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Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):995-1000. doi: 10.1073/pnas.0811964106. Epub 2009 Jan 14.

Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry.

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  • 1Department of Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.

Abstract

Protein phosphorylation is central to the understanding of cellular signaling, and cellular signaling is suggested to play a major role in the regulation of human embryonic stem (ES) cell pluripotency. Here, we describe the use of conventional tandem mass spectrometry-based sequencing technology--collision-activated dissociation (CAD)--and the more recently developed method electron transfer dissociation (ETD) to characterize the human ES cell phosphoproteome. In total, these experiments resulted in the identification of 11,995 unique phosphopeptides, corresponding to 10,844 nonredundant phosphorylation sites, at a 1% false discovery rate (FDR). Among these phosphorylation sites are 5 localized to 2 pluripotency critical transcription factors--OCT4 and SOX2. From these experiments, we conclude that ETD identifies a larger number of unique phosphopeptides than CAD (8,087 to 3,868), more frequently localizes the phosphorylation site to a specific residue (49.8% compared with 29.6%), and sequences whole classes of phosphopeptides previously unobserved.

PMID:
19144917
[PubMed - indexed for MEDLINE]
PMCID:
PMC2633571
Free PMC Article
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