Characterization of transcription factors by mass spectrometry and the role of SELDI‐MS

I. Introduction 419 II. Genomics, Proteomics, and MS 420 III. Regulatory Networks and the Traditional Study of Transcription Factors 421 IV. Identification of Transcription‐Factor Complexes 422 V. Structural Characterization of Transcription Factors 423 VI. Determination of Binding Sites and Stoichiometry of Binding 423 VII. Post‐Translational Modifications 426 VIII. Assessing Metal Binding and Activity 427 IX. Affinity Capture and Identification of Transcription Factors Using MS 429 X. Role of SELDI‐MS to Characterize Transcription Factors 430 XI. Other Applications of SELDI‐MS 433 XII. Conclusion and Future Prospects 434 Acknowledgments 434 References 434 Over the last decade, much progress has been made in the field of biological mass spectrometry, with numerous advances in technology, resolution, and affinity capture. The field of genomics has also been transformed by the sequencing and characterization of entire genomes. Some of the next challenges lie in understanding the relationship between the genome and the proteome, the protein complement of the genome, and in characterizing the regulatory processes involved in progressing from gene to functional protein. In this new age of proteomics, development of mass spectrometry methods to characterize transcription factors promises to add greatly to our understanding of regulatory networks that govern expression. However, at this time, regulatory networks of transcription factors are mostly uncharted territory. In this review, we summarize the latest advances in characterization of transcription factors by mass spectrometry including affinity capture, identification of complexes of DNA‐binding proteins, structural characterization, determination of protein–DNA and protein–protein interactions, assessment of modification sites and metal binding, studies of functional activity, and the latest chip technologies that use SELDI‐MS that allow the rapid capture and identification of transcription factors.