Particle induced X-ray emission (PIXE) at microprobe of Jožef Stefan Institute is used to measure two-dimensional quantitative elemental maps of biological tissue. To improve chemical and biological understanding of the processes in vivo, supplementary information about chemical bonding and/or molecular distributions could be obtained by heavy-ion induced molecular desorption and a corresponding mass spectroscopy with Time-Of-Flight (TOF) mass spectrometer. As the method combines the use of heavy focused ions in MeV energy range and TOF Secondary Ion Mass Spectrometry, it is denoted as MeV SIMS. At Jožef Stefan Institute, we constructed a linear TOF spectrometer and mount it to our multipurpose nuclear microprobe. A beam of 8MeV 35Cl7+ could be focused to a diameter of better than 3μm×3μm and pulsed by electrostatic deflection at the high-energy side of accelerator. TOF mass spectrometer incorporates an 1m long drift tube and a double stack microchannel plate (MCP) as a stop detector positioned at the end of the drift path. Secondary ions are focused at MCP using electrostatic cylindrical einzel lens. Time of flight spectra are currently acquired with a single-hit time-to-digital converter. Pulsed ion beam produces a shower of secondary ions that are ejected from positively biased target and accelerated towards MCP. We start our time measurement simultaneously with the start of the beam pulse. Signal of the first ion hitting MCP is used to stop the time measurement. Standard pulses proportional to the time of flight are produced with time to analog converter (TAC) and fed into analog-to-digital converter to obtain a time histogram. To enable efficient detection of desorbed fragments with higher molecular masses, which are of particular interest, we recently implemented a state-of art Field Programmable Gate Array (FPGA)-based multi-hit TOF acquisition. To test the system we used focused 8MeV 35Cl7+ ion beam with pulse length of 180ns. Mass resolution of measured SIMS spectra, dominantly determined by the duration of the beam pulse, is in good agreement with resolution estimated from pulse length. With improved high-voltage switching ability that will enable beam pulses with duration of 50ns, a mass resolution of better than 500 is anticipated.