PROTEOMICS

The Proteomics Core is located at Pacific Northwest National Laboratory (Richland, Washington). Teaming with PNNL provides the Center with world-class mass spectrometry instrumentation and state-of-the-art technology development. Key to the Center's proteomics efforts is the use of highly sensitive Fourier transform ion cyclotron resonance (FTICR) mass spectrometry, which enables the profiling of protein abundance changes using biopsy samples that provide only limited protein yields. Quantitative proteomic analyses are performed using stable isotope labeling and label-free comparative absolute quantification methods. PNNL provides the computational resources and data analysis pipeline for accurate peptide identification and quantification. Higher-order analyses are performed by Center biologists using software systems provided by the Bioinformatics & Biostatistics Core.

We are also leveraging increases in PNNL's throughput capabilities to extend our quantitative proteomic studies to multiple HCV and HIV-1 model systems. In addition, we are exploiting recent technological and methodological advances that now permit in-depth proteome coverage of high dynamic range samples to analyze additional biological materials, such as human plasma samples. The data generated from these studies will support efforts to provide a detailed molecular portrait of the protein abundance changes that occur during disease progression and are likely to yield improved diagnostic methods, markers of disease progression, and novel approaches to therapeutic intervention.