Phase correction of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry data allows the spectra to be presented in absorption mode. Absorption mode spectra offer superior mass resolving power (up to a factor of 2), mass accuracy, and sensitivity over the conventional magnitude mode. Hitherto, the use of absorption mode in FT-ICR mass spectrometry has required either specially adapted instrumentation or a manually intensive process of phase correction or has ignored the potentially significant effects of image charge and the associated frequency shifts. Here we present an algorithm that allows spectra recorded on unadapted FT-ICR mass spectrometers to be phase corrected, their baseline deviations removed, and then an absorption mode spectrum presented in an automated manner that requires little user interaction.