Kihyung Song & Riccardo Spezia 
Theoretical Mass Spectrometry [PDF ebook] 
Tracing Ions with Classical Trajectories

This book discusses fragmentation mechanisms of molecules under mass spectrometry conditions and the resulting peaks observed in ESI-MS/MS experiments. The underlying principles are used to understand everything from small molecules to biological poly-peptides collision induced dissociation. In a theoretical approach, gas phase reactivity of molecular ions is coupled with chemical dynamics simulations.