The invention generally relates to systems and methods for collision induced dissociation of ions in an ion trap. In certain aspects, the invention provides a system that includes a mass spectrometer having an ion trap, and a central processing unit (CPU). The CPU includes storage coupled to the CPU for storing instructions that when executed by the CPU cause the system to generate one or more signals, and apply the one or more signals to the ion trap in a manner that all ions within the ion trap are fragmented at a same Mathieu q value.