Florida State University Libraries Electronic Theses, Treatises and Dissertations The Graduate School 2013 Application of FT-ICR Mass Spectrometry in Study of Proteomics, Petroleomics and Fragmentomics Yuan Mao Follow this and additional works at the FSU Digital Library. For more information, please contact [email protected] THE FLORIDA STATE UNIVERSITY COLLEGE OF ARTS AND SCIENCES APPLICATION OF FT-ICR MASS SPECTROMETRY IN STUDY OF PROTEOMICS, PETROLEOMICS AND FRAGMENTOMICS By YUAN MAO A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy Degree Awarded: Spring Semester, 2013 Yuan Mao defended this dissertation on April 1, 2013. The members of the supervisory committee were: Alan G. Marshall Professor Directing Dissertation Michael Blaber University Representative Naresh S. Dalal Committee Member Michael G. Roper Committee Member The Graduate School has verified and approved the above-named committee members, and certifies that the dissertation has been approved in accordance with university requirements. ii ACKNOWLEDGEMENTS I would first and foremost like to thank my advisor Dr. Alan G. Marshall for all the help, guidance, patience, encouragement, and motivation throughout my graduate career, enabling me to a better scientist. I am fortunate to become a part of his group; he always expected the best and led me to be an independent thinker. I would also like to thank Dr. Michael Blaber, Dr. Naresh S. Dalal, and Dr. Michael G. Roper for serving on my dissertation committee members. I appreciate the time they spent for evaluating this thesis. I specially thank Dr. Christopher L. Hendrickson for his great mentoring, support and help throughout my entire Ph.D. life in Tallahassee, FL. He kept questioning me and taught me to think critically before I started my projects. I greatly thank Dr. Nicolas. L. Young for his numerous discussions and guidance in the biological projects. I want to thank Dr. Jeremiah D. Tipton, Dr. Joshua J. Savory and Dr. Nathan K. Kaiser for their help in FT-ICR MS instrumentation and many useful discussions. I appreciate John Quinn’s help in the instrument maintenance for my experiments. I thank those whom I have collaborated in research during my graduate career, including Dr. Neil L. Kelleher, Dr. Leonid Zamdborg, and Dr. Jason C. Rouse for countless discussions on phosphoproteomics and top-down characterization of monoclonal antibody. I want to thank Dr. Ryan Rodgers and Dr. Greg Blakney for their helpful suggestion for my presentation in scientific conference. I also want to thank all graduate students and postdocs in Dr. Marsahll’s group. I would like to thank Dr. Qianwei Xia and Dr. Ning Li for giving me the opportunity of summer internship at Regeneron Pharmaceuticals, Inc. and Yao Lv, Lichao Zhang, Chen Li, Haibo Qiu, Qilie Luo, Shivkumar Raidas, and Berny Mullappally for their kindly guidance in biochemical and analytical techniques during my internship. My research projects are supported NSF Division of Materials Research through DMR-0654118, and the State of Florida. iii TABLE OF CONTENTS List of Tables.................................................................................................................................vii List of Figures ..............................................................................................................................viii Abstract .........................................................................................................................................xii 1. HIGH MASS ACCURACY FOURIER TRANSFORM ION CYCLOTRON RESONANCE MASS SPECTROMETRY........................................................................................................1 Mass accuracy, mass resolution and mass resolving power ...................................................1 The need for high mass accuracy and high resolving power………………………………...2 External calibration, internal calibration and post-acquisition calibration ...……………….3 Fourier transform ion cyclotron resonance mass spectrometry ..............................................4 High mass accuracy in proteomics, fragmentomics and petroleomics………………….......10 2. VALENCE PARITY TO DISTINGUISH C AND Z● IONS FROM ELECTRON CAPTURE DISSOCIATION/ELECTRON TRANSFER DISSOCIATION OF PEPTIDES: EFFECTS OF ISOMERS, ISOBARS, AND PROTEOLYSIS SPECIFICITY ..............................................19 Introduction ......................................................................................................................19 Methods.................................................................................................................................20 Results and discussion ..........................................................................................................22 Conclusions...........................................................................................................................29 3. IDENTIFICATION OF PHOSPHORYLATED HUMAN PEPTIDES BY ACCURATE MASS MEASUREMENT ALONE………………………….………………….…….…......31 Introduction …………………………………………………………………………..........31 Methods.................................................................................................................................34 Results and discussion ..........................................................................................................34 Conclusions...........................................................................................................................41 4. IMPLEMENTATION OF DUAL ELECTROSPRAY ELECTRON TRANSFER DISSOCIATION WITH A FOURIER TRANSFER ION CYCLOTRON RESONANCE MASS SPECTROMETRY ………………………………………………………………….42 Introduction ......................................................................................................................42 Experimental procedures ......................................................................................................43 Results and discussion ..........................................................................................................47 iv Conclusions...........................................................................................................................54 5. AUTOMATION OF “SPACING” CALIBRATION FOR IMPROVEMENT OF MASS MEASUREMENT ACCURACY OF TANDEM FOURIER TRANSFORM ION CYCLOTRON RESONANCE MASS SPECTROMETRY ………………………………...56 Introduction ………………………………………………………………………........56 Experimental procedures ......................................................................................................59 Results and discussion ..........................................................................................................62 Conclusions...........................................................................................................................67 6. HOW MUCH MASS RESOLUTION IS NECESSARY: COUNTING THE COMMON MASS DOUBLETS FOR CcHhNnOoSs ELEMENTAL COMPOSITIONS…………………72 Introduction ……………………………………………………………………………72 Experimental procedures …………………………………………………………....73 Results and discussion .....................................................................……………………….76 Conclusions...........................................................................................................................80 7. IDENTIFICATION OF ALL POSSIBLE COMPONENTS IN COMPLEX MIXTURES: NUMBER OF ELEMENTAL COMPOSITIONS, MASS ACCURACY AND MASS RESOLUTION……………………………………………………………………………….82 Introduction ……………………………………………………………………………...82 Methods …………………………………………………………………………………….84 Results and discussion ..........................................................................................................86 Conclusions.........................................................................................................................100 8. TOP-DOWN STRUCTURAL ANALYSIS OF AN INTACT MONOCLONAL ANTIBODY BY ELECTRON CAPTURE DISSOCIATION FOURIER TRANSFORM ION CYCLOTRON RESONANCE MASS SPECTROMETRY………………………………..101 Introduction ……………………………………………………………………………….101 Experimental procedures ............................................................ …………………………104 Results and discussion ........................................................................................................105 Conclusions.........................................................................................................................113 APPENDICES v A. VALENCE PARITY TO DISTINGUISH C’ AND Z● IONS FROM ELECTRON CAPTURE DISSOCIATION/ELECTRON TRANSFER DISSOCIATION OF PEPTIDES: EFFECTS OF ISOMERS, ISOBARS, AND PROTEOLYSIS SPECIFICITY ............................................116 B. IDENTIFICATION OF PHOSPHORYLATED HUMAN PEPTIDES BY ACCURATE MASS MEASUREMENT ALONE…………………………………………………………………117 REFERENCES............................................................................................................................118 BIOGRAPHICAL SKETCH.......................................................................................................132 vi LIST OF TABLES 2.1 Accurate masses of 20 common amino acids, 5 chemical elements and c/z● ion caps…..21 2.2 The 22 lowest mass compositional isomers derived from amino acids, and their corresponding integer residue monoisotopic masses……………………………………..27 3.1 The accurate atomic masses and corresponding mass defects for five elements found in amino acids. Note the large negative mass defect for element of phosphorous 31P………………………………………………………………………….........................34