A streamlined approach to high-throughput proteomics

Abstract

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.

Keywords::

• bioinformatics
• gel electrophoresis
• isoelectric focusing
• laboratory information management system
• mass spectrometry
• Proteome Systems
• proteomics

Acknowledgements

This work was supported by the Australian Research Council. The authors are grateful to Marc Wilkins for insightful suggestions and critical evaluation of this manuscript, to Michael Hsu and Emma Richards for providing data from ChIP experiments, and to Proteome Systems for the use of their ProteomIQ platform

•	Proteomics research generates very large and diverse data sets, which require a coordinated approach to data collection and analysis.
•	High-throughput proteomics requires integration for storing, manipulating and mining large amounts of data, and automation for consistent sample handling on a large scale.
•	The application of new, integrated start-to-finish automated proteomics platforms such as ProteomIQ™ (Proteome Systems Ltd) simplifies proteomic analyses and facilitates rapid and efficient data collection, analysis and archiving.
•	Increased detection sensitivity, new adjuncts to 2D gel electrophoresis technology and more integrated informatics approaches will continue to drive proteomics research and aid in the identification of new biomarkers for diagnostic and therapeutic applications.

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