The goal of translational proteomics is to identify putative protein markers that may define a biological condition and incorporate the protein-based markers into routine, quantitative assays. This requires an integrated analytical approach designed to identify and verify peptide surrogates in a small cohort as well as determine differential expression ratios across biological groups. Experimental methods incorporate well-characterized sample preparation, separation, and liquid chromatography coupled to mass spectrometry (LC-MS) methods which collectively facilitate global qualitative and quantitative determinations across all samples. The primary challenge is to develop robust data acquisition schemes providing the greatest breadth of detection while extending depth for qualitative and quantitative measurements. We will present a hybrid data acquisition method, pSMART, that utilizes high-resolution/accurate mass (HR/AM) detection of precursors with narrow window data independent acquisition (DIA) methods on the Q Exactive mass spectrometer. Incorporating both acquisition schemes increase the breadth of detection and quantification while satisfying reproducible product ion generation for sequence confirmation. In addition, the pSMART method provides unique flexibility to adapt to different chromatographic parameters. Differential protein expression analysis for targeted pathways from complex biological samples will be presented using the pSMART method.
For research use only. Not for use in diagnostic procedures.
Scott Peterman, Senior Application Scientist with Thermo Fisher Scientific, has developed and coordinated software development for targeted protein quantitation market supporting new mass spectrometry and consumables as well as integrating with existing proteomics software. He currently consults with customers to optimize integrated mass spectrometry based research strategies for clinical translational with a focus on targeted protein quantitation that includes quality control, reference standards, and software support.
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