ADVANCED STRUCTURAL AND SPATIAL ANALYSIS OF LIPIDS USING ION MOBILITY – MASS SPECTROMETRY By Michal Kliman 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 August, 2011 Nashville, Tennessee Approved: Professor John A. McLean Professor Terry P. Lybrand Professor H. Alex Brown Professor Christopher J. Janetopoulos Dedicated to Viera, my loving wife, my companion and best friend, our loves Peter, Agatha and Esther, Dad Cyril, Mom Marianna, Sister Mariana, and the Brothers and Sisters in Faith. ii ACKNOWLEDGEMENTS I would like to first thank my advisor, Dr. John A. McLean, for unwavering encouragement, superb advice and for exemplifying and leading in the art of telling a good story. I was fortunate to join Dr. McLean’s laboratory when it first formed, and helped to set up and christen by work the first instruments and optics with and alongside great coworkers Larissa Fenn, Whitney Ridenour, Randi Gant-Branum, Sophie Zhao, Josh Kerr, Sevugarajan Sundarapandian, Ablatt Mahsut, Jeff Enders, Cody Goodwin, Jody May, Jay Forsythe, Seth Byers, Kelly Hines, and Alyssa Granger. I have since witnessed the growth and success of this group, and savored every fruitful conversation and collaboration within and without the laboratory. My academic journey was greatly enriched through training with Eric Dawson, Jarrod Smith, and Jonathan Sheehan, through collaborative work with Niranjana Vijayakrishnan, Dr. Kendal Broadie, Gus Wright, Libin Xu, Keri Tallman, Dr. Ned Porter, Dr. David Hercules, Dr. Zeljka Korade, and Dr. Brian Bachmann. Colleagues from outside of Vanderbilt campus, including Misha Ugarov, Tom Egan, Dr. J. Albert Schultz and Dr. Amina Woods, were always ready to lavishly share their expertise. I also thank my committee members, Dr. Terry Lybrand, Dr. H. Alex Brown and Dr. Christopher Janetopoulos, for their engaging advice, clarity of vision and thought, their contagious enthusiasm, and for their selfless mentor-collaborator time investment. iii I feel forever indebted to those special educators who took time to properly channel, encourage and cherish my youthful enthusiasm for chemistry. I thank Dr. Charles Baldwin, my fabulously motivating undergraduate advisor; I also thank Dr. Randy Johnston, the originator of the many sparks and later fires of appreciation for analytical chemistry at Union University and beyond. I thank the visionary educators and academic administrators of the Faculty of Chemical Engineering of the Slovak Technical University in Bratislava, Slovakia, for jump- starting an English only program of study, which accelerated my ability to transfer to a BSc. chemistry program in the United States. I thank Mgr. Agáta Vozárová, a patient, properly strict, yet always encouraging secondary school teacher for her enthusiastic acknowledgment of hard work. My personal and family growth and transition from immigrant to citizen has been made a sweet perpetual reality because of special wise friends who have showed true southern hospitality including John and Leeba Curlin, Charles and Elizabeth Barnett, Joe Jordan, Greg and Melinda Jordan, Ray and Sue Smith, David and Cathy Shelton, Reza Rejaei, Emily Shipper, Randall and Lynn Page, Howard and Mary Keas, and Judy Williams. Of our peers, I thank those who steered us toward a balance of work and all those other important past times. I thank especially T.J. and Michelle Luschen, Ralf Müller and Dina Ghomein, Doug and Kerstin Clark, Randy and Amber Grantham, Toni and Teresa Chiareli, Chris and Elise Welsch, Pieter and Mandy DeGraff, Greg and Cathy Franklin, Akira and Sumiko Furusawa, Ashby and Mandy Tillery, David and Mia Curlin and Greg and Lisa Allison. My hearts thanks also go to our Village Chapel family, iv especially pastor Jim Thomas and the Tuesday band of brothers for shepherding us well. I thank my nuclear family, dad Cyril Kliman, the progenitor of the family chemistry genes, mom Marianna Klimanova, who birthed and fanned my interest in English, my sister Mariana, my parents in law Michal and Viera Olejcek, brother in law Martin for their steady support and their many talents and drive to do every task well. I lavish my thanks and affection on Viera my courageous, strong and loving companion and best friend for her overflowing heart and soul approach to the wellbeing of dad, and our loves Peter, Agatha, and Esther. I gratefully acknowledge the sources of financial support during my graduate career provided by the Vanderbilt University College of Arts and Sciences, GAANN Fellowship, the Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Ionwerks, Inc. (Houston, TX), SBIR contracts from the National Institutes Of Health (NIH/ NIDA #HHSN271200800020C (N43DA-8-7764) and #HHSN271200700012C (N44DA-7-7756)) to Ionwerks, Inc., the Dissertation Enhancement Award, the National Science Foundation NSF (CHE-0717067), Vanderbilt Kennedy Center for Research on Human Development, the National Institutes of Health (NIH/NIDA #HHSN2712006 – 77593C; HHSN271200677563C, and NIH (ES013125)), the US Defense Threat Reduction Agency (HDTRA-09-1-0013), and Waters Inc. v TABLE OF CONTENTS Page DEDICATION ........................................................................................................ ii ACKNOWLEDGEMENTS .....................................................................................iii LIST OF TABLES ................................................................................................ xi LIST OF FIGURES...............................................................................................xii LIST OF ABBREVIATIONS.................................................................................xiv Chapter I. INTRODUCTION ........................................................................................ 1 1.1 Challenges of contemporary lipidomics ......................................... 1 1.1.2 Challenge of high spatial resolution in lipid analysis............... 4 1.2 Biomolecular ion mobility-mass spectrometry overview.................. 5 1.2.1 Types of ion mobility .............................................................. 7 1.2.1.1 Drift tube ion mobility...................................................... 9 1.2.1.2 Traveling wave ion mobility ......................................... 10 1.2.1.3 Asymmetric field ion mobility spectrometry .................. 11 1.2.2 Motion of ions within neutral gases....................................... 12 1.2.3 Foundational principles of ion mobility structural separations.................................................................................... 12 1.2.4 Computational approaches for interpretation of structure .... 16 1.3 Characterization of lipids by IM-MS .............................................. 20 1.4 Summary and objectives .............................................................. 21 vi References.......................................................................................... 24 II. ION MOBILITY-MASS SPECTROMETRY CONFORMATIONAL LANDSCAPE OF ANHYDROUS BIOMOLECULES................................. 33 2.1 Introduction................................................................................... 33 2.2 Experimental................................................................................. 35 2.2.1 Samples and preparation...................................................... 35 2.2.1.1 Oligonucleotides........................................................... 35 2.2.1.2 Carbohydrates.............................................................. 35 2.2.1.3 Lipids............................................................................ 36 2.2.2 Instrumentation..................................................................... 37 2.2.3 Molecular dynamics simulations ........................................... 37 2.3 Results and discussion ................................................................. 39 2.4 Conclusions................................................................................... 46 2.5 Acknowledgements....................................................................... 47 References.......................................................................................... 48 III. STRUCTURAL SELECTIVITY OF ANHYDROUS SPHINGOLIPIDS AND GLYCEROPHOSPHOLIPIDS IN ION MOBILITY-MASS SPECTROMETRY ANALYSIS ................................................................. 52 3.1 Introduction................................................................................... 52 3.2 Experimental................................................................................. 54 3.2.1 Lipid samples and preparation.............................................. 54 vii 3.2.2 IM-MS and MS analysis........................................................ 55 3.2.3 Collision cross-section (CCS) determination ........................ 56 3.2.4 Computational modeling....................................................... 58 3.3 Results and discussion ................................................................. 59 3.4 Conclusions................................................................................... 69 3.5 Acknowledgements....................................................................... 70 References.......................................................................................... 70 IV. STRUCTURAL MASS SPECTROMETRY ANALYSIS OF