Technological advances are enabling proteomics measurements that are increasingly effective, comprehensive and higher throughput. The challenges associated with proteomics measurements include identifying and quantitating large sets of proteins where components of interest may have relative abundances that span more than six orders of magnitude, vary broadly in chemical and physical properties, have transient and low levels of modifications, and are subject to endogenous proteolytic processing. The utility of proteomics data depends significantly on the quality of the data; both the confidence of protein identifications as well as the quantitative utility of the data.
This presentation will describe advanced nanoscale separations and mass spectrometric (MS) instrumentation being developed at applied at Pacific Northwest National Laboratory for making comprehensive, quantitative, and high throughput proteomic measurements. A key element of the approach involves the identification of peptide markers for proteins that are then used for subsequent high throughput mass spectrometric measurements (i.e. without the need for tandem mass spectrometry). The use of stable isotope labels or relative MS peak intensities of these peptide markers provides the basis for quantitation. Initial applications have focused on microbial systems, including Deinococcus radiodurans, Shewanella oneidensis, Rhodobacter sphaerodies and Yersina pesti.
More recent work is extending the application of these proteomics technologies to mammalian systems, including the human blood plasma proteome with its broad biomedical applications. The effectiveness of disease diagnosis and subsequent therapeutic treatment using information contained within the plasma proteome is particularly challenging due to its complexity and large dynamic range of relative protein abundances (>10 orders of magnitude). Initial characterization of the blood plasma proteome at PNNL has provided confident identification peptide markers for many more proteins from plasma than previously detected. These plasma proteome measurements potentially provide the basis for development of biomarkers or signatures for virtually any disease state, and initial collaborative efforts are underway e.g. to identify distinctive biomarkers for the early detection of cancers where much more effective treatment is feasible.
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