The Proteomics Core enhances the research productivity of KCI members by providing the equipment and trained personnel necessary for analysis of cellular proteome composition, protein modification, protein quantitation and protein interaction. The Proteomics Core is grouped in the Basic Research Core Cluster which, in addition to the Proteomics Core, includes the Microscopy, Imaging and Cytometry Resources Core and the Animal Model and Therapeutics Evaluation Core. The services provided by the Proteomics Core have contributed to 16 peer-reviewed publications during the current review period. Proteome profiling and protein identification services utilize state-of-the-art mass spectrometer-based methods. The platforms for analyses are the Thermo Fisher Orbitrap Fusion equipped with Electron Transfer Dissociation and the Thermo Fisher Q Exactive Orbitrap. Isolated protein, gel plug and full proteome analysis are supported. Sample preparation is achieved by robotic or manual depletion of high abundance proteins, chemical labeling, digestion and solid phase extraction (SPE). A full range of sorbents including specialized sorbents such as TiO2 for isolation of phosphopeptides are available for SPE. Nanoflow HPLC from Easy-nLC 1000 and Michrom H4 platforms is utilized for analyses with a Triversa Nanomate robot available as needed. Data analysis is achieved using Mascot, Sequest-HT, X!Tandem, MaxQuant and PEAKS algorithms with secondary data analysis by Scaffold Q+ and Scaffold PTM. Results are distributed electronically using our ftp server. The Core enhances research productivity by providing a clear and easily accessible process for protein identification and for relative quantitation of proteins based on isotopic labels. Quantitation technologies supported include Spectral Counting, cICAT, iTraq, TMT, SILAC and Multiple Reaction Monitoring (MRM). Analysis of isotopically labeled samples is achieved using Proteome Discoverer, MaxQuant and the Mascot Quantitation package as appropriate. MRM analysis is achieved using the TSQ Vantage with Skyline software for experimental design and data analysis. The protein identification and quantitation component of the Proteomics Core provides KCI members access to technology for protein identification, proteomic profiling and biomarker identification. The protein interactions component of the Core provides instrumentation and services for detection of protein binding by Fluorescence Polarization (FP). The instruments in the Core produce sensitive, accurate and real time measurements of protein binding events. Thus, the protein interactions component of the Core supports investigators in interrogating protein-protein interactions and the effects of those interactions on signaling pathways and cellular function.
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