Mass spectrometry for human kinome analysis

Abstract Kinases are involved in numerous critical cell signaling processes, and dysregulation in kinase signaling is implicated in many human diseases. Therefore, comprehensive analysis of protein expression and activation of kinases at the entire proteome scale is important for developing drugs for the treatment of human diseases. Over the past few decades, mass spectrometry has evolved into a powerful and indispensable bioanalytical tool for the facile identification and quantification of proteins. Mass spectrometry-based proteomic methods are now widely employed in human kinome analysis, and these methods offer quantitative information about the expression levels and ATP-binding affinities of more than 300 kinases. In this chapter, we review the applications of various mass spectrometry-based proteomic methods, including label-free and metabolic/chemical labeling approaches, for interrogating quantitatively the human kinome. We also survey the utilizations of different types of data acquisition methods, including data-dependent and data-independent acquisition (DDA and DIA), as well as targeted proteomic approaches, relying on multiple- and parallel-reaction monitoring (MRM and PRM), for the comprehensive assessment of the human kinome.