Quantum oscillation amplitudes of multiband metals, such as high-T_c superconductors in the normal state, heavy fermions or organic conductors, are generally determined through Fourier analysis of the data even though the oscillatory part of the signal is field dependent. It is demonstrated that the amplitude of a given Fourier component can strongly depend on both the nature of the windowing (either flat, Hahn or Blackman window) and, since oscillations are obtained within a finite field range, the window width. Consequences on the determination of the Fourier amplitudes, hence of the effective masses, are examined in order to determine the conditions for reliable data analysis.