Charge ratio analysis method to interpret high resolution electrospray Fourier transform-ion cyclotron resonance mass spectra

The charge ratio analysis method (CRAM) is a new approach for the interpretation of high resolution Fourier transform ion cyclotron resonance (FT-ICR) electrospray mass spectral data. The high resolution capability of FT-MS provides resolved isotopic peaks of multiply charged ions of biopolymers enabling their accurate and monoisotopic molecular mass determination. It does, however, require that the correct charge and isotope composition of these ions be assigned in order for this accuracy to be realized. The unique feature of the CRAM in processing the FT-ICR data is that the charge states of ions are identified from analysis of the ratios of m/z values of isotopic peaks of different multiply charged ions. In addition, the CRAM process correlates the isotopic peaks of different multiply charged ions that share the same isotopic composition. As the size of biopolymers increases, their isotope patterns become more uniform and more difficult to discern from one another. This impacts on the correct matching of a theoretical isotope distribution to experimental data particularly in the case of biopolymers of unknown elemental compositions. The significance of the CRAM is demonstrated in terms of correlating theoretical isotopic distributions to experimental data where this correlation could not always be achieved based on the relative intensities of isotopic peaks alone. While for high resolution FT-ICR mass spectral data, the ion charge can be otherwise determined from the reciprocal of the m/z difference between adjacent isotopic peaks, the CRAM approach is superior and determines ion charge with several orders of magnitude higher accuracy. The CRAM has been applied to high resolution FT-ICR mass spectral for several proteins (ubiquitin, cytochrome c, transthyretin, lysozyme and calmodulin) to demonstrate the general utility of this approach and its application to proteomics. The results have been discussed in terms of internally calibrated ions versus external calibration where the CRAM approach was superior in both cases.