Comparison of methods for identifying experimental proteomes. Experimental proteomes were determined using MALDI MS or nano-electrospray MS following 2D gel protein separation (2D gel), 1D liquid chromatography peptide separation with nano-electrospray MS (1D LC), or 2D peptide separation by 2D chromatography (strong cation exchange and reverse phase chromatography) with nano-electrospray MS (MUDPIT). 'Proteome' represents all predicted yeast proteins. Protein length in residues (A), isoelectric point (B), and codon adaption index, CAI (C), are shown. MUDPIT data were obtained from reference 6 and our laboratory; 1D LC data are from our laboratory; 2D gel data are from references 14 and 15.