The Sanford-Burnham Medical Research Institute, La Jolla, CA, USA.
Stem Cell Rev Rep. 2012 Mar;8(1):16-31. doi: 10.1007/s12015-011-9317-8.
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.
细胞信号转导在很大程度上受蛋白质磷酸化控制。这种翻译后修饰（PTM）在研究影响细胞信号转导的一个或几个蛋白质磷酸化事件时已经得到了广泛分析。然而，由蛋白激酶驱动的信号网络，包括总（磷酸化）蛋白质组，在很大程度上控制着细胞命运。因此，大规模分析差异调节的蛋白质磷酸化对于阐明复杂的细胞事件至关重要，包括多能性的维持和胚胎干细胞（ESCs）的分化。目前用于总磷酸蛋白质组和总蛋白质组加总磷酸蛋白质组（称为（磷酸化）蛋白质组）分析的首选技术是多维液相色谱-（MDLC）串联质谱（MS/MS）。近年来，MDLC 用于分离总（磷酸化）蛋白质组、磷酸肽富集、富集馏分分离以及通过 MS/MS 定量肽鉴定的肽的技术进步非常迅速，质谱仪的灵敏度、速度和准确性也得到了提高。（磷酸化）蛋白质组深度覆盖的增加允许更好地理解蛋白质磷酸化网络的变化，因为细胞对刺激的反应并从一种未分化或分化状态转变为另一种状态。虽然 MDLC-MS/MS 研究非常强大，但理解数据的解释非常重要，并且需要针对总（磷酸化）蛋白质组分析提供的生物学预测进行有针对性的实验研究。此时，多能干细胞的磷酸蛋白质组学分析还处于起步阶段。然而，这些研究已经开始有助于更好和更快地理解基本的多能干细胞信号转导和命运控制，特别是在系统生物学水平上。
