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Molecular & Cellular Proteomics 5:1899-1913, 2006.
© 2006 by The American Society for Biochemistry and Molecular Biology, Inc.

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Other Diseases and Conditions

High Dynamic Range Characterization of the Trauma Patient Plasma Proteome^*,S

Tao Liu, Wei-Jun Qian, Marina A. Gritsenko, Wenzhong Xiao, Lyle L. Moldawer^¶, Amit Kaushal, Matthew E. Monroe, Susan M. Varnum, Ronald J. Moore, Samuel O. Purvine, Ronald V. Maier^||, Ronald W. Davis, Ronald G. Tompkins^**, David G. Camp, II, Richard D. Smith^, the Inflammation and the Host Response to Injury Large Scale Collaborative Research Program

From the Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, California 94304, ^¶ Department of Surgery, University of Florida College of Medicine, Gainesville, Florida 32610, ^|| Department of Surgery, Harborview Medical Center and University of Washington, Seattle, Washington 98104, and ^** Department of Surgery, Shriners Burn Center, and Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114

Although human plasma represents an attractive sample for disease biomarker discovery, the extreme complexity and large dynamic range in protein concentrations present significant challenges for characterization, candidate biomarker discovery, and validation. Herein we describe a strategy that combines immunoaffinity subtraction and subsequent chemical fractionation based on cysteinyl peptide and N-glycopeptide captures with two-dimensional LC-MS/MS to increase the dynamic range of analysis for plasma. Application of this "divide-and-conquer" strategy to trauma patient plasma significantly improved the overall dynamic range of detection and resulted in confident identification of 22,267 unique peptides from four different peptide populations (cysteinyl peptides, non-cysteinyl peptides, N-glycopeptides, and non-glycopeptides) that covered 3654 different proteins with 1494 proteins identified by multiple peptides. Numerous low abundance proteins were identified, exemplified by 78 "classic" cytokines and cytokine receptors and by 136 human cell differentiation molecules. Additionally a total of 2910 different N-glycopeptides that correspond to 662 N-glycoproteins and 1553 N-glycosylation sites were identified. A panel of the proteins identified in this study is known to be involved in inflammation and immune responses. This study established an extensive reference protein database for trauma patients that provides a foundation for future high throughput quantitative plasma proteomic studies designed to elucidate the mechanisms that underlie systemic inflammatory responses.

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