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I know adding zeros will not increase the frequency resolution. I have couple of waveforms in time domain measured over months. I take the fft of the waveforms to find frequency components. The problem is I get several points around each peak, but only based on visual check i found that the real peak is not the one hit by discrete frequency points.

To shovel this, 1. I can add zeros to get finer structure so that the frequency points are more close to the real peak points.

My question is: I can perform the same procedure for all waveforms. But can I really compare the peaks identified with such zero padding so that I can get the conclusion about whether there is peak shift over time or not in terms of frequency.

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Zero-padding can be used to more accurately estimate the frequency of a single sinusoid in zero noise. Since a zero-padded FFT produces a smoother looking plot, and thus shallower peaks, if there are any subtle changes in the inflections and thus peak location caused by noise, those shifts will be magnified by the zero-padded FFT, perhaps from a fraction of a FFT result bin to several bins of random shift.

So, one needs to have a good estimate of the S/N ratio to know whether and how much zero-padded will produce a usefully more accurate frequency peak estimate of a sinusoidal (or narrow band) signal.

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