An isotope labeling strategy for quantifying the degree of phosphorylation at multiple sites in proteins

J Am Soc Mass Spectrom. 2004 May;15(5):647-53. doi: 10.1016/j.jasms.2003.12.019.


A procedure for determining the extent of phosphorylation at individual sites of multiply phosphorylated proteins was developed and applied to two polyphosphorylated proteins. The protocol, using simple chemical (Fischer methyl-esterification) and enzymatic (phosphatase) modification steps and an accessible isotopic labeling reagent (methyl alcohol-d(4)), is described in detail. Site-specific phosphorylation stoichiometries are derived from the comparison of chemically identical but isotopically distinct peptide species analyzed by microspray liquid chromatography-mass spectrometry (microLC-MS) using a Micromass Q-TOF2 mass spectrometer. Ten phosphorylation sites were unambiguously identified in tryptic digests of both proteins, and phosphorylation stoichiometries were determined for eight of the ten sites using the isotope-coded strategy. The extent of phosphorylation was also estimated from the mass spectral peak areas for the phosphorylated and unmodified peptides, and these estimates, when compared with stoichiometries determined using the isotope-coded technique, differed only marginally (within approximately 20%).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Arabidopsis
  • CDC2 Protein Kinase
  • Calcium-Calmodulin-Dependent Protein Kinases / chemistry
  • Cyclin-Dependent Kinases / chemistry
  • Escherichia coli
  • Isotope Labeling / methods*
  • Molecular Sequence Data
  • Phosphorylation
  • Proteins / chemistry*
  • Protozoan Proteins
  • Sensitivity and Specificity


  • Proteins
  • Protozoan Proteins
  • Calcium-Calmodulin-Dependent Protein Kinases
  • CDC2 Protein Kinase
  • Cyclin-Dependent Kinases