A Nanofluidic/Microfluidic System for Enhanced Low-Input and Single-Cell Proteomics

Within living cells, proteins are the primary cellular machinery, performing most biological functions. Aberrant protein expression or modification often leads to cellular dysfunction that causes illness and disease. Thus, an improved understanding of how proteins change within cells in response to disease progression is needed. These quantitative measurements of changes in proteins and their modifications are necessary for improved biological models of cellular function. More accurate and detailed mechanisms of disease transformation will improve diagnostics and allow rational design of new treatments. To gain as complete a picture as possible of cellular state, proteomics aims to identify and characterize all the proteins and their proteoforms in a biological sample. Such proteomic analyses are challenging due to the large number of proteins expressed, the large dynamic range of protein relative abundance, the dynamic nature of protein expression, the numerous biologically essential modifications, and the loss of proteins by surface adsorption. The diverse structures and complexity of cells complicates the initial purification and preparation of proteomic samples. Currently, there is a movement within the field of proteomics to improve single cell analyses to better understand cellular heterogeneity, which is critical to understanding the mechanisms of disease and response to treatment. To help overcome these challenges, a new microfluidic/nanofluidic sample preparation platform is proposed to provide efficient extraction of proteins from the cellular milieu, removal of contaminants, and protein denaturation. This platform will be integrated into both top-down and bottom-up workflows and is expected to overcome the longstanding challenge of reliably providing solubilized proteins with negligible contaminants and ion-suppressing agents for top-down proteomics. For bottom-up proteomics, an additional advantage of improved protein denaturation is anticipated. Additionally, the proposed microfluidic/nanofluidic systems are well-suited for the preparation of samples down to the single-cell level. The Aims include fundamental studies of the protein purification process and measurement of the anticipated improvement in both top-down and bottom-up proteome analyses. If successful, this application will provide a widely accessible system for low input and single-cell proteomics sample preparation that will significantly improve the depth of proteome coverage and speed of single-cell proteomics.