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Fundamental Studies of Protein Ionization for Improved Analysis by Electrospray Ionization Mass Spectrometry and Related Methods

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Fundamental Studies of Protein Ionization for Improved Analysis by Electrospray Ionization Mass Spectrometry and Related Methods Western Michigan University ScholarWorks at WMU Dissertations Graduate College 4-2014 Fundamental Studies of Protein Ionization for Improved Analysis by Electrospray Ionization Mass Spectrometry and Related Methods Kevin A. Douglass Western Michigan University, [email protected] Follow this and additional works at: https://scholarworks.wmich.edu/dissertations Part of the Organic Chemistry Commons Recommended Citation Douglass, Kevin A., "Fundamental Studies of Protein Ionization for Improved Analysis by Electrospray Ionization Mass Spectrometry and Related Methods" (2014). Dissertations. 240. https://scholarworks.wmich.edu/dissertations/240 This Dissertation-Open Access is brought to you for free and open access by the Graduate College at ScholarWorks at WMU. It has been accepted for inclusion in Dissertations by an authorized administrator of ScholarWorks at WMU. For more information, please contact [email protected]. FUNDAMENTAL STUDIES OF PROTEIN IONIZATION FOR IMPROVED ANALYSIS BY ELECTROSPRAY IONIZATION MASS SPECTROMETRY AND RELATED METHODS by Kevin A. Douglass A dissertation submitted to the Graduate College in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Chemistry Western Michigan University April 2014 Doctoral Committee: Andre R. Venter, Ph.D., Chair John B. Miller, Ph.D. Yirong Mo, Ph.D. Blair R. Szymczyna, Ph.D. Bruce Bejcek, Ph.D. FUNDAMENTAL STUDIES OF PROTEIN IONIZATION FOR IMPROVED ANALYSIS BY ELECTROSPRAY IONIZATION MASS SPECTROMETRY AND RELATED METHODS Kevin A. Douglass, Ph.D. Western Michigan University, 2013 Mass spectrometry (MS) is an analytical technique in which a sample is converted to gas-phase ions that are subsequently separated and detected. It offers great speed, selectivity, and sensitivity during analysis, characteristics which have enabled it to become a leading method for the study of proteins. The applications of MS for these biologically significant macromolecules range from accurately determining identity and sequence to shedding light on post-translational modifications and protein-molecule interactions. As a first step towards analysis by MS, gas-phase protein ions must be formed. A common method for ionization is electrospray ionization (ESI), where a liquid sample including the protein is charged, nebulized, and evaporated, resulting in bare protein ions. Although ESI has been used in this way for over two decades, many aspects of the protein charging mechanism remain unclear. To address this problem, my research has focused on (1) identifying the factors that determine the extent of protein multiple charging during ESI and (2) improving the ionization of proteins by desorption electrospray ionization (DESI). DESI is a method similar to ESI, except that the sample is desorbed from a surface by the spray instead of being present in it from the onset. As a result of (1), a simple model was developed that enables the accurate prediction of protein multiple charging observed during ESI-MS if the protein sequence is known. Furthermore, the enhancement of multiple charging that is observed upon the addition of certain organic reagents, a phenomenon known as supercharging, was investigated and a novel mechanism of protein supercharging was proposed. For (2), the difficulty in analyzing large proteins by DESI-MS was studied using an innovative approach where DESI was separated into its individual sub-processes and their individual contributions to the DESI process were evaluated. As a result, core limitations to the DESI-MS of large proteins were identified. The results of my cumulative research efforts should lead to the improved MS analysis of proteins by spray ionization methods, including ESI and DESI. Copyright by Kevin A. Douglass 2014 ACKNOWLEDGMENTS It is hard to believe that I’m already finishing my dissertation, preparing to defend, and anticipating life after death doctorate. Joking aside, I have enjoyed my time at Western Michigan University immensely, in no small part to the wonderful faculty and friends I have met there. I owe everyone at least a small “thank you” for the support and encouragement they have provided me; most deserve more. I would like to especially thank: Dr. Andre Venter, for pushing me to achieve beyond what I would have on my own. You’ve helped me to be confident in my abilities and to think outside the confines of popular thought. My success as a student is a reflection of your success as an advisor. My labmates. Shashank, Afrand, Benedicte, Amy, Kari, Gregg, Elahe, Sepideh, and Wisam, it has been a pleasure working beside you. I wish you all the best. Pam McCartney and Robin Lenkart. Thank