Multidimensional chromatography coupled to mass spectrometry is an emerging technique for the analysis of complex protein mixtures. One approach in this general category, multidimensional protein identification technology (MudPIT), couples biphasic or triphasic microcapillary columns to high-performance liquid chromatography, tandem mass spectrometry, and database searching. The integration of each of these components is critical to the implementation of MudPIT in a laboratory. MudPIT can be used for the analysis of complex peptide mixtures generated from biofluids, tissues, cells, organelles, or protein complexes. The information described in this chapter will provide researchers with details for sample preparation, column assembly, and chromatography parameters for complex peptide mixture analysis.