SBIR Phase II: A dual mass spectrometry and fluorescence microarray platform for proteomics

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The broader impact/commercial potential of this Small Business Innovation Research (SBIR) Phase II project will be to develop an analytical assay to enable measurement of biological samples by mass spectrometry and fluorescence. The assay will be based on a microarray platform, for applications in the areas of targeted quantitative proteomics, enzymatic activity assays, and combinatorial chemistry. Targeted quantitative proteomics measures changes in the concentration of a specific protein biomarker across multiple samples, such as cell lines, tissues, or biofluids. In the pharmaceutical industry, this method is widely used to assess efficiency of a drug candidate compound as well as its potential toxicity. Researchers are especially interested in the multiplexed approaches to quantitative proteomics that could provide detailed information on the state of various cellular biochemical networks. The significance of this project is the newly developed capability to rapidly separate, purify, and concentrate a large number of proteomic biomarkers for multiplexed quantitative analysis by mass spectrometry. This will result in the assay miniaturization to help lower the costs of the drug development process. Outside of the pharmaceutical field, the technology can be utilized in the clinical settings for performing minimally invasive diagnostics. It also can be extended to basic biology research to study a wide range of important biological interactions including antibody-antigen, drug candidate-drug target, enzyme-substrate, receptor-ligand, and others. This SBIR Phase II project proposes to develop a new analytical technology for life sciences termed Bead-Assisted Mass Spectrometry (BAMS). BAMS is a microarray platform that enables independent data acquisition by fluorescence and mass spectrometry. It applies the method of image cytometry to rapidly screen thousands of microbeads arrayed inside individual wells on a miniaturized microwell plate (picotiter plate). It is the first technology to incorporate high throughput analysis by mass spectrometry into bead-based bioassays, which in their current form are measured primarily on flow cytometry instruments. The dual detection capability is particularly important in proteomics where mass spectrometry can be applied to distinguish protein isoforms and proteins with different patterns of post-translational modifications such as phosphorylation. This project will utilize mass spectrometry imaging in combination with two- and three-dimensional fluorescence imaging, and will perform complementary analysis of bead arrays on the MALDI TOF and ESI MS platforms to achieve greater sequence coverage. This technology will provide researchers with far more options with respect to designing custom multiplex bead assays than currently possible. In addition, BAMS may be used to measure optically encoded beads, mass tag-encoded beads, and even non-encoded beads such as combinatorial peptide bead libraries.