Multiplexed and microparticle‐based analyses: Quantitative tools for the large‐scale analysis of biological systems

Abstract

While the term flow cytometry refers to the measurement of cells, the approach of making sensitive multiparameter optical measurements in a flowing sample stream is a very general analytical approach. The past few years have seen an explosion in the application of flow cytometry technology for molecular analysis and measurements using microparticles as solid supports. While microsphere-based molecular analyses using flow cytometry date back three decades, the need for highly parallel quantitative molecular measurements that has arisen from various genomic and proteomic advances has driven the development in particle encoding technology to enable highly multiplexed assays. Multiplexed particle-based immunoassays are now common place, and new assays to study genes, protein function, and molecular assembly. Numerous efforts are underway to extend the multiplexing capabilities of microparticle-based assays through new approaches to particle encoding and analyte reporting. The impact of these developments will be seen in the basic research and clinical laboratories, as well as in drug development. q 2006 International Society for Analytical CytologyKey terms: microarray; systems biology; proteomics; protein array; high throughput screening; drug discovery; diagnostics A major goal for biomedical research in the 21st century will be to collect and integrate molecular information about genes, proteins, and numerous other biomolecules into the working models of cell and organism function from which predictions can be made. The rationale for pursuing such an ambitious goal stems from the very significant advances in molecular analysis that enable the sequencing of whole genomes, the highly parallel analysis of gene expression levels, and large scale identification of proteins in complex samples. These advances resulted from new molecular reagents and assay chemistries, new instrumentation with improved sensitivity and throughput, new computational tools, and a significant change in focus for experimental biology from one that focuses on individual molecules to one that considers the abundance and interactions of many different molecules as they function in networks of biochemical pathways in living systems.However, just as these new technologies have enabled the rapid acceleration of data collection and interpretation, continued progress toward transforming this information into biological understanding is dependent on continued improvement in analytical technologies. In particular, it is critical to augment qualitative analysis methods that allow the identification of important molecules with quantitative measurements of their abundance and function. The ability to make quantitative measurements of the concentrations of many individual proteins, their interactions and the formation of macromolecular assemblies, and the measurement of these assemblies in live cells and organisms represent major challenges in understanding the systems of molecular networks and pathways that underlie physiology and disease. These challenge...

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