Measuring Phosphorylation-Specific Changes in Response to Kinase Inhibitors in Mammalian Cells Using Quantitative Proteomics

Many cancers have been associated with the deregulation of kinases, and thus, kinases have become a prime target for the development of cancer treatments. This focus on kinases has resulted in the approval of several small-molecule kinase inhibitors for cancer treatments. Further, the use of these inhibitors as tools to study cancer has provided valuable information about biological mechanisms. However, to date, not much is known about the global effects of kinases on the proteome or phosphoproteome. In this protocol, we describe methodology to study the impact of kinase inhibitors on the proteome and phosphoproteome using mass spectrometry-based quantitative proteomics. More specifically, we focus on the effects of Aurora B kinase inhibitors on the proteome, cytoskeleton proteome, the phosphoproteome, and the cytoskeleton phosphoproteome during cell cycle. This methodology is easily extended to other biological studies whose aim is to study the global proteomic effects of a kinase inhibitor.