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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

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Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS.

Hong Wang¹, Chee-Hong Wong, Alice Chin

¹Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. hongwang@fhcrc.org

Journal of Proteome Research

|October 13, 2009

Summary

This study introduces a dual stable isotope coding (DSIC) method for enhanced protein quantification in complex samples. DSIC significantly increases the number of identified and quantified proteins compared to single labeling techniques.

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Area of Science:

Proteomics
Analytical Chemistry
Biochemistry

Background:

Stable isotope labeling coupled with mass spectrometry is crucial for protein identification and quantification in complex mixtures.
Existing methods face limitations in maximizing protein yield while maintaining labeling efficiency.

Purpose of the Study:

To develop and validate a novel Dual Stable Isotope Coding (DSIC) methodology.
To enhance protein quantification yield and labeling efficacy in complex biological samples like sera.

Main Methods:

Intact proteins in sera were sequentially labeled with acrylamide for Cysteine (Cys) and succinic anhydride for Lysine (Lys) residues.
Labeled proteins underwent online 2D-HPLC fractionation.
Resolved fractions were digested with trypsin and analyzed via nano LC-MS/MS.

Main Results:

DSIC achieved 100% labeling efficiency for Cys and 98% for Lys.
Compared to single labeling (104 quantified proteins), DSIC identified 185 proteins and quantified 174.
DSIC significantly increased the number of quantified proteins from complex sera samples.

Conclusions:

The DSIC technique offers a superior approach for protein identification and quantification.
This method enhances proteomic analysis by increasing the yield of quantifiable proteins from biological samples.