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Biological Sciences

Quantitative Proteomics


Label-free quantification is a method in mass spectrometry that aims to determine the differential expression level of proteins in two or more biological samples. Unlike other methods for protein quantification, label-free quantification does not use a stable isotope-containing compound to chemically bind to and thus label the protein

The ability to quantitatively measure protein abundances is essential for elucidating complex cellular processes and understanding cellular machineries. PNNL has focused on the development and application of 16O/18O labeling[1,2] and "label free" quantitation based on direct MS-intensities. More recently, we have focused on the development and application of a targeted quantitative strategy using selected reaction monitoring (SRM) mass spectrometry.

Our quantitative proteomic approaches have been broadly applied to different biomarker discovery and mechanistic studies by quantifying changes in protein abundances and posttranslational modifications.

The model systems being investigated included many bacterial and plant organisms relevant to relevant to DOE research mission areas in bioenergy, bioremediation, and carbon sequestration as well as many different cells, tissues, and biofluids from mice or human relevant to the National Institutes of Health.

Relevant Publications

Qian W, ME Monroe, T Liu, JM Jacobs, GA Anderson, Y Shen, RJ Moore, DJ Anderson, R Zhang, SE Calvano, SF Lowry, W Xiao, LL Moldawer, RW Davis, RG Tompkins, DG Camp, II, and RD Smith. 2005. "Quantitative Proteome Analysis of Human Plasma Following in vivo Lipopolysaccharide Administration using O-16/O-18 Labeling and the Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics 4(5):700-709.

Qian W, T Liu, VA Petyuk, MA Gritsenko, BO Petritis, AD Polpitiya, A Kaushal, W Xiao, CC Finnerty, MG Jescheke, N Jaitly, ME Monroe, RJ Moore, LL Moldawer, RW Davis, RG Tompkins, DN Hemdon, DG Camp, II, and RD Smith. 2009. "Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an O-18-Labeled "Universal" Reference Sample." Journal of Proteome Research 8(1):290-299.

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