A Novel Proteomic Approach for Specific Identification of Tyrosine Kinase Substrates Using [13C]Tyrosine

Nieves Ibarrola, Henrik Molina, Akiko Iwahori, Akhilesh Pandey

Research output: Contribution to journalArticle

86 Citations (Scopus)

Abstract

Proteomic studies to find substrates of tyrosine kinases generally rely on identification of protein bands that are "pulled down" by antiphosphotyrosine antibodies from ligand-stimulated samples. One can obtain erroneous results from such experiments because of two major reasons. First, some proteins might be basally phosphorylated on tyrosine residues in the absence of ligand stimulation. Second, proteins can bind non-specifically to the antibodies or the affinity matrix. Induction of phosphorylation of proteins by ligand must therefore be confirmed by a different approach, which is not always feasible. We have developed a novel proteomic approach to identify substrates of tyrosine kinases in signaling pathways studies based on in vivo labeling of proteins with "light" (12C-labeled) or "heavy" (13C-labeled) tyrosine. This stable isotope labeling in cell culture method enables the unequivocal identification of tyrosine kinase substrates, as peptides derived from true substrates give rise to a unique signature in a mass spectrometry experiment. By using this approach, from a single experiment, we have successfully identified several known substrates of insulin signaling pathway and a novel substrate, polymerase I and transcript release factor, a protein that is implicated in the control of RNA metabolism and regulation of type I collagen promoters. This approach is amenable to high throughput global studies as it simplifies the specific identification of substrates of tyrosine kinases as well as serine/threonine kinases using mass spectrometry.

Original languageEnglish (US)
Pages (from-to)15805-15813
Number of pages9
JournalJournal of Biological Chemistry
Volume279
Issue number16
DOIs
StatePublished - Apr 16 2004
Externally publishedYes

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Proteomics
Protein-Tyrosine Kinases
Tyrosine
Substrates
Proteins
Ligands
Mass Spectrometry
Labeling
Mass spectrometry
Isotope Labeling
Antibody Affinity
Protein-Serine-Threonine Kinases
Phosphorylation
Collagen Type I
Antibodies
Experiments
Cell culture
Metabolism
Isotopes
Cell Culture Techniques

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

A Novel Proteomic Approach for Specific Identification of Tyrosine Kinase Substrates Using [13C]Tyrosine. / Ibarrola, Nieves; Molina, Henrik; Iwahori, Akiko; Pandey, Akhilesh.

In: Journal of Biological Chemistry, Vol. 279, No. 16, 16.04.2004, p. 15805-15813.

Research output: Contribution to journalArticle

Ibarrola, Nieves ; Molina, Henrik ; Iwahori, Akiko ; Pandey, Akhilesh. / A Novel Proteomic Approach for Specific Identification of Tyrosine Kinase Substrates Using [13C]Tyrosine. In: Journal of Biological Chemistry. 2004 ; Vol. 279, No. 16. pp. 15805-15813.
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