Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC)

Ramars Amanchy, Dario E. Kalume, Akiko Iwahori, Jun Zhong, Akhilesh Pandey

Research output: Contribution to journalArticle

97 Scopus citations

Abstract

Identification of phosphorylated proteins remains a difficult task despite technological advances in protein purification methods and mass spectrometry. Here, we report identification of tyrosine-phosphorylated proteins by coupling stable isotope labeling with amino acids in cell culture (SILAC) to mass spectrometry. We labeled HeLa cells with stable isotopes of tyrosine, or, a combination of arginine and lysine to identify tyrosine phosphorylated proteins. This allowed identification of 118 proteins, of which only 45 proteins were previously described as tyrosine-phosphorylated proteins. A total of 42 in vivo tyrosine phosphorylation sites were mapped, including 34 novel ones. We validated the phosphorylation status of a subset of novel proteins including cytoskeleton associated protein 1, breast cancer anti-estrogen resistance 3, chromosome 3 open reading frame 6, WW binding protein 2, Nice-4 and RNA binding motif protein 4. Our strategy can be used to identify potential kinase substrates without prior knowledge of the signaling pathways and can also be applied to profiling to specific kinases in cells. Because of its sensitivity and general applicability, our approach will be useful for investigating signaling pathways in a global fashion and for using phosphoproteomics for functional annotation of genomes.

Original languageEnglish (US)
Pages (from-to)1661-1671
Number of pages11
JournalJournal of Proteome Research
Volume4
Issue number5
DOIs
StatePublished - Sep 1 2005

Keywords

  • EGF receptor signaling
  • Phosphoproteomics
  • SILAC
  • Tandem mass spectrometry
  • Tyrosine phosphorylation

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

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