Combined with high and ultra high pressure liquid chromatography, mass spectrometry-based peptide and protein structure analysis requires high resolution and mass accuracy achievable within short ion detection time. Although Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) offers highest resolution and mass accuracy among all types of mass spectrometers, it is unacceptably slow for many applications in proteomics requiring on-line sample pre-fractionation. Multiple frequency detection promises to increase the speed of ion detection in FT-ICR MS without the loss of resolving power, but its application to peptide and, especially, protein analysis has been negligible. In this report, we show that double frequency detection in high field FT-ICR MS indeed allows faster acquisition of high resolution mass spectra of proteins. (C) 2010 Elsevier B.V. All rights reserved.