High-Throughput Comparative Proteome Analysis Using a Quantitative Cysteinyl-peptide Enrichment Technology

Tao Liu,† Wei-Jun Qian,† Eric F. Strittmatter, David G. Camp, II, Gordon A. Anderson, Brian D. Thrall, and Richard D. Smith*
Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352
Anal. Chem., 2004, 76 (18), pp 5345–5353
DOI: 10.1021/ac049485q
Publication Date (Web): August 5, 2004
Copyright © 2004 American Chemical Society
†

 Authors who contributed equally to this work.

,
*

In papers with more than one author, the asterisk indicates the name of the author to whom inquiries about the paper should be addressed.

Abstract

A new quantitative cysteinyl-peptide enrichment technology (QCET) was developed to achieve higher efficiency, greater dynamic range, and higher throughput in quantitative proteomics that use stable-isotope labeling techniques combined with high-resolution liquid chromatography (LC)−mass spectrometry (MS). This approach involves 18O labeling of tryptic peptides, high-efficiency enrichment of cysteine-containing peptides, and confident protein identification and quantification using the accurate mass and time tag strategy. Proteome profiling of naïve and in vitro-differentiated human mammary epithelial cells using QCET resulted in the identification and quantification of 603 proteins in a single LC−Fourier transform ion cyclotron resonance MS analysis. Advantages of this technology include the following:  (1) a simple, highly efficient method for enriching cysteinyl-peptides; (2) a high-throughput strategy suitable for extensive proteome analysis; and (3) improved labeling efficiency for better quantitative measurements. This technology enhances both the functional analysis of biological systems and the detection of potential clinical biomarkers.

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History

  • Published In Issue September 15, 2004
  • Received for review April 2, 2004. Accepted June 23, 2004.

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