We collected 41 E. coli total cell extracts, digested, analysed them using a new FTICR - ion trap cluster. By combining ion trap and FTICR data we identified 4,333 unique peptides corresponding to 948 proteins. The use of high-field FTICR with high resolving power, mass accuracy and dynamic range provides significantly better quantitative precision for label-free proteomics than ion trap data alone. Quantitative proteomic data agrees with microarray gene expression data for glucose- lactose diauxie in E. coli, for instance the [3-galactosidase and lacZ expression profiles were similar. Proteins taking part in the same metabolic pathways as beta-galactosidase were also upregu- lated. The data analysis methods should be further refined, using automatic internal calibration [7, 8] and more sophisticated chromatographic peak finding and integration methods for quantitation.
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