Proteomics

PROJECT SUMMARY (See instructions): The Proteomics Shared Resource provides AECC researchers with comprehensive mass spectrometry technologies for analysis of proteins, peptides, carbohydrates, lipids and. unknowns. Staff scientists plan and execute proteomics-based analyses, carry out intensive data analysis, and interact closely with AECC scientists on all aspects of their experiments. Services include: MALDI-TOF, ESI- and FT-ICR mass spectrometry; bioinformatics searches and customized data analysis; 2D-gels, 2D-DIGE and high-resolution HPLC; rapid turnaround time for protein ID from gel bands, immunoaffinity isolations or specialty preparations; identification of components of protein complexes; post-translational modifications of proteins; protocols and training in methods and data acquisition; quantitative proteomics using SILAC, SILAM, ^?0, iTRAQ and label-free methods; protein dynamics and biomolecular interactions using hydrogen/deuterium exchange-mass spectrometry; confirmation of synthetic and recombinant molecules; and high-resolution analysis by FT-ICR-MS of metabolites, drugs, peptides and small molecules. Quantitative mass spectrometry experiments have assumed new importance in the past project period, and are anticipated to continue to increase. New services include: (i) imaging mass spectrometry, whereby frozen tissue sections can be analyzed for small proteins or small molecules, transmitters or metabolites and (ii) triple quadrupole mass spectrometry for the quantitative analysis of drugs and their metabolites in biological fluids. The science of the AECC members helps to drive the technology offered in the facility. For example, the demand for imaging mass spectrometry led to the successful shared instrumentation grant application that awarded funds for its implementation. Studies of protein dynamics involve close interactions with several AECC faculty and have been helpful in designing new drug candidates. Analysis of kinetic isotope effects (KIE) is utilized in the design of transition- state inhibitors. The Proteomics Shared Resource provides training on the analytical tools available to users such as the MASCOT search engine and associated modules. Protein Scaffold, ProteolQ, MSnbase to integrate quantitative proteomics with statistical analysis, and specialized software for Selected Reaction Monitoring. A Proteomics course is offered which provides instruction in advanced data analysis.