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A more recent version of this article appeared on October 1, 2006.
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Submitted on May 2, 2006
Revised on July 25, 2006
Accepted on August 3, 2006

Advances and challenges in liquid chromatography-mass spectrometry based proteomic profiling for clinical applications

Wei-Jun Qian, Jon M. Jacobs, Tao Liu, David G. Camp II, and Richard D. Smith

Macromolecular Structure & Dynamics, Pacific Northwest National Laboratory, Richland, WA 99352

Corresponding Author: rds{at}pnl.gov

Recent advances in proteomic technologies provide tremendous opportunities for biomarker-related clinical applications; however, the unique characteristics of human biofluids such as the high dynamic range in protein abundances, and extreme complexity of the proteomes present tremendous challenges. In this review we summarize recent advances in LC-MS based proteomic profiling and its applications in clinical proteomics, as well as discuss the major challenges associated with implementing these technologies for more effective candidate biomarker discovery. Developments in immunoaffinity depletion and various fractionation approaches in combination with substantial improvements in LC-MS platforms have enabled the plasma proteome to be profiled with considerably greater dynamic range of coverage, allowing many proteins at low ng/mL levels to be confidently identified. Despite these significant advances and efforts, major challenges associated with the dynamic range of measurements and extent of proteome coverage, confidence of peptide/protein identifications, quantitation accuracy, analysis throughput, and the robustness of present instrumentation must be addressed before a proteomic profiling platform suitable for efficient clinical applications can be routinely implemented


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