Matthew J. Rardin Matthew J. Rardin, Ph.D., is currently a postdoctoral fellow in the laboratory of Dr. Brad Gibson at the Buck Institute for Research on Aging. Originally from Colorado, he received a B.S. in Microbiology at Colorado State University and obtained a Ph.D. in 2008 from the University of California San Diego in the laboratory of Dr. Jack Dixon where he studied the role of phosphorylation in mitochondria. His postdoctoral work in the Gibson lab is focused on developing techniques for the identification and quantitation of proteins and post-translational modifications in a variety of mitochondrial paradigms using mice as a model system. Recently his work has focused on the use of label free quantitation including MS1-Filtering and SWATH for studying the role of lysine acetylation in mitochondria from SIRT3 knockout animals and how it regulates signaling mechanisms within this dynamic organelle.

Label free quantitation of proteomic data using MS1 Filtering and MS/MSALL with SWATH acquisition

Recently, we developed a label free quantitation tool called MS1 Filtering using expanded features in Skyline. MS1 Filtering processes precursor ion intensity chromatograms of peptide analytes from full scan mass spectral data acquired during data dependent acquisitions by HPLC MS/MS. In contrast data independent acquisitions such as SWATH can quantify product ion analytes from the MS2 scan when a spectral library is available. Interestingly, during each SWATH acquisition cycle on the Triple TOF 5600 mass spectrometer an MS1 scan is acquired providing two independent methods for quantifying analytes in a single acquisition or experiment. We have carried out a series of experiments to examine the utility of using both methods for interrogation of proteomic data sets. This presentation will focus on our efforts to explore the utility of MS1 and MS2 quantitation, either alone or in combination, using Skyline.

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