Quantitative phosphoproteomics strategies for understanding protein kinase-mediated signal transduction pathways

Abstract

Protein phosphorylation is a central regulatory mechanism of cell signaling pathways. This highly controlled biochemical process is involved in most cellular functions, and defects in protein kinases and phosphatases have been implicated in many diseases, highlighting the importance of understanding phosphorylation-mediated signaling networks. However, phosphorylation is a transient modification, and phosphorylated proteins are often less abundant. Therefore, the large-scale identification and quantification of phosphoproteins and their phosphorylation sites under different conditions are one of the most interesting and challenging tasks in the field of proteomics. Both 2D gel electrophoresis and liquid chromatography-tandem mass spectrometry serve as key phosphoproteomic technologies in combination with prefractionation, such as enrichment of phosphorylated proteins/peptides. Recently, new possibilities for quantitative phosphoproteomic analysis have been offered by technical advances in sample preparation, enrichment, separation, instrumentation, quantification and informatics. In this article, we present an overview of several strategies for quantitative phosphoproteomics and discuss how phosphoproteomic analysis can help to elucidate signaling pathways that regulate various cellular processes.

Keywords::

• 2D-DIGE
• cell signaling
• iTRAQ/TMT
• liquid chromatography-mass spectrometry
• phosphoproteomics
• phosphorylation
• prefractionation
• protein kinase
• SILAC
• two-dimensional gel electrophoresis

Financial & competing interests disclosure

This work was supported in part by a Grant-in-Aid for Scientific Research (20570177) from the Ministry of Education, Culture, Sports, Science and Technology of Japan and by a grant from the Nagase Science and Technology Foundation to Hidetaka Kosako. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Notes

iTRAQ: Isobaric tag for relative and absolute quantitation; SILAC: Stable isotope labeling by amino acids in cell culture; TMT: Tandem mass tag.