Top-down Thermal Proteome Profiling using Mass Spectrometry on Human Plasma Proteins

Abstract

Proteins play vital roles in biological systems; hence, the characterization of protein function is crucial for better understanding of complex cellular systems. The study of biological function of proteins at the proteome level is called functional proteomics. One way to probe functionality of proteins is to measure stability via the measurement of protein unfolding as a result of chemical or thermal denaturation. My research is focused on developing and applying novel thermal proteome profiling (TPP) technologies to measure protein thermal stability by heating proteins using a temperature gradient. Traditionally, TPP is conducted using a bottom-up approach in which proteins are enzymatically digested into peptides for mass spectrometry (MS) analysis. Here, a top-down TPP approach was applied to analyze the stability of intact proteoforms and observe the effect of protein modifications that might be obscured due to protein digestion. We applied this top-down TPP method to human plasma to observe the stability of functional proteoforms of low-abundance, clinically relevant proteins. However, it is challenging to elucidate such proteins in human plasma because high-abundant proteins often mask the detection of low-abundant proteins. We systematically evaluated and optimized a depletion protocol to efficiently remove high-abundant proteins in human plasma samples prior to proteomics analysis. Overall, my research illustrates the feasibility of studying functional proteomes in human plasma through a novel platform that integrates the depletion of high-abundant proteins and top-down TPP applications.