Proteomics has rapidly become an important tool for life science research, allowing the integrated analysis of global protein expression from a single experiment. To accommodate the complexity and dynamic nature of any proteome, researchers must use a combination of disparate protein biochemistry techniques, often a highly involved and time-consuming process. Whilst highly sophisticated, individual technologies for each step in studying a proteome are available, true high-throughput proteomics that provides a high degree of reproducibility and sensitivity has been difficult to achieve. The development of high-throughput proteomic platforms, encompassing all aspects of proteome analysis and integrated with genomics and bioinformatics technology, therefore represents a crucial step for the advancement of proteomics research. ProteomIQ (Proteome Systems) is the first fully integrated, start-to-finish proteomics platform to enter the market. Sample preparation and tracking, centralized data acquisition and instrument control, and direct interfacing with genomics and bioinformatics databases are combined into a single suite of integrated hardware and software tools, facilitating high reproducibility and rapid turnaround times. This review will highlight some features of ProteomIQ, with particular emphasis on the analysis of proteins separated by 2D polyacrylamide gel electrophoresis.