WaNPRC Macaque Proteomics for Models of Influenza Infection and AIDS
EMSL Project ID
27798
Abstract
Abstract for PNNL Project 49651 - Resource OwnerUnder PNNL Project 49561 the Biological Systems Analysis and Mass Spectrometry (BSAMS) group is the Proteomics Core for the NIH NCRR P51 Washington National Primate Research Center (WaNPRC), University of Washington, Seattle. The specific aims for the PNNL BSAMS group within the Center are as follows.
Aim 1. Provide resources for proteomic analysis of macaque tissues. The Proteomics Core will provide resources and support through the multiple stages of acquiring proteomics data, from initial construction of reference accurate mass and time (AMT) tag databases through quantitative analyses of multiple samples taken during the course of animal studies. Peptide coverage in AMT tag databases will be enhanced by advanced separation methods pioneered at PNNL to reduce sample complexity. High-throughput quantitative analyses will be accomplished with the AMT tag paradigm for protein identifications using LC-MS, a process that offers high mass accuracy, high quantitative precision, and small sample-size requirements. Protein quantification will be obtained using 16O/18O stable isotope labeling and label-free absolute intensity methods that are under continual refinement at PNNL. In developing these resources, the Core will perform protein measurements on macaque influenza infection and AIDS models that are available through internal and external collaborations. These studies will track the molecular features of the viral disease model at the protein level, enhancing our understanding of viral virulence, pathogenesis, and the host response.
Aim 2. Provide bioinformatics resources for proteomics data, including methods for integrative proteomic and transcriptomic analysis. The large volume of proteomics data generated by this project will require an extensive computational infrastructure for data management, archiving, and analysis. PNNL will provide resources for the upstream informatics aspects, such as peptide identification and quantification. Functions provided at the WaNPRC will include protein abundance calculations and error estimates using the Elucidator system (Rosetta Biosoftware); this software will also perform clustering operations and other statistical analyses. Datasets and results will be stored in the Division's database system, where it can be served to higher-order analytical packages for extracting biological pathways or network development. Informatics approaches will also be explored for integrating proteomics results with corresponding microarray measurements.
Project Details
Start Date
2007-09-12
End Date
2010-09-12
Status
Closed
Released Data Link
Team
Principal Investigator