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Molecular & Cellular Proteomics 4:700-709, 2005.
© 2005 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

Quantitative Proteome Analysis of Human Plasma following in Vivo Lipopolysaccharide Administration Using ¹⁶O/¹⁸O Labeling and the Accurate Mass and Time Tag Approach^*,S

Wei-Jun Qian, Matthew E. Monroe, Tao Liu, Jon M. Jacobs, Gordon A. Anderson, Yufeng Shen, Ronald J. Moore, David J. Anderson, Rui Zhang, Steve E. Calvano, Stephen F. Lowry, Wenzhong Xiao^¶, Lyle L. Moldawer^||, Ronald W. Davis^¶, Ronald G. Tompkins^**, David G. Camp, II, Richard D. Smith^, and 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 99352, the Department of Surgery, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Brunswick, New Jersey 08901, the ^¶ Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, California 94304, the ^|| Department of Surgery, University of Florida College of Medicine, Gainesville, Florida 32610, and the ^** Department of Surgery, Shriners Burn Center and Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114

Identification of novel diagnostic or therapeutic biomarkers from human blood plasma would benefit significantly from quantitative measurements of the proteome constituents over a range of physiological conditions. Herein we describe an initial demonstration of proteome-wide quantitative analysis of human plasma. The approach utilizes postdigestion trypsin-catalyzed ¹⁶O/¹⁸O peptide labeling, two-dimensional LC-FTICR mass spectrometry, and the accurate mass and time (AMT) tag strategy to identify and quantify peptides/proteins from complex samples. A peptide accurate mass and LC elution time AMT tag data base was initially generated using MS/MS following extensive multidimensional LC separations to provide the basis for subsequent peptide identifications. The AMT tag data base contains >8,000 putative identified peptides, providing 938 confident plasma protein identifications. The quantitative approach was applied without depletion of high abundance proteins for comparative analyses of plasma samples from an individual prior to and 9 h after lipopolysaccharide (LPS) administration. Accurate quantification of changes in protein abundance was demonstrated by both 1:1 labeling of control plasma and the comparison between the plasma samples following LPS administration. A total of 429 distinct plasma proteins were quantified from the comparative analyses, and the protein abundances for 25 proteins, including several known inflammatory response mediators, were observed to change significantly following LPS administration.

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