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Originally published In Press as doi:10.1074/mcp.M700132-MCP200 on July 20, 2007.
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Molecular & Cellular Proteomics 6:1809-1817, 2007.
© 2007 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

High Sensitivity Detection of Plasma Proteins by Multiple Reaction Monitoring of N-Glycosites*,S

Jianru Stahl-Zeng{ddagger},§, Vinzenz Lange§,¶,||, Reto Ossola, Katrin Eckhardt||, Wilhelm Krek||, Ruedi Aebersold,**,{ddagger}{ddagger} and Bruno Domon,§§

From {ddagger} Applied Biosystems, 64293 Darmstadt, Germany, Institute of Molecular Systems Biology and || Competence Center for Systems Physiology and Metabolic Diseases, Institute of Cell Biology/ETH Zurich, CH-8093 Zurich, Switzerland, ** Faculty of Sciences, University of Zurich, CH-8006 Zurich, Switzerland, and {ddagger}{ddagger} Institute for Systems Biology, Seattle, Washington 98103

The detection and quantification of plasma (serum) proteins at or below the ng/ml concentration range are of critical importance for the discovery and evaluation of new protein biomarkers. This has been achieved either by the development of high sensitivity ELISA or other immunoassays for specific proteins or by the extensive fractionation of the plasma proteome followed by the mass spectrometric analysis of the resulting fractions. The first approach is limited by the high cost and time investment for assay development and the requirement of a validated target. The second, although reasonably comprehensive and unbiased, is limited by sample throughput. Here we describe a method for the detection of plasma proteins at concentrations in the ng/ml or sub-ng/ml range and their accurate quantification over 5 orders of magnitude. The method is based on the selective isolation of N-glycosites from the plasma proteome and the detection and quantification of targeted peptides in a quadrupole linear ion trap instrument operated in the multiple reaction monitoring (MRM) mode. The unprecedented sensitivity of the mass spectrometric analysis of minimally fractionated plasma samples is the result of the significantly reduced sample complexity of the isolated N-glycosites compared with whole plasma proteome digests and the selectivity of the MRM process. Precise quantification was achieved via stable isotope dilution by adding 13C- and/or 15N-labeled reference analytes. We also demonstrate the possibility of significantly expanding the number of MRM measurements during one single LC-MS run without compromising sensitivity by including elution time constraints for the targeted transitions, thus allowing quantification of large sets of peptides in a single analysis.

§§ To whom correspondence should be addressed. Tel.: 41-44-633-2088; Fax: 41-44-633-2052; E-mail: domon{at}imsb.biol.ethz.ch


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