Abstract: A method for fully automated deconvolution of electrospray ionization mass spectra of multiply-charged biomolecular ions is disclosed. The method comprises preparing a biomolecular sample and performing mass spectrometry to generate mass spectrum data. This data is processed by a data processor to create a short-time Fourier transform (STFT) spectrogram of frequency versus mass-to-charge (m/z). Signal peaks at integer-value frequencies are grouped, and charge state values are assigned to selected pixels within the spectrogram associated with the grouped series. A preliminary deconvolved mass spectrum is generated via an inverse STFT, followed by an automated refinement process. The refinement includes performing a secondary STFT transform on the preliminary spectrum, excluding signal data at non-integer frequencies, and applying a subsequent inverse STFT to produce absolute mass distribution data.