The document describes research using secondary-ion mass spectrometry (SIMS) to study the fragmentation of organic molecules desorbed from surfaces. It discusses three types of fragmentation mechanisms - direct desorption, desorption then fragmentation, and ion-beam induced fragmentation. It also summarizes the development of an automated time-of-flight SIMS machine for optimizing experimental parameters and collecting high-speed data. Experiments were conducted using a model Cu(100) surface with adsorbed CD3SH molecules to understand the effects of surface orientation on fragmentation patterns.