Global discovery of protein kinases and other nucleotide-binding proteins by mass spectrometry.
Nucleotide-binding proteins, such as protein kinases, ATPases and GTP-binding proteins, are among the most important families of proteins that are involved in a number of pivotal cellular processes. However, global study of the structure, function, and expression level of nucleotide-binding proteins as well as protein-nucleotide interactions can hardly be achieved with the use of conventional approaches owing to enormous diversity of the nucleotide-binding protein family. Recent advances in mass spectrometry (MS) instrumentation, coupled with a variety of nucleotide-binding protein enrichment methods, rendered MS-based proteomics a powerful tool for the comprehensive characterizations of the nucleotide-binding proteome, especially the kinome. Here, we review the recent developments in the use of mass spectrometry, together with general and widely used affinity enrichment approaches, for the proteome-wide capture, identification and quantification of nucleotide-binding proteins, including protein kinases, ATPases, GTPases, and other nucleotide-binding proteins. The working principles, advantages, and limitations of each enrichment platform in identifying nucleotide-binding proteins as well as profiling protein-nucleotide interactions are summarized. The perspectives in developing novel MS-based nucleotide-binding protein detection platform are also discussed. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 35:601-619, 2016.
Department of Chemistry, University of California, Riverside, CA, 92521-0403.
Yongsheng
Y
Xiao
Department of Chemistry, University of California, Riverside, CA, 92521-0403.
Yinsheng
Y
Wang
D002352:Carrier Proteins; D013058:Mass Spectrometry; D009711:Nucleotides; D011494:Protein Kinases / Q000737:chemistry*; D020543:Proteome; D040901:Proteomics
D002352:Carrier Proteins; D009711:Nucleotides; D020543:Proteome; D011494:Protein Kinases
affinity purification; kinome; multiple-reaction monitoring; protein kinases; protein quantification