In this work, we have presented an analytical model that allows us to detect unique fingerprints of oligopeptides using potential and capacitance in FET based sensor. These unique signatures allow us to differentiate between oligopeptides or any possible change (mutations) in the sequence of the oligopeptide itself. Moreover, the developed model can extract the population of a single short peptide even in the presence of other oligopeptides in the solution. The effect of silanol sites, on the sensor surface, in the presence of oligopeptides, is also studied. Such simulation results provide a solution to extract the actual signal and linearize the sensor output. We have developed further the simulation methodology by considering noise in the system. We have proposed a novel noise reduction technique that can help us to filter out the noise while pinpointing the fingerprints which can be used as parallel processing of experimental signals in measuring instruments.