This paper describes data acquisition system for Time-of-Flight Mass Spectrometer based on a commercial high-speed signal averager AP100 (AcqirisTM). Counting Mode for AP100 ADC has been characterized. Feasibility of acquisition system has been tested with two different instruments. First instrument is a home-built Time-of-Flight Mass Spectrometer used in our lab for biochemical studies. Second instrument is a prototype of Multi Reflection Time-of-Flight mass Spectrometer with long (about 10 milliseconds) time of flight. All experiments were controlled by our data acquisition software, which includes fast compression algorithms and allows storing large arrays of LC-MC experimental data without any losses. Our studies show that AP100 based data acquisition system is satisfying requirements of TOF tandems with 2D parallel MS-MS analysis.