Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2015 GUMBOS as Matrices for Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry Hashim Abdullah Al Ghafly Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Chemistry Commons Recommended Citation Al Ghafly, Hashim Abdullah, "GUMBOS as Matrices for Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry" (2015). LSU Doctoral Dissertations. 3253. https://digitalcommons.lsu.edu/gradschool_dissertations/3253 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. GUMBOS AS MATRICES FOR MATRIX-ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Chemistry by Hashim Al Ghafly B.S., King Saudi University Riyadh, 1997 M.S., University of Nebraska Omaha, 2009 May 2015 To my Parents Abdullah Al Ghafly and Norah Bouhlaqa To my children, my wife and my friends for their continuous love, encouragement and support throughout the years. ii ACKNOWLEDGEMENTS I deeply appreciate the excellent guidance, dedicated teaching, constant encouragement, kind assistance, and the precious time devoted by my supervisor, Professor Isiah M. Warner. I am confident that the experience I gained in the Warner lab will tremendously help me to succeed in my future endeavors. I also express thanks to the members of my doctoral committee i.e. Professors Graca Vicente and Hsiao-Chun Wu for their time and helpful suggestions. Next, I am grateful to Professor Kermit K. Murray for helping me learn about mass spectrometry and for his guidance and encouragement. I also want to recognize Dr. Jeonghoon Lee and Ms. Connie David at the Louisiana State University Mass Spectrometry Facility for their training on the mass spectrometers. In addition, I acknowledge the guidance of former and current members of Professor Warner’s research group, especially the postdoctoral researchers: Dr. Noureen Siraj, Dr. Susmita Das, and Dr. Farhana Hasan for teaching me the relevant instrumental techniques utilized for the synthesis and characterization of ionic liquids. I also appreciate them for their helpful suggestions and assistance with proofreading my dissertation and published manuscripts. Finally, I thank the Culture Mission of the Royal Embassy of Saudi Arabia, and the National Science Foundation (NSF) grants CHE-1307611 and CHE-1152106 for financial support. Overall, I dedicate this work to my lovely wife, Dr. Zahra Al Ghafli, and our children, Kawthar, Fatimah, Ali, and Haydar for their love, support, and prayers, which enabled me to successfully complete this research. iii TABLE OF CONTENTS ACKNOWLEDGEMENTS ............................................................................................... iii LIST OF TABLES ............................................................................................................ vii LIST OF FIGURES .......................................................................................................... viii ABSTRACT ..................................................................................................................... xiv CHAPTER 1: THE EVALUATION OF MASS SPECTROMETRY AND THE POTENTIAL OF IONIC LIQUIDS FOR MALDI MATRECES ...................................... 1 1.1 Mass Spectrometry ................................................................................................ 1 1.2 Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) ......................................................................................................... 2 1.2.1 Operational Mode of MALD IMS .................................................................. 3 1.2.2 Time of Flight Mass Spectrometry (TOFMS) ................................................. 4 1.2.3 Matrix Ionization ............................................................................................ 9 1.2.4 Sample Preparation ........................................................................................ 9 1.3 MALDI Matrices .................................................................................................. 11 1.3.1 Organic Matrices .......................................................................................... 11 1.3.2 Inorganic Matrices ........................................................................................ 14 1.3.3 Liquid Matrices ............................................................................................ 14 1.4 Ionic Liquids ....................................................................................................... 15 1.4.1 Synthesis of Ionic Liquids ............................................................................ 17 1.4.2 Physical and Chemical Properties of Ionic Liquids ..................................... 19 1.5 Group of Uniform Materials Based on Organic Salts (GUMBOS) .................... 19 1.6 Tissue Imaging Using MALDI .......................................................................... 20 1.6.1 Tissue Preparation ........................................................................................ 21 1.6.2 Matrix Selection and Application ................................................................ 22 1.7 Additional Analytical Techniques ....................................................................... 24 1.7.1 Ultraviolet-Visible Spectroscopy ................................................................. 24 1.7.2 Fluorescence Spectroscopy .......................................................................... 25 1.7.2.1 Intrinsic Protein Fluorescence ................................................................... 26 1.7.2.2 Binding Isotherm Models .......................................................................... 27 1.7.3 Fluorescence Anisotropy .............................................................................. 28 1.8 Scope of the Dissertation ..................................................................................... 29 1.9 References ............................................................................................................ 29 CHAPTER 2: GUMBOS MATRICES OF VARIABLE HYDROHOBICITY FOR MALDI MASS SPECTROMETRY ................................................................................ 39 2.1 Introduction ......................................................................................................... 39 2.2 Experimental Section .......................................................................................... 42 2.2.1 Materials ....................................................................................................... 42 2.2.2 Synthesis and Characterization of GUMBOS .............................................. 43 2.2.3 Determination of Relative Hydrophobicity .................................................. 43 2.2.4 Sample Preparation for MALDI ................................................................... 44 iv 2.2.5 MALDI-TOF-Mass Spectrometry Data Acquisition ................................... 44 2.3 Results and Discussion ........................................................................................ 44 2.3.1 Preparation and Characterization of AP-based Materials ............................ 44 2.3.2 Evaluation of the Performance of AP and AP-based GUMBOS as MALDI Matrices for Hydrophobic and Hydrophilic Peptide Detection ................................ 52 2.3.3 Analysis of Hydrophobic and Hydrophilic Peptide Mixtures ...................... 64 2.4 Conclusions ......................................................................................................... 69 2.5 References ........................................................................................................... 70 CHAPTER 3: SELECTIVE BINDING AFFINITIES OF AP AND AP-BASED GUMBOS FOR HYDROPHOBIC AND HYDROPHILIC PEPTIDES IN MALDI MS 75 3.1 Introduction ......................................................................................................... 75 3.2 Experimental ....................................................................................................... 77 3.2.1 Materials ....................................................................................................... 77 3.2.2 Instrumentation .............................................................................................. 77 3.2.2.1 MALDI-TOF-MS Analysis ....................................................................... 77 3.2.2.2 Fluorescence Spectra ................................................................................. 78 3.2.2.3 Determination of Binding Parameters of CHCA, AP, and AP-based GUMBOS to Peptides ........................................................................................... 78 3.2.2.4 Determination of Fluorescence Anisotropy of CHCA, AP, and AP-based GUMBOS to Peptides ..........................................................................................