tionation in the first dimension, followed by RP chromatography in the second dimension to generate a 2-dimensional image of the protein content. The MALDI-TOF MS analysis of the second dimension fractions

The discovery stage of proteome profiling for disease or expression proteomics typically involves the comparison of different states of a cell, tissue or plasma. In order to obtain better reproducibility and quantitate proteins, 2-dimensional LC liquid separation technique, ProteomeLab PF2D is presented. This method uses chromatofocusing to produce pI fractionation in the first dimension, followed by RP chromatography in the second dimension to generate a 2-dimensional image of the protein content. The MALDI-TOF MS analysis of the second dimension fractions is also discussed. Additionally, CE-ESI-MS utility in the protein identification and carbohydrate chain conformation analysis is presented. The triptic digested protein and the labeled oligosaccharides were elegantly analyzed by MS-MS. Also the labeled oligosaccharides analysis by CE system with laser-induced fluorescence detecting provided the additional information. The CE-ESI-MS technique complements LC-MS as a new powerful analytical tool for the fields of proteomics and glycomics to analyze the conformation of the N-linked oligosaccharides.