The Use of a Quantitative Cysteinyl-Peptide Enrichment Technology for High-Throughput Quantitative Proteomics

Quantitative proteomic measurements are of significant interest in studies aimed at discovering disease biomarkers and providingnew insights into biological pathways. A quantitative cysteinyl-peptide enrichment technology (
QC
ET) can be employed to achievehigher efficiency, greater dynamic range, and higher throughput in quantitative proteomic studies based on the use of stableisotope-labeling techniques combined with high-resolution capillary or nano-scale liquid chromatography-mass spectrometry(LC-MS) measurements. The QCET approach involves specific
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O/
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O-labeling of tryptic peptides, high-efficiency enrichment of cysteinyl-peptides, and confident protein identification andquantification using high mass accuracy LC-Fourier transform ion cyclotron resonance mass spectrometry (FTICR) measurementsand a previously established database of accurate mass and LC elution time information for the labeled peptides. This methodologyhas been initially demonstrated by using proteome profiling of na�ve and in vitro-differentiated human mammary epithelialcells as an example, which initially resulted in the identification and quantification of 603 proteins in a single LC-FTICRanalysis. QCET provides not only highly efficient enrichment of cysteinyl-peptides for more extensive proteome coverage andimproved labeling efficiency for better quantitative measurements, but more importantly, a high-throughput strategy suitablefor quantitative proteome analysis where extensive or parallel proteomic measurements are required, such as in time coursestudies of specific pathways and clinical sample analyses for biomarker discovery.