U2-Physicians 3F Hall Hub Back-hero

MCW Researcher Develops Breakthrough Protein Analysis to Enable Drug Discovery, Clinical Analyses

The study of all proteins in a biological system, or proteomics, enables an unbiased assessment of protein quantities. Proteome analysis is an important tool for clinicians and biologists to build hypotheses about how protein changes associated with disease can lead to new therapeutics. Proteomics technology continues to improve, but relatively low throughput prevents its application to problems that require thousands of samples, such as clinical biomarker discovery or drug discovery.

In an article published in Nature Methods, a new professor in the MCW Biochemistry Department has developed a groundbreaking protein analysis technique that enables quantification of proteins in seconds instead of the usual tens of minutes or hours.

“This is a significant breakthrough that will decrease the time required for proteomic analysis, which translates to lower cost per sample,” said Jesse G. Meyer, PhD, assistant professor of Biochemistry at MCW and lead researcher of this study. “That means we can start thinking about collecting data from thousands of proteomes, which is needed for drug discovery and clinical analyses.”

Due to the incredible complexity of proteins in any biological system, proteomics technology typically relies on separation of protein pieces called peptides before their analysis by mass spectrometry. This pre-fractionation of peptides is usually done in the liquid phase based on the “greasiness” or hydrophobicity of peptides. Peptide separation is the rate limiting factor in proteomics experiments. The key advancement of this new proteomic technology is a shift to separate the peptide parts of proteins in the gas phase, which is achieved in milliseconds.

Preliminary experiments demonstrated that this new method – “Direct Infusion – Shotgun Proteome Analysis ” (DI-SPA) – could quantify 3-4 proteins per second. The researchers showed that the quantitative values from DI-SPA were similar to those from traditional proteomic methods.

To demonstrate its utility, Natalie Niemi and Dave Pagliarini, assistant professor and professor, respectively, at Washington University Saint Louis, devised experiments testing whether the method could reveal interactions between nutrients, toxin treatments, and a genetic mutation. A total of 44 unique conditions were tested in triplicate, and data was collected from 132 samples in only about 4 hours. Traditional proteomics methods would require at minimum nearly one week. They found that DI-SPA detected many of the expected proteome remodeling, and that the data could reveal relationships between experimental factors.

The study also showed that the new method is well suited to analyze purified mitochondria, the power plants inside cells. They further showed that DI-SPA can follow over 100 proteins from human plasma, an analysis that could be theoretically completed in only ~30 seconds per sample. Thus, the new proteome analysis method opens up possibilities for analysis of thousands of patient samples in clinical cohorts.

“This project is a perfect marriage of technology development, informatics, and high throughput screening,” said Dr. Meyer. “The combination of these technologies, and the diverse expertise from everyone involved, produced something greater than the sum of the parts. I am grateful to be part of such a talented team of scientists.”

These findings are described in the article entitled “Quantitative Shotgun Proteome Analysis by Direct Infusion”, recently published in the journal Nature Methods. This work was conducted by Jesse Meyer, PhD, of the Medical College of Wisconsin, Natalie Niemi, PhD, and Dave Pagliarini, PhD, of Washington University Saint Louis, and Josh Coon, PhD of University of Wisconsin-Madison.