“Molecular phenotyping of therapeutic responses and mammalian aging with quantitative proteomics”

Highlights:

• Proteins act as the effector molecules of cells – carrying out most of the structural, regulatory, and enzymatic functions. Proteins themselves are often regulated through direct interaction with ligands, including metals, lipids, other proteins, and drugs. These protein-ligand interactions are fundamental to diverse biological processes. Yet, technologies to explore these interactions are limited in terms of both throughput and their ability to scale. We are building tools and methods to rapidly quantify these interactions and determine mechanisms of action for diverse species of ligands.
• Intelligent data acquisition in mass spectrometry driven proteomics can enhance the accuracy and efficiency of proteomics data collection. Using methods like real-time data base searching (search a spectra in less than 10 milliseconds) we are building adaptive strategies to harness spectral data to determine quantitative disparities between cellular states.
• Modern proteomics enables quantitation of up to 10,000 proteins from complex cellular matrices. At the interface of cell biology, biochemistry and proteomics, we are attempting to understand how proteins govern key cellular pathways involved in normal cellular function and disease (e.g. cancer).

Dr. Schweppe began his research career working for Dr. Charles Lovett at Williams College. He then pursued doctoral work with Dr. Scott Gerber at Dartmouth Medical School, followed by postdoctoral work with Dr. James Bruce (UW) and Dr. Steven Gygi (Harvard Medical School). Starting in 2020, Devin began his research group here at the University of Washington in the Department of Genome Sciences.
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Dr. Schweppe’s research interests focus on the implementation of millisecond informatics to enable intelligent data acquisition strategies. His research group applies these technologies to quantify proteins as a readout for diverse cell states with broad interests spanning microbial protein interactions, small-molecule binding events, pre-clinical proteomics, and profiling primary tissue samples. Dr. Schweppe’s research group builds on the application of sample multiplexing and real-time search to achieve high efficiency instrument acquisition for both discovery and targeted proteomics platforms. Along with the methods and technology development focus, the group has worked to build applications and resources to disseminate large-scale proteomics datasets to the research community, these efforts include work the crosslinking mass spectrometry repository XLinkDB, the cysteine oxidation explorer for OxiMouse, and the BioPlex human interactome explorer.