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Lydia Nuwaysir, Applied Biosystems
"Development and Applications in Targeted Quantitative Proteomics"

Abstract:

Global proteomics experiments in mass spectrometry attempt to identify or characterize as many components as possible in a sample through acquisition methods that theoretically allow observation and selection of any peak for detection. In practice, certain criteria are typically used for selecting peaks with favorable attributes, but in general this approach provides an overall view of components within a sample. However, because of the way global experiments are performed, as sample complexity increases, reproducibility can suffer due to the inherent variability in the automated peak selection process.  In contrast to global discovery strategies, a hypothesis driven approach can provide more direct answers to specific biological questions.  In this approach, additional information can be used to design more intelligent experiments to generate only the data of interest on a much faster timescale.  Multiple reaction monitoring (MRM) is a mass spectrometry experiment that is used for hypothesis driven experiments and allows very fast, sensitive and specific detection and quantitation of targeted analytes in complex mixtures.  Experiments using MRM have found widespread use in the pharmaceutical industry as an analytical tool in drug development. More recently, MRM experiments have been used for biomarker verification, protein/peptide confirmation and characterization, and pathway mapping (e.g., tracking changes in phosphorylation signaling networks during various cellular perturbations).  In this talk, applications in targeted quantitative proteomics such as those mentioned above will be discussed using a hybrid quadrupole linear ion trap system.  The hybrid system’s ability to perform highly sensitive MS/MS scans within the same MRM experiment provide a unique additional capability that enables confirmation of the detected species and increases the overall confidence in the experimental results.