Purdue University Purdue e-Pubs Open Access Dissertations Theses and Dissertations Winter 2015 Instrumentation and development of a mass spectrometry system for the study of gas-phase biomolecular ion reactions Ziqing Lin Purdue University Follow this and additional works at: https://docs.lib.purdue.edu/open_access_dissertations Part of the Biomedical Engineering and Bioengineering Commons, and the Chemistry Commons Recommended Citation Lin, Ziqing, "Instrumentation and development of a mass spectrometry system for the study of gas-phase biomolecular ion reactions" (2015). Open Access Dissertations. 503. https://docs.lib.purdue.edu/open_access_dissertations/503 This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. INSTRUMENTATION AND DEVELOPMENT OF A MASS SPECTROMETRY SYSTEM FOR THE STUDY OF GAS-PHASE BIOMOLECULAR ION REACTIONS A Dissertation Submitted to the Faculty of Purdue University by Ziqing Lin In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2015 Purdue University West Lafayette, Indiana ii ACKNOWLEDGEMENTS I am deeply thankful to my PhD advisor, Prof. Zheng Ouyang. He is more than a mentor or supervisor, but a kind friend, giving me a fantastic PhD experience at Purdue. His passion, courage and extraordinary vision in scientific research makes him an outstanding scientist and engineer. Prof. Ouyang works hard day and night, while on the other side providing a free and comfortable environment for me and other colleagues in the group to do research and raise opinions without pressure. These precious characteristics no doubt affect me in my professional life. When we first met in Tsinghua, he told me that PhD life is a best opportunity to test our boundary of capabilities. I learnt a lot during my PhD study, not only in terms of technical knowledge but the determination and belief in solving a problem. Five years is not a short period, I truly appreciate his supervision and encouragement for me to explore the scientific world and ii myself. It is my honor to know Zheng as a person and have the opportunity to work with each other for both research and teaching experiences. I sincerely wish him good luck for his future endeavors. I would also like to extend my thanks to Prof. Yu Xia in Department of Chemistry. I received a lot of valuable suggestions and comments from her for gas-phase ion chemistry. Prof. Xia is very sophisticated and precise about her scientific findings. Her dedication and persistence shows me how one could possibly be devoted to her career. Moreover, Dr. Xia has a charismatic personality and always welcomes discussions at any iii time. She also allowed me to use the nanospray tip puller and the commercial mass spectrometer in her laboratory, which was a great favor during my PhD study. It is my privilege to have Prof. Kinam Park and Prof. Corey Neu in my thesis committee, who are always trying to do everything to help. Prof. R. Graham Cooks, although not in my committee, has offered tremendous guidance and support in different perspectives of my graduate studies. I would also like to thank Prof. Mingji Dai, Dr. Yang Yang from Purdue University, Prof. František Tureček from University of Washington, Prof. Barney Ellison, Prof. Veronica M. Bierbaum from University of Colorado, Prof. Michael L. Gross from Washington University, and Dr. Amber L. Russell from Badger Technical Services for their kind help in organic synthesis, theoretical calculation, and tips for the pyrolysis nozzle. I am indebted to all the group members and alumni in Prof. Ouyang, Xia and Cooks’ research group. It has been a wonderful experience to have such a close relationship with so many people. Dr. Tsung-Chi Chen, Dr. Wei Xu, Chien-Hsun Chen and Linfan Li are the colleagues who helped me to build my instrument. Jason Duncan was a technician in iii Cooks’ group, always delivering solid supports when I asked for different electronic controls to achieve varies functions. Lei Tan is a close collaborator in Xia’s group with whom I worked together on gas-phase ion chemistry. Besides, it is always inspiring and pleasant to discuss with group members such as Dr. He Wang, Dr. Qian Yang, Dr. Sandilya Garimella, Dr. Xiaoyu Zhou, Xiao Wang, Yue Ren, Melodie Du, Yuan Su, etc. Without all your help, I would not have been able to finish my PhD program. I would also like to take the time to acknowledge my parents who have been supporting me mentally and financially throughout my student life in China and my PhD iv abroad. They have been extremely patient and understanding and I would like to thank them for all the amazing opportunities they have given me over the years. Last but not least, I owe my deepest gratitude to my lovely girlfriend and dance partner Esther Foo, who shares with me tears and laughter, sadness and joy in my life and for being supportive throughout this journey. Having blessed with a strong memory where I could recall minute details in my everyday life, I’m glad that I would have the chance to remember all the wonderful moments in my PhD life, and for this, I am eternally grateful. iv v TABLE OF CONTENTS Page LIST OF TABLES ............................................................................................................ vii LIST OF FIGURES ......................................................................................................... viii ABBREVIATIONS .......................................................................................................... xv ABSTRACT…. .............................................................................................................. xviii CHAPTER 1. INTRODUCTION ..................................................................................... 1 1.1 Gas-phase biomolecular ion reactions and mass spectrometry instrumentations .................................................................................................................. 1 1.1.1 Tandem mass spectrometry in gas-phase ion reactions .......................5 1.1.2 Gas-phase biomolecular ion/radical reactions at atmospheric pressure 7 1.1.3 Instrumentations for gas-phase ion reactions in vacuum ...................13 1.2 Conclusion ...............................................................................................38 1.3 References ................................................................................................40 v CHAPTER 2. INSTRUMENTATION AND CHARACTERIZATION OF A HOME- BUILT DAPI-RIT-DAPI MASS SPECTROMETER FOR GAS-PHASE ION/MOLECULE AND ION/ION REACTIONS ........................................................... 50 2.1 Introduction ..............................................................................................50 2.2 Instrumentation ........................................................................................52 2.3 Materials ...................................................................................................54 2.4 Results and discussion .............................................................................54 2.4.1 System configuration .........................................................................54 2.4.2 Pressure effect on gas-phase ion reactions ........................................59 2.4.3 Dynamic gas flow effect on gas-phase ion reactions .........................62 2.5 Conclusion ...............................................................................................69 vi Page 2.6 References ................................................................................................70 CHAPTER 3. Gas-Phase Reactions of C3H2 with Protonated Alkyl Amines: formation of a c-n covalent bond ....................................................................................................... 73 3.1 Introduction ..............................................................................................73 3.2 Instrumentation ........................................................................................74 3.3 Materials ...................................................................................................78 3.4 Results and discussion .............................................................................79 3.4.1 Carbene reaction with protonated alkylamines ..................................79 3.4.2 Theoretical calculation of the reaction mechanism ...........................83 3.4.3 Experimental evidences of the reaction mechanism ..........................86 3.5 Conclusion ...............................................................................................91 3.6 Appendix ..................................................................................................92 3.7 References ..............................................................................................106 CHAPTER 4. Gas-Phase c-C3H2 carbene reactions with biomolecular ions ............... 109 4.1 Introduction ............................................................................................109 4.2 Experimental section ..............................................................................110 4.3 Results and discussion ...........................................................................110 4.3.1 Nucleobases and nucleosides ...........................................................110 4.3.2 Amino acids, peptides, proteins, and lipids .....................................117 vi 4.4 Conclusion .............................................................................................131