In clinical and diagnostic proteomics that requires an analysis of a large number of human samples, it is essential to develop a comprehensive and robust system for proteome analysis. Our strategy for quantitative protein profiling has been performed by two approaches; both “gel-based” and “shotgun” proteomics. Gel-based proteomics consists of two-dimensional polyacrylamide-gel electrophoresis (2-D PAGE) for quantitative analysis of the separated intact proteins and mass spectrometry for protein identification. Simultaneously, shotgun proteomics has been conducted by the quantitative protein profiling approach for peptide fragments after digestion of whole protein mixture, based on multi-dimensional liquid chromatography and tandem mass spectrometry (LC/MS/MS). Therefore, we have constructed high-throughput and -sensitive 1-D LC/MS/MS systems with a micro-flow LC system and a linear ion-trap mass spectrometer for an approach using 2-D PAGE. Additionally, high-resolution and fully automated online 2-D LC/MS/MS systems have been constructed for comprehensive protein profiling. Currently, we have applied Fourier-transform mass spectrometry (FT-MS) to our protein profiling system. These LC/MS/MS systems described here are capable of high resolution peptide mapping, which is sufficient to comprehensively identify highly complex biological mixture with a reasonably high throughput. These integrated systems could be used as a promising technical platform toward bedside practice of clinical proteomics.