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Phosphoproteomic Analysis: An Emerging Role in Deciphering Cellular Signaling in Human Embryonic Stem Cells and Their Differentiated Derivatives

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Abstract

Cellular signaling is largely controlled by protein phosphorylation. This post-translational modification (PTM) has been extensively analyzed when examining one or a few protein phosphorylation events that effect cell signaling. However, protein kinase-driven signaling networks, comprising total (phospho)proteomes, largely control cell fate. Therefore, large-scale analysis of differentially regulated protein phosphorylation is central to elucidating complex cellular events, including maintenance of pluripotency and differentiation of embryonic stem cells (ESCs). The current technology of choice for total phosphoproteome and combined total proteome plus total phosphoproteome (termed (phospho)proteome) [1] analyses is multidimensional liquid chromatography- (MDLC) tandem mass spectrometry (MS/MS). Advances in the use of MDLC for separation of peptides comprising total (phospho)proteomes, phosphopeptide enrichment, separation of enriched fractions, and quantitative peptide identification by MS/MS have been rapid in recent years, as have improvements in the sensitivity, speed, and accuracy of mass spectrometers. Increasingly deep coverage of (phospho)proteomes is allowing an improved understanding of changes in protein phosphorylation networks as cells respond to stimuli and progress from one undifferentiated or differentiated state to another. Although MDLC-MS/MS studies are powerful, understanding the interpretation of the data is important, and targeted experimental pursuit of biological predictions provided by total (phospho)proteome analyses is needed. (Phospho)proteomic analyses of pluripotent stem cells are in their infancy at this time. However, such studies have already begun to contribute to an improved and accelerated understanding of basic pluripotent stem cell signaling and fate control, especially at the systems-biology level.

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Acknowledgements

We apologize to those whose work was not cited due to space constraints.

Support was provided by the SBMRI-NCI Cancer Center Support Grant 5 P30 CA30199-28, the La Jolla Interdisciplinary Neuroscience Center Cores Grant 5 P30 NS057096 from NINDS, RC2 MH090011 from NIMH and by the UCSD Dept. of Psychiatry NIMH T32.

Conflicts of Interest

The authors declare no potential conflicts of interest.

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  1. The Sanford-Burnham Medical Research Institute, La Jolla, CA, USA

    Brian T. D. Tobe, Junjie Hou, Andrew M. Crain, Ilyas Singec, Evan Y. Snyder & Laurence M. Brill

  2. Proteomics, Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Rd., La Jolla, CA, 92037, USA

    Laurence M. Brill

  3. Program for Stem Cell and Regenerative Biology, Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Rd., La Jolla, CA, 92037, USA

    Evan Y. Snyder

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Correspondence to Evan Y. Snyder or Laurence M. Brill.

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Tobe, B.T.D., Hou, J., Crain, A.M. et al. Phosphoproteomic Analysis: An Emerging Role in Deciphering Cellular Signaling in Human Embryonic Stem Cells and Their Differentiated Derivatives. Stem Cell Rev and Rep 8, 16–31 (2012). https://doi.org/10.1007/s12015-011-9317-8

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