you for patiently helping me to stay afloat amidst the murky sea of administration. I’m sure I’ll only bother you each a dozen more times before I graduate. My committee members. I would like to thank Dr. John B. Miller, Dr. Yirong Mo, Dr. Blair Szymczyna, and Dr. Bruce Bejcek for many thoughtful discussions and the times you have each given me advice on my projects. The Department of Chemistry faculty. Regardless of whether you were part of my committee or not, you were always there to give me advice or simply talk about school, ii Acknowledgments - Continued work, or life. Some of my best memories over the last few years are of conversations I had with faculty members. Sean Bashaw and Dr. Kevin Blair. It’s your hard work and dedication to the students, more so than the nuts and bolts, that keep the instruments in this department together. Finally and most of all, I would like to thank my amazing wife, Jessi. Your continuous love and support have helped me get through these last four years with most of my sanity remaining. Marrying you will always be the greatest accomplishment of my life. Kevin A. Douglass iii TABLE OF CONTENTS ACKNOWLEDGEMENTS ....................................................................................... ii LIST OF TABLES ..................................................................................................... x LIST OF FIGURES ................................................................................................... xi LIST OF ACRONYMS ............................................................................................. xiv PREFACE .................................................................................................................. 1 CHAPTER 1. INTRODUCTION ......................................................................................... 1 1.1 A Brief History of Electrospray Ionization .............................................. 2 1.2 The Dissertation Structure ....................................................................... 5 1.3 References ................................................................................................ 6 2. FUNDAMENTALS OF PROTEIN IONIZATOIN BY ELECTROSPRAY IONIZATION ................................................................ 9 2.1 Introduction to Electrospray Ionization ................................................... 9 2.2 The Formation of Charged Droplets ........................................................ 10 2.3 The Disintegration of Charged Droplets .................................................. 11 2.4 Analyte Ionization .................................................................................... 13 2.5 Protein Multiple Charging ....................................................................... 13 2.6 References ................................................................................................ 15 3. A NEW ALGORITHM FOR CHARGE STATE PREDICTION ................. 18 3.1 Introduction .............................................................................................. 18 iv Table of Contents---Continued CHAPTER 3.2 General Background of the Extent of Protein Multiple Charging ........... 19 3.3 Experimental Details ................................................................................ 23 3.4 Results and Discussion ............................................................................ 24 3.4.1 Coulombic Repulsion and Protein Charging .................................. 24 3.4.2 Determining the Optimum Separation between Charged Residues ......................................................................................... 26 3.4.3 A Detailed Example of the Counting Algorithm ............................ 27 3.4.4 Evaluating the Accuracy of the Algorithm ..................................... 32 3.4.5 Implications of the New Model on Protein Charging by ESI ......... 35 3.5 Conclusion ............................................................................................... 36 3.6 References ................................................................................................ 37 4. CHARGE STATE MODIFICATION: SULFOLANE ADDUCTS AND SUPERCHARGING ............................................................................ 41 4.1 Introduction .............................................................................................. 41 4.2 Modification of the Charge State Distribution ......................................... 42 4.3 Experimental Details ................................................................................ 44 4.4 Investigating Supercharging of Cytochrome c by Sulfolane Addition .... 46 4.4.1 Concentration Dependence ............................................................. 46 4.4.2 Comparison of Supercharging in the Positive and Negative Ion Modes .....................................................................................
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