Proteomics of transcription factors

Peptide mass spectrometry (MS) is an invaluable analytical method in biological and medical research. It is the only technique that, when integrated with liquid chromatography (LC) and database search tools, allows a highly sensitive qualitative characterization and highly accurate quantitative comparison of proteomes. Although many proteomes are much more complex than their corresponding genomes, due to, for example, extreme differences in protein abundance and post-translational modifications, continuous technical advances in MS instrumentation and peptide pre-fractionation techniques lead to increasing fractions of proteomes that can be covered. Nevertheless, the targeted analysis of subsets of proteomes defined by post-translational modifications (PTMs), for example phosphorylation, acetylation, or glycosylation, using specialized enrichment techniques, is required to gain insight into cellular processes that would be inadequately covered by analysis of the full proteome alone. The technological progression in proteomics also benefits the analysis of protein complexes and other relatively small ensembles of proteins. With modern MS instrumentation, a targeted analysis is mostly not required to create a comprehensive picture of protein complexes, including PTMs and protein isoforms. Selected core technologies of proteomics are introduced in Chapter 1. It is mainly focused on MS instrumentation and database searching, but also covers aspects like peptide fragmentation and methods in quantitative proteomics. In this chapter we also give a brief introduction to the general transcription factors (GTFs) TFIID and SAGA and put them into their broader biological context.