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Biomolecular Signatures of Disease Via Ion Mobility And BIOMOLECULAR SIGNATURES OF DISEASE VIA ION MOBILITY AND MASS SPECTROMETRY TECHNIQUES By Kelly M. Hines Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Chemistry May, 2014 Nashville, Tennessee Approved: John A. McLean, Ph.D. David E. Cliffel, Ph.D. Donna J. Webb, Ph.D. Eva M. Harth, Ph.D. ACKNOWLEDGEMENTS Firstly, I would like to thank my dissertation advisor Dr. John A. McLean for allowing me to explore my own interests, and for providing encouragement and direction in times when I was uncertain in my abilities or the merits of my research. The advice to not “let perfection get in the way of good enough,” has been particularly helpful. Thank you for being an excellent mentor. I would like to thank my dissertation committee members Dr. David E. Cliffel, Dr. Donna J. Webb, and Dr. Eva M. Harth for their guidance and advice, and for challenging me to see the broader impacts of my work. I would like to acknowledge the many collaborators who have contributed to my dissertation research: Dr. John P. Wikswo, Dr. Dana R. Marshall, Dr. Donna J. Webb, Dr. Kristie L. Rose, Dr. Jeffrey M. Davidson, and Dr. Susan R. Opalenik. I learned many new things through our work together. I would like to thank my colleagues, past and present, in the McLean lab for being good co-workers and good friends. In particular, I would like to thank Dr. Jeffrey R. Enders, Dr. Michal Kliman and Dr. Cody Goodwin for their help, advice and patience. Special thanks to Dr. Jay G. Forsythe for being a great friend in and out of lab. Many thanks to all my friends and family for their love and support. I would have never made it to this point without you. Thank you to my parents and siblings for always being there to listen, no matter the time of day or night, for their continual encouragement and advice, and for reminding me everything will work out when I couldn’t see it for myself. To my best friends Sarah Moravia, Amelia Null, and Carlee Murphy: thank you ii for befriending me in French class and still being here all these years later (Go Gators!). Finally, thanks to Bert Stone for being my rock, and for all the happiness and love you have brought me. Lastly, I would like to acknowledge the entities which provided financial support for this work: the Vanderbilt University College of Arts and Sciences, the Vanderbilt Institute of Chemical Biology, the Vanderbilt Institute of Integrative Biosystems Research and Education, the U.S. Defense Threat Reduction Agency (HDTRA-09-1- 0013 and DTRA100271 A-5196), and the National Institutes of Health (R01GM092218, RC2DA028981 and UH2TR000491). iii TABLE OF CONTENTS Page ACKNOWLEDGEMENTS ................................................................................................ ii LIST OF TABLES ............................................................................................................ vii LIST OF FIGURES ......................................................................................................... viii LIST OF ABBREVIATIONS ..............................................................................................x Chapter I. MULTIDIMENSIONAL SEPARATIONS BY ION-MOBILITY- MASS SPECTROMETRY..............................................................................................1 1.1. IM-MS: Multidimensional Gas Phase Separations .....................................1 1.1.1. The Evolution of IM Technology ......................................................2 1.1.2. The Correlation of IM and MS Dimensions ......................................7 1.1.2.1. Tailoring the Configuration of Multidimensional Separations ............................................................................9 1.1.2.2. Advantages for Complex Biological Sample Analysis ........12 1.1.3. Structural Information from 2D Conformation Space .....................14 1.1.3.1. Relating Mobility Drift Time to CCS ..................................15 1.1.3.2. Correlating Empirical and Computational CCSs .................17 1.2. Instrumental Configurations of Modern IM-Mass Spectrometers .............18 1.2.1. Impact of Ion Source Selection on IM Arrangement .......................19 1.2.2. IM-Time-of-Flight Mass Spectrometers ..........................................21 1.2.2.1. MALDI-IM-TOFMS ..........................................................21 1.2.2.2. ESI-IM-TOFMS .................................................................24 1.2.2.3. Traveling Wave IM-TOFMS ..............................................24 1.3. Applications of IM-MS ..............................................................................27 1.3.1. Conformation Space Analysis..........................................................27 1.3.1.1. Mapping Conformation Space of Biomolecules ................28 1.3.1.2. Utilizing Conformation Space with IM shift reagents .......32 1.3.2. Integrating Omics Analysis by IM-MS............................................37 1.3.2.1. Proteomics ..........................................................................38 1.3.2.2. Glycomics ...........................................................................42 iv 1.3.2.3. Lipidomics ..........................................................................46 1.3.3. Structural Biology by IM-MS ..........................................................49 1.4. Conclusions ................................................................................................53 1.5. Summary and Objectives of Dissertation Research ...................................54 1.6. Acknowledgements ....................................................................................56 1.7. References ..................................................................................................57 II. BIOMOLECULAR SIGNATURES OF DIABETIC WOUND HEALING BY STRUCTURAL MASS SPECTROMETRY .........................................................76 2.1. Introduction ................................................................................................76 2.2. Experimental ..............................................................................................79 2.3. Results and Discussion ..............................................................................85 2.4. Conclusions ..............................................................................................100 2.5. Acknowledgements ..................................................................................102 2.6. References ................................................................................................103 III. STRUCTURAL MASS SPECTROMETRY OF TISSUE EXTRACTS TO DISTINGUISH CANCEROUS AND NON-CANCEROUS BREAST DISEASES ...........................................................................................................108 3.1. Introduction ..............................................................................................108 3.2. Experimental ............................................................................................112 3.3. Results and Discussion ............................................................................118 3.4. Conclusions ..............................................................................................132 3.5. Acknowledgements ..................................................................................133 3.6. References ................................................................................................134 IV. PHOSPHORYLATION OF SERINE 106 IN ASEF2 REGULATES CELL MIGRATION AND ADHESION TURNOVER .................................................140 4.1. Introduction ..............................................................................................140 4.2. Experimental ............................................................................................142 4.3. Results and Discussion ............................................................................150 4.4. Conclusions ..............................................................................................163 4.5. Acknowledgements ..................................................................................164 4.6. References ................................................................................................165 v V. PERSPECTIVES ON EMERGING AND FUTURE DIRECTIONS .................169 5.1. Summary ..................................................................................................169 5.2. Future Directions .....................................................................................171 5.2.1. Biomolecular Signatures of Diabetic Wound Healing...................171 5.2.2. Distinguishing Cancerous and Noncancerous Breast Diseases .....171 5.2.3. Characterizing the Phosphorylation of Asef2 ................................172 5.3. Conclusions ..............................................................................................173 Appendix A. References of Adaptation for Chapters ................................................................175 B. Supporting Information for Chapter II .................................................................176 C. Supporting Information for Chapter III ...............................................................183 D. Supporting Information for Chapter IV ...............................................................232 E. Curriculum Vitae .................................................................................................256
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