In-Depth Profiling of Post-Translational Modifications on the Related Transcription Factor Complexes TFIID and SAGA Nikolai Mischerikow,†,§ Gianpiero Spedale,‡,§ A. F. Maarten Altelaar,†,§ H. Th. Marc Timmers,‡,§ W. W. M. Pim Pijnappel,‡,§ and Albert J. R. Heck*,†,§,| Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, Department of Physiological Chemistry, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands, Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands, and Centre for Biomedical Genetics, Padualaan 8, 3584 CH Utrecht, The Netherlands Received May 20, 2009
The basal transcription factor TFIID and the chromatin-modifying complex SAGA, which have several subunits in common, are crucial for transcription regulation. Here, we describe an in-depth profiling of post-translational modifications (PTMs) on both TFIID and SAGA from yeast. We took a multipronged approach using high-resolution mass spectrometry (LC-MS) in combination with the proteases Trypsin, Chymotrypsin and Glu-C. The cumulative peptide identification data, at a false discovery rate
