Probing proteomes using capillary isoelectric focusing-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Unlike the genome, the proteome is exquisitely sensitive to cellular condit ions and will consist of proteins having abundances dependent upon stage in the cell cycle, cell differentiation, response to environmental conditions (nutrients, temperature, stress, etc.), or disease state(s). Therefore, th e study of proteomes under well-defined conditions can provide a better und erstanding of complex biological processes and inference of protein functio n. Thus, much faster, more sensitive, and precise capabilities for the char acterization of cellular constituents are desired. We describe progress in the development and initial application of the powerful combination of capi llary isoelectric focusing (CIEF) and Fourier transform ion cyclotron reson ance (FTICR) mass spectrometry for measurements of the proteome of the mode l system Escherichia coli. Isotope depletion of the growth media has been u sed to improve mass measurement accuracy, and the comparison of CIEF-FTICR results for the analysis of cell lysates harvested from E. coli cultured in normal and isotopically depleted media are presented. The initial studies have revealed 400-1000 putative proteins in the mass range 2-100 kDa from t otal injections of similar to 300 ng off. coli proteins in a single CIEF-FT ICR analysis.