ABSTRACT
Regulatory Pathways........................................................................ 208 11.2 Current Analyses .......................................................................................... 211
11.2.1 Identification of Transcriptional Regulators from Complex Mixtures............................................................................ 211
11.2.2 Enrichment of Nuclear Proteins Using Subcellular Fractionation ................................................................. 213
11.2.3 Proteomics and Subnuclear Components ........................................ 215 11.2.4 Analysis of Transcriptional Regulatory Complexes Following
Affinity Purification ......................................................................... 217 11.3 Future Prospects........................................................................................... 219 References.............................................................................................................. 220
The application of mass spectrometry to studies of biological pathways has become an indispensable tool in elucidating the function and regulation of proteins in the context of a cell. These studies have allowed for the identification of protein interaction partners as well as the rapid identification of multiple post-translational modifications such as phosphorylation and acetylation. This type of analysis can be extremely useful for the study of complex biological processes such as the regulation of transcription in the nucleus. In recent years, the application of microarray technology has led to
the ability to identify genome-wide changes in mRNA levels in response to changes in environmental stimuli and the mutation or deletion of individual target proteins. These studies have been useful in the identification of novel members of signaling pathways and target genes, but do not give a complete picture of the state of the cell under various conditions. With the application of mass spectrometry to complex biological mixtures in combination with microarray technologies, we can now gain a more complete picture of the effects of gene expression on the overall abundance and modification of proteins under different cellular conditions.
