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)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Specialized Center (P50)
Project #
5P50GM076547-07
Application #
8539500
Study Section
Special Emphasis Panel (ZGM1-CBCB-3)
Project Start
Project End
Budget Start
2013-09-01
Budget End
2014-08-31
Support Year
7
Fiscal Year
2013
Total Cost
$443,387
Indirect Cost
$197,061
Name
Institute for Systems Biology
Department
Type
DUNS #
135646524
City
Seattle
State
WA
Country
United States
Zip Code
98109
Peterson, Eliza J R; Ma, Shuyi; Sherman, David R et al. (2016) Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis. Nat Microbiol 1:16078
Cromie, Gareth A; Tan, Zhihao; Hays, Michelle et al. (2016) Dissecting Gene Expression Changes Accompanying a Ploidy-Based Phenotypic Switch. G3 (Bethesda) :
Gatto, Laurent; Hansen, Kasper D; Hoopmann, Michael R et al. (2016) Testing and Validation of Computational Methods for Mass Spectrometry. J Proteome Res 15:809-14
Plaisier, Christopher L; O'Brien, Sofie; Bernard, Brady et al. (2016) Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis. Cell Syst 3:172-86
Vialas, Vital; Sun, Zhi; Reales-Calderón, Jose A et al. (2016) A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage. J Proteomics 131:122-30
Deutsch, Eric W; Sun, Zhi; Campbell, David S et al. (2016) Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics. J Proteome Res 15:4091-4100
Stittrich, Anna B; Ashworth, Justin; Shi, Mude et al. (2016) Genomic architecture of inflammatory bowel disease in five families with multiple affected individuals. Hum Genome Var 3:15060
Zhou, Joseph Xu; Samal, Areejit; d'Hérouël, Aymeric Fouquier et al. (2016) Relative stability of network states in Boolean network models of gene regulation in development. Biosystems 142-143:15-24
Xue, Ting; Liu, Ping; Zhou, Yong et al. (2016) Interleukin-6 Induced ""Acute"" Phenotypic Microenvironment Promotes Th1 Anti-Tumor Immunity in Cryo-Thermal Therapy Revealed By Shotgun and Parallel Reaction Monitoring Proteomics. Theranostics 6:773-94
McDermott, Suzanne M; Luo, Jie; Carnes, Jason et al. (2016) The Architecture of Trypanosoma brucei editosomes. Proc Natl Acad Sci U S A 113:E6476-E6485

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