This paper presents digital signal processing for a miniature, multi-channel, multi-sensor detection system, based on chemically functionalized COMB micro-capacitors and low noise integrated analog electronics. The presented system is capable of detecting traces of different molecules in the air. Currently, it is possible to detect less than 3ppt of target molecules in the atmosphere at room temperature in a 1 Hz bandwidth. For such multi-channel measurements with extreme requirements regarding sensitivity, it is necessary to have the appropriate analog signal processing electronics, as well as digital signal processing hardware, algorithms, and software. The complete architecture of the DSP part of a multi-channel sensor measurement system is explained, together with some simulation and the measured results.