XLIC). We thank HZB for the allocation of synchrotron radiation beamtime.
517030-L-sub01-bw-Egorov 517030-L-sub01-bw-Egorov 517030-L-sub01-bw-Egorov 517030-L-sub01-bw-Egorov Processed on: 8-2-2018 Processed on: 8-2-2018 Processed on: 8-2-2018
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Photoionization and excitation
processes in proteins and peptides
Proefschrift
ter verkrijging van de graad van doctor aan de Rijksuniversiteit Groningen
op gezag van de
rector magnificus prof. dr. E. Sterken en volgens besluit van het College voor Promoties.
De openbare verdediging zal plaatsvinden op maandag 12 maart 2018 om 14.30 uur
door
Dmitrii Egorov
geboren op 25 oktober 1988 te 6LQW3HWHUVEXUJ, 5XVODQG
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Prof. dr. ir. R.A. Hoekstra
Copromotor
Dr. T.A. Schlathölter
Beoordelingscommissie
3URIGU/$YDOGL
Prof. dr. B. Noheda Pinuaga Prof. dr. J. Oomens
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Table of Contents
INTRODUCTION ... 1
1.1 Biological damage ... 2
1.2 Astrobiology ... 3
1.3 X-ray microscopy and crystallography ... 3
1.4 Photon absorption experiments ... 6
1.5 Peptides and proteins ... 8
1.6 Thesis outline ... 11
Bibliography ... 12
CHAPTER 2 EXPERIMENT ... 15
2.1 PAULTJE ... 16
2.2 Nanocluster trap setup ... 18
2.3 Optimization of the high-fluence ESI source ... 20
2.3.1 Ion funnel basics ... 20
2.3.2 Ion inlet system improvement ... 21
2.3.3 Ion funnel and octupole ion transmission experiments ... 21
2.3.4 RF ion funnel SIMION simulation ... 26
2.4 Microchannel plate sensitivity ... 30
2.5 BESSY II synchrotron facility... 31
Bibliography ... 34
NEAR-EDGE X-RAY ABSORPTION MASS-SPECTROMETRY OF GAS-PHASE PROTEINS: THE INFLUENCE OF PROTEIN SIZE... 37
3.1 Introduction ... 38
3.2 Experiment ... 39
3.3 Results and discussion ... 43
3.3.1 Photoabsorption and auger ionization ... 43
3.3.2 Mass spectra ... 44
3.3.3 Electronic excitation and internal temperature ... 53
3.3.4 Partial ion yields ... 56
3.4 Conclusions ... 61
Acknowledgements ... 62
517030-L-sub01-bw-Egorov 517030-L-sub01-bw-Egorov 517030-L-sub01-bw-Egorov 517030-L-sub01-bw-Egorov Processed on: 8-2-2018 Processed on: 8-2-2018 Processed on: 8-2-2018
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MASS-SPECTROSCOPY STUDY ON PROTONATED PEPTIDES OF
DIFFERENT SIZE ... 65
4.1 Introduction ... 66
4.2 Experiment ... 67
4.3 Results and discussion ... 70
4.3.1 Valence ionization and excitation ... 70
4.3.2 Mass spectra ... 74 4.3.3 [YG10F+H]+... 74 4.3.4 [Gramicidin A+2H]2+ ... 75 4.3.5 [Melittin+3H]3+... 75 4.3.6 [YG5F+H]+... 78 4.3.7 [Angiotensin I+2H]2+ ... 79 4.3.8 [PK26-P+3H]3+ ... 79 4.3.9 [Melittin+4H]4+... 80
4.4 Peptide size effects ... 82
4.5 Conclusion ... 88
Acknowledgements ... 89
Bibliography ... 90
NEAR-EDGE SOFT X-RAY MASS SPECTROMETRY OF PROTONATED MELITTIN ... 93
5.1 Introduction ... 94
5.2 Experimental ... 95
5.2.1 The Groningen tandem mass-spectrometer ... 96
5.2.2 The NanoClusterTrap at HZB ... 96
5.2.3 Electrospray ... 97
5.3 Results and discussion ... 97
5.3.1 Soft X-ray spectra for non-dissociative and double ionization ... 97
5.3.2 Small neutral losses ... 104
5.3.3 Formation of sequence ions ... 106
5.4 Conclusion ... 112 Acknowledgements ... 113 Bibliography ... 114 ... 117 SAMENVATTING... 121 LIST OF PUBLICATIONS ... 125
