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A more recent version of this article appeared on October 1, 2007. Originally published In Press as doi:10.1074/mcp.M700132-MCP200 on July 20, 2007.
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Submitted on March 23, 2007
Revised on June 21, 2007
Accepted on July 18, 2007

High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites

Jianru Stahl-Zeng, Vinzenz Lange, Reto Ossola, Ruedi Aebersold, and Bruno Domon

Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093

Corresponding Author: domon{at}imsb.biol.ethz.ch

The detection and quantification of plasma (serum) proteins at or below the ng/mL concentration range is 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 immuno-assays 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, while 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 five 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 to 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 constrains for the targeted transitions, thus allowing quantification of large sets of peptides in a single analysis.


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