Ionization Mechanisms in UV-MALDI:
An Introduction to General Principles and the Coupled Chemical and Physical Dynamics Model

by Richard Knochenmuss

1. Introduction

2. The Desorption / Ablation Event

3. The Coupled Physical and Chemical Dynamics (CPCD) Model
            About the name
            It is not a "Gas Phase" Model
            Primary ionization- creating the first ions
                    Table 1. Ionization Potentials
            Secondary ionization- ion-molecule reactions
                    Table 2, Proton Affinities
                    Table 3, Cation Affinities

4. The Quantitative CPCD Rate Equation Model
            Primary Ionization
                    Successfully predicted phenomema
            Secondary Ionization
                    Successfully predicted phenomema
            Loss Mechanisms
            Example Results
                    Analyte Concentration
                    Analyte Molecular Weight
                    Charge Transfer Thermodynamics
                    Positive / Negative Analyte Ratios

5. The Quantitative CPCD Molecular Dynamics Model
            Motivation for MD
            Implementation
            Ion Recombination
            Results
            Movies

6. Surface Phenomena
            Metal Surfaces: photoelecton emission
            Metal Surfaces: enhanced MALDI signal
            Structured Substrates

7. Literature

1. Introduction
Matrix-assisted laser desorption/ionization (MALDI) is a widespread modern analytical method, invented in the 1980s by F. Hillenkamp and M. Karas, but many users know little about how it works.

MALDI is a complex phenomenon involving multiple interacting physical and chemical processes. Each of these aspects will be addressed, quantitative models for UV MALDI will be presented (the only ones currently available), some example results shown, and compared to experiment. The purpose of this tutorial is to summarize and explain these models, it is not a general review (see the Analyst paper below). The CPCD have been more successful than expected when this work was started, but are certainly not the last word on the subject. Hopefully readers will better understand UV MALDI, better plan and interpret their MALDI experiments, and be motivated to help improve our understanding of how MALDI works.

It is assumed that readers have some basic knowledge of the MALDI method: Analyte is mixed with an excess of matrix material, usually by co-crystallization from solution. This mixture is irradiated with tens to hundreds of microjoules of energy from a laser, usually in the ultraviolet range, but infrared is also used. Only ultraviolet mechanisms are considered here. The resulting ions may be analyzed by many different methods, but time-of-flight is typical.