1. Mechanism of Ionization in Matrix-Assisted Laser Desorption Ionization (MALDI): How does proton transfer occur Ajax Group http://pslc.ws/mactest/maldi.htm Joshua P. Layfield Jordan C. Vincent Desiree M. Bates Ashley K. Tucker Sara E. Ray Ron C. Estler

2. MALDI Overview MALDI is a soft ionization technique that has revolutionized high-molecular weight mass spectrometry Technique used to measure the molecular weights of a number of systems Proteins Polysaccharides Glyco-lipids Synthetic Polymers Nobel Prize Awarded to Fenn and Tanaka in 2002 for the development of soft ionization techniques http://www.magnet.fsu.edu/education /tutorials/tools/ionization_maldi.html

3. Advantages Used for Disease Diagnosis Used for Disease Diagnosis Able to Ionize Large molecules Able to Ionize Large molecules Accurate / Rapid Analysis Accurate / Rapid Analysis Fast Technique Fast Technique MALDI Overview Disadvantages Lack of Reproducibility Lack of Reproducibility –Sample Hot Spots Lack of proper Matrix Molecules Lack of proper Matrix Molecules Poor Fundamental Understanding of the Mechanism Poor Fundamental Understanding of the Mechanism Lack of Rational Design Lack of Rational Design

4. Cluster Ionization Cluster Ionization –Ionization occurs after desorption from the matrix –Proton transfer occurs in the gas-phase or in small matrix clusters Proposed Mechanisms

5. Photoionzation Photoionzation –Multiple matrix molecule photon absorption –Energy transferred to the analyte in the solid-phase or the gas-phase Proposed Mechanisms

6. Methods Run a MD canonical simulation (CHARMM) to determine the general structure of the matrix protein interactions Run a MD canonical simulation (CHARMM) to determine the general structure of the matrix protein interactions Optimize the structures of potentially relevant matrix/analyte conformations using electronic structure theory Optimize the structures of potentially relevant matrix/analyte conformations using electronic structure theory Study the energetics of the proton transfer reactions using intrinsic-reaction- coordinate electronic structure studies for a test set of amino acid/benzoic acid derivatives Study the energetics of the proton transfer reactions using intrinsic-reaction- coordinate electronic structure studies for a test set of amino acid/benzoic acid derivatives

7. Methods

8. Future Challenges Move beyond pure molecular mechanics Move beyond pure molecular mechanics Investigate other possibilities for matrix molecules Investigate other possibilities for matrix molecules Move beyond the gas phase for the MD simulations Move beyond the gas phase for the MD simulations Testing new matrix molecules for predictive recommendations to experimentalists Testing new matrix molecules for predictive recommendations to experimentalists

9. Special Thanks…