A novel means of simultaneous ion injection and mass scanning has been studied. Classic injection methods for ion trap mass spectrometry proceed by loading the trap and scanning out in mutually exclusive time segments. This mode implicitly imparts a duty cycle and acquisition rate limit to ion trap mass analysis. Using digital frequency scanning methods without the use of discrete injection phases, we demonstrate continuous injection and acquisition rates up to 1000 Hz (averaging 400,000 Th/s) in a 3D ion trap configuration showing an alternatively faster control of ions over the classic voltage ramping mass-selective instability scanning method. The digital frequency scanning method may accommodate current advances in high-speed separation [e.g., ultraperformance liquid chromatography (UPLC), two-dimensional gas chromatography (GC×GC), ion mobility spectrometry (IMS), and capillary electrophoresis (CE)] and ion transfer efficiency (e.g., ion funnels). These ion sources may comprise high ion currents with compositions that change quickly and require high-speed mass analysis. Though resolution is compromised with higher acquisition rates, the frequency scanning mode permits a more flexible platform to accomplish the optimal trade-off of speed and mass spectral quality.