Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), followed by protein extraction and characterization with chemical sequencing or mass spectrometry (MS), is the most commonly used method to analyze complex protein systems such as cells and organella. Many reports appeared on the improvements of these processes of information-collection, to establish a system with higher performance. However, it is claimed that 2-D PAGE-based methods are slow and labor-intensive and also need subsequent efforts for one-by-one identification of proteins. Combined methods of Fourier transform ion cynclotron resonance (FTICR) mass spectrometry with preceding separation techniques such as capillary isoelectric focusing or capillary liquid chromatography was introduced to be promising for the analysis of the protein systems. Also, the works to overcome the disadvantages of 2-D PAGE-based methods, combining the results obtained by non-denaturing 2-D PAGE and by denaturing 2-D PAGE to integrate protein information, were introduced.