RATIONALE: Peak picking algorithms in mass spectrometry face the challenge of picking the correct signals from a mass spectrum. In some cases signal wiggles (side lobes) are also chosen in the produced mass list as if they were real signals. Constraints which are defined in such algorithms do not always guarantee wiggle free accurate mass list generation out of raw mass spectra. This problem intensifies with acquisitions, which are accompanied with longer transients. Thus, the problem represents a contemporary issue, which propagates with modern high memory digitizers and exists in both MS and MS/MS spectra. METHODS: A solariX FTMS mass spectrometer with an Infinity ICR cell (Bruker Daltonics, Bremen, Germany) coupled to a 12 Tesla magnet (Magnex, UK) was used for the experimental study. Time domain transients of several different data point lengths 512k, 1M, 2M, 4M, 8M were obtained and are Fourier transformed to obtain frequency spectra which show the effect of the transient truncation on sinc wiggle developments in the FT-ICR-MS. MATLAB Simulations were also performed to investigate the origin of the Fourier Transform (FT) artifacts. RESULTS: A new filter is developed to identify and remove FT artifacts (sinc side lobes) from both frequency and mass spectra. The newly developed filter is based on distinguishing between the FWHM of the correct frequency/mass signals and the FWHM of their corresponding wiggles. The filter draws a reliable confidence limit of resolution range, within which a correct frequency/mass signal is identified. The filter is applicable over a wide mass range of metabolic interest (100-1200) amu. CONCLUSIONS: The origin of FT artifacts due to time-domain transient truncations was thoroughly investigated both experimentally and by simulations in this study. A new solution for this problem with automatic recognition and elimination of these FT artifacts (side lobes / wiggles) is provided, which is independent of any intensity thresholds, magnetic field strengths and time-domain transient lengths.