We report a system for automated protein analysis. In the system, proteins are labeled with the fluorogenic reagent 3-(2-furoyl)quinoline-2-carboxaldehyde, which reacts with lysine residues and creates a highly fluorescent product. These labeled proteins are analyzed by submicellar capillary electrophoresis at pH 7.5 to perform a first dimension separation. Once the first components migrate from the capillary, a fraction is transferred to a second dimension capillary, where electrophoresis is performed at pH 11.1 to further separate the proteins. Laser-induced fluorescence is used as an ultrasensitive detector of the separated proteins. Successive fractions are transferred from the first dimension capillary to the second dimension capillary for further separation to generate, in serial fashion, a twodimensional electropherogram. The transfer of fractions is computer-controlled; there is no operator intervention once the sample has been injected. Zeptomoles of labeled proteins are detected, providing exquisite sensitivity. The resolution of complex samples into components requires sophisticated technology. Most separation techniques are capable of resolving, at most, several dozen components. Cal Giddings (1) recognized that the combination of two separation techniques is important in the resolution of complex mixtures. If the two separation techniques are based on unrelated characteristics of the sample, then the number of resolution elements is given by the product of the resolution elements of both separation steps. For example, isoelectric focusing and SDS-polyacrylamide gel electrophoresis can, individually, resolve ϳ50 components in a protein sample. Their combination, in two-dimensional electrophoresis, can resolve several thousand components (2).Unfortunately, classic two-dimensional electrophoresis requires manual manipulation of the sample. These manipulations, although reasonable for occasional use, are very tedious when performed in large-scale protein analysis projects. Furthermore, detection sensitivity is limited, and relatively large amounts of sample are required to detect weakly expressed components.Column-switching technology is an alternative means of performing two-dimensional separations and is commonly used in chromatographic resolution of complex samples. Most simply, a fraction containing the compound of interest is captured as it elutes from the first column and is transferred to another chromatographic column for additional resolution; fractionation is repeated with different chromatographic methods to achieve the desired purity.In multidimensional chromatography, also known as comprehensive chromatography, a second column is used to sequentially separate all fractions from the first column. These two-dimensional techniques are particularly useful when characterizing extremely complex samples. An early report used two successive chromatographic steps to purify peptides generated from the proteolytic digest of a human immunoglobulin (3).Jorgenson and others (4 -12) have developed elegant...