Quantitative Protein Analysis by Solid Phase Isotope Tagging and Mass Spectrometry

  • Huilin Zhou
  • Rosemary Boyle
  • Ruedi Aebersold
Part of the Methods in Molecular Biology book series (MIMB, volume 261)


Here we describe a method for stable isotope labeling and solid-phase capture of cysteinyl peptides from complex protein mixtures. Site-specific, quantitative labeling of cysteine residues with tags that differ in isotopic content enables quantification of relative peptide abundance between samples. Labeling on a solid phase provides for simultaneous simplification of a complex peptide mixture by isolating cysteinyl, and subsequently tagged, peptides. Peptides from proteolytic digests of protein samples are labeled in preparation for analysis by microcapillary liquid chromatography and tandem mass spectrometry (μLC-MS/MS) to determine their sequences and relative abundance between samples. This approach enables rapid identification and accurate quantification of relative abundance of individual proteins from different biological contexts.

Key Words

Protein quantification protein-protein interaction mass spectrometry proteomics solid phase chemistry isotope tagging protein identification comparative protein analysis photo-cleavable chemistry 


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Copyright information

© Humana Press Inc., Totowa, NJ 2004

Authors and Affiliations

  • Huilin Zhou
    • 1
  • Rosemary Boyle
    • 2
  • Ruedi Aebersold
    • 3
  1. 1.Department of Chemistry & BiochemistryUniversity of California-San DiegoSan Diego
  2. 2.Department of Genome SciencesUniversity of WashingtonSeattle
  3. 3.Institute for Systems BiologySeattle

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