Overview. The proteomics core provides cutting-edge proteomics capabilities to the Center, ISB and many collaborators locally and worldwide. Recent accomplishments include: development of analytical and computational tools enabling comprehensive and systematic analysis of proteomes, subproteomes, and post translational modifications;development of software suites for evaluation and validation of proteomic datasets;and the design and implementation of targeted quantitative mass spectrometry (MS) experiments to analyze proteomes and subcellular proteomes. The core equipped with state-of-the-art MS technologies (see Resources) and will continue to disseminate and promote tools for high quality quantitative data acquisition and rapid implementation of new technologies. The core provides training and assistance on MS operation and experimental design, and assists with the Proteomics Informatics course (See Education and Training). Because the core is so integral to Center research, we provide below a description of ongoing technology development. Quantitative Proteomics. The core is a world leader in the development and application of both label and label-free quantitative proteomics for expression profiling and analysis of macromolecular assemblages. For example, the core, in collaboration with the Aitchison group, developed a novel automated approach to quantify peptides in SILAC experiments (QTIPs) along with new approaches for isolation of macromolecular complexes. These approaches significantly improved the identification of in vivo relevant interactions and led to extensive definition of signaling networks involved in peroxisome induction.

Agency
National Institute of Health (NIH)
Type
Specialized Center (P50)
Project #
5P50GM076547-08
Application #
8735161
Study Section
Special Emphasis Panel (ZGM1)
Project Start
Project End
Budget Start
Budget End
Support Year
8
Fiscal Year
2014
Total Cost
Indirect Cost
Name
Institute for Systems Biology
Department
Type
DUNS #
City
Seattle
State
WA
Country
United States
Zip Code
98109
Wurtmann, Elisabeth J; Ratushny, Alexander V; Pan, Min et al. (2014) An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Mol Microbiol 92:369-82
Sangar, Vineet; Funk, Cory C; Kusebauch, Ulrike et al. (2014) Quantitative proteomic analysis reveals effects of epidermal growth factor receptor (EGFR) on invasion-promoting proteins secreted by glioblastoma cells. Mol Cell Proteomics 13:2618-31
Tyler, Anna L; Crawford, Dana C; Pendergrass, Sarah A (2014) Detecting and Characterizing Pleiotropy: New Methods for Uncovering the Connection Between the Complexity of Genomic Architecture and Multiple phenotypes. Pac Symp Biocomput :183-187
Mohamadlou, Hamid; Shope, Joseph C; Flann, Nicholas S (2014) Maximizing Kolmogorov Complexity for accurate and robust bright field cell segmentation. BMC Bioinformatics 15:32
Ashworth, Justin; Plaisier, Christopher L; Lo, Fang Yin et al. (2014) Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction. PLoS One 9:e107863
Carpp, Lindsay N; Rogers, Richard S; Moritz, Robert L et al. (2014) Quantitative proteomic analysis of host-virus interactions reveals a role for Golgi brefeldin A resistance factor 1 (GBF1) in dengue infection. Mol Cell Proteomics 13:2836-54
Kusebauch, Ulrike; Deutsch, Eric W; Campbell, David S et al. (2014) Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Curr Protoc Bioinformatics 46:13.25.1-13.25.28
Schoggins, John W; MacDuff, Donna A; Imanaka, Naoko et al. (2014) Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity. Nature 505:691-5
Kusebauch, Ulrike; Ortega, Corrie; Ollodart, Anja et al. (2014) Mycobacterium tuberculosis supports protein tyrosine phosphorylation. Proc Natl Acad Sci U S A 111:9265-70
Vialas, Vital; Sun, Zhi; Loureiro y Penha, Carla Veronica et al. (2014) A Candida albicans PeptideAtlas. J Proteomics 97:62-8

Showing the most recent 10 out of 186 publications