PFI:AIR - TT: Development of a universal protein and peptide cleanup kit

Carnegie Mellon University, Pittsburgh PA

Investigators

Abstract

This PFI: AIR Technology Translation project focuses on translating the development of novel technologies for the field of proteomics. Proteomics is the high throughput study of proteins produced by organisms, tissues or cells. Proteomics methods enable biomedical researchers in industry and academia to discover the following knowledge: what proteins differ between normal development and diseased states, what proteins are affected by exposure to different drugs or treatments, and what proteins potentially serve as disease biomarkers. Proteomics methods have been applied to a wide range of organisms under an enormous number of conditions. It a relatively new field that has numerous technological hurdles to cross in order to meet its full potential. Scientists working in the field of proteomics have indicated that protein and peptide sample preparation is one of the greatest experimental hurdles they face. More than a million of such proteomics samples are prepared for analysis per year in the U.S. and reproducible, reliable and automatable sample preparation is important. Currently, the existing sample preparation methods lack universality, they are biased towards particular classes of proteins and peptides that results in significant sample loss, and the current methods are difficult to automate for industrial applications. This award develops a prototype of a "Universal Protein and Peptide Isolation and Cleanup Kit" (UPICK) that targets a ubiquitous feature of all proteins and peptides, thus it is universal and unbiased. UPICK is amenable to automation, enabling adoption into high-throughput, industrial workflows, while minimizing handling errors and environmental contamination. UPICK will allow researchers to perform their proteomics experiments with far greater reliability, repeatability and standardization, thus enhancing biomedical discovery. This project addresses the following technology gap(s) as it translates from research discovery toward commercial application. Two novel reagents will be developed for the protein cleanup kit. One is the development of a completely reversible protein/peptide tag that is capable of chemically coupling to the second novel feature, which is ultra-high capacity magnetic beads. Together, these reagents will be used to first tag all proteins or peptides in solution and then covalently bind the tagged proteins/peptides to magnetic beads. The beads will then be washed to remove endogenous and exogenous non-protein contaminants, such as DNA, RNA, salts, detergents and denaturants. The goal is to create a UPICK prototype to distribute for beta-testing. Graduate students and a team of undergraduates will be involved in developing the kits and testing the efficacy and ease of use of the kits both in-house and with beta-test partners. In addition, the students will have the opportunity to participate in Carnegie Mellon?s Tepper School of Business Innovation Scholars Program that develops the entrepreneurial skills of non-business school, graduate students.