eCRAM computer algorithm for implementation of the charge ratio analysis method to deconvolute electrospray ionization mass spectra

A computer program (eCRAM) has been developed for automated processing of electrospray mass spectra based on the charge ratio analysis method. The eCRAM algorithm deconvolutes electrospray mass spectra solely from the ratio of mass-to-charge (m/z) values of multiply charged ions. The program first determines the ion charge by correlating the ratio of m/z values for any two (i.e., consecutive or non-consecutive) multiply charged ions to the unique ratios of two integers. The mass, and subsequently the identity of the charge carrying species, is further determined from m/z values and charge states of any two ions. For the interpretation of high-resolution electrospray mass spectra, eCRAM correlates isotopic peaks that share the same isotopic compositions. This process is also performed through charge ratio analysis after correcting the multiply charged ions to their lowest common ion charge. The application of eCRAM algorithm has been demonstrated with theoretical mass-to-charge ratios for proteins lysozyme and carbonic anhydrase, as well as experimental data for both low and high-resolution FT-ICR electrospray mass spectra of a range of proteins (ubiquitin, cytochrome c, transthyretin, lysozyme and calmodulin). This also included the simulated data for mixtures by combining experimental data for ubiquitin, cytochrome c and transthyretin.