\(B\rho\) -defined Isochronous Mass Spectrometry ( \(B\rho\) -IMS) based on heavy-ion storage rings is a newly developed technique for precision mass measurements of short-lived nuclides. Two time-of-flight detectors are installed in a straight section of the storage ring, measuring the revolution time and the velocity of the stored ions to achieve a high precision of mass measurement. Electromagnetic noise from the detection system constitutes a primary source of uncertainty in \(B\rho\) -IMS mass values. In the development of \(B\rho\) -IMS, a digital Fourier denoising analysis was applied to analyze the full-waveform timing signals sampled by a digital oscilloscope. Several periodic electrical components were unexpectedly discovered in the timing signals, and the corresponding frequencies were exactly integer submultiples of the oscilloscope sampling rate. Through this analysis, the systematic deviation existing in the re-determined mass values was removed at \(1\sigma\) confidence level for nuclei with \(Z\ge 15\) , and the precision of measured velocities and ion masses was improved by a comparable magnitude, ranging from 7% to 20%. In further investigation, the amplitudes of these periodic components were correlated with the voltage sampling range of the oscilloscope and varied quasi-periodically in different hours over a day. Given the widespread use of digital oscilloscopes, this finding is relevant to experiments employing similar electronic equipment.