Phosphoproteomic analysis: an emerging role in deciphering cellular signaling in human embryonic stem cells and their differentiated derivatives.
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) 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.
The Sanford-Burnham Medical Research Institute, La Jolla, CA, USA.
Brian T D
BT
Tobe
Junjie
J
Hou
Andrew M
AM
Crain
Ilyas
I
Singec
Evan Y
EY
Snyder
Laurence M
LM
Brill
D000818:Animals; D002458:Cell Fractionation / Q000379:methods; D002853:Chromatography, Liquid / Q000379:methods; D019295:Computational Biology; D053595:Embryonic Stem Cells / Q000378:metabolism*; D006801:Humans; D010446:Peptide Fragments / Q000737:chemistry; D010750:Phosphoproteins / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism*; D010766:Phosphorylation; D011499:Protein Processing, Post-Translational; D040901:Proteomics; D015398:Signal Transduction; D053719:Tandem Mass Spectrometry / Q000379:methods
D010446:Peptide Fragments; D010750:Phosphoproteins