Abstract
We suggest a line of work for improving the current state-of-the art in computational methods for mass spectrometry. Our main focus is on increasing the chemical realism of the modeling of the fragmentation process. Two core ingredients of our proposal are i) describing the individual fragmentation reactions via graph transformation rules and ii) expressing the dynamics of the system via reaction rates and quasi-equilibrium theory. We use graph transformation rules both for specifying the possible core fragmentation reactions, and for characterizing the reaction sites when learning values for the rates. We employ a strategy framework in order to systematically expand the chemical space of fragments. We think that this approach in terms of chemical modeling is more mechanistically explicit than previous ones, and believe this can lead to both better spectrum prediction and more explanatory power. Our modeling of system dynamics also allows better separation of instrument dependent and instrument independent parameters of the model.
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