In Silico Tandem Mass Spectrometer: an Analytical and Fundamental Tool

In this article, we summarize some aspects of the recently developed computational approach to model and predict collision induced dissociation mass spectra. In particular, we describe how initial conditions can be set to model fragmentation conditions and then obtain different results from the analysis of an ensemble of reactive trajectories. This approach was studied and validated on different systems, from small organic molecules to large biomolecules. Recently an iterative procedure was proposed to increase the fragmentation sampling, reducing computational time and providing a more comprehensive fragmentation pattern. All these fundamental developments are at the basis of the application of this approach to analytical problems. One important and possible outcome will be in creating an in silico data base which will be an useful complement to the experimental ones. This is discussed within other possible future outlooks.