Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors.
Mass spectrometry-based approaches are commonly used to identify proteins from multiprotein complexes, typically with the goal of identifying new complex members or identifying post-translational modifications. However, with the recent demonstration that spectral counting is a powerful quantitative proteomic approach, the analysis of multiprotein complexes by mass spectrometry can be reconsidered in certain cases. Using the chromatography-based approach named multidimensional protein identification technology, multiprotein complexes may be analyzed quantitatively using the normalized spectral abundance factor that allows comparison of multiple independent analyses of samples. This study describes an approach to visualize multiprotein complex datasets that provides structure function information that is superior to tabular lists of data. In this method review, we describe a reanalysis of the Rpd3/Sin3 small and large histone deacetylase complexes previously described in a tabular form to demonstrate the normalized spectral abundance factor approach.
Florens
Laurence
L
Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA.
Carozza
Michael J
MJ
Swanson
Selene K
SK
Fournier
Marjorie
M
Coleman
Michael K
MK
Workman
Jerry L
JL
Washburn
Michael P
MP
D042002:Chromatin Assembly and Disassembly / Q000502:physiology*; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods*; D046912:Multiprotein Complexes / Q000302:isolation & purification*; D011499:Protein Processing, Post-Translational / Q000502:physiology*; D040901:Proteomics / Q000295:instrumentation / Q000379:methods*; D013329:Structure-Activity Relationship
D046912:Multiprotein Complexes