Two-dimensional (2D) gel electrophoresis is the most common protein separation method in proteomics research. It can provide high resolution and high sensitivity. However, 2D gel methods have several limitations, such as labor-intensive procedures, poor reproducibility, and limited dynamic range of detection. In fact, many investigators have returned to couple the one-dimensional (1D) SDS-PAGE with mass spectrometry for protein identification. The limitation of this approach is the increased protein complexity in each one-dimensional gel band. To overcome this problem and provide reproducible quantitative information, we describe here a 2D method for protein mixture separation using a combination of high performance liquid chromatography (HPLC) and 1D SDS-PAGE. The study shows that the step-gradient fractionation method we have applied provides excellent reproducibility. In addition, high mass accuracy of LC-FTICR-MS can allow more confident protein identifications by high resolution and ultra-high mass measurement accuracy. This approach was applied to comparative proteomics since protein abundance level changes can be easily visualized with side-by-side vertical comparison in one gel. Furthermore, separation of multi-samples in the same gel significantly reduces run-to-run variation, as is shown with differential image gel electrophoresis (DIGE). Finally, this approach readily incorporates immunological methods to normalize relative abundances of multiple samples within a single gel. This paper presents the results of our developments and our initial application of this strategy for mapping protease function of beta amyloid cleaving enzyme (BACE) in biological systems.