The study of macromolecular complexes by quantitative proteomics

ABSTRACT We describe a generic strategy for determining the specific composition, changes in the composition, and changes in the abundance of protein complexes. It is based on the use of

isotope-coded affinity tag (ICAT) reagents1 and mass spectrometry to compare the relative abundances of tryptic peptides derived from suitable pairs of purified or partially purified protein

complexes. In a first application, the genuine protein components of a large RNA polymerase II (Pol II) preinitiation complex (PIC) were distinguished from a background of co-purifying

proteins by comparing the relative abundances of peptides derived from a control sample and the specific complex that was purified from nuclear extracts by a single-step promoter DNA

affinity procedure2. In a second application, peptides derived from immunopurified STE12 protein complexes isolated from yeast cells in different states were used to detect quantitative

changes in the abundance of the complexes, and to detect dynamic changes in the composition of the samples. The use of quantitative mass spectrometry to guide identification of specific

complex components in partially purified samples, and to detect quantitative changes in the abundance and composition of protein complexes, provides the researcher with powerful new tools

for the comprehensive analysis of macromolecular complexes. Access through your institution Buy or subscribe This is a preview of subscription content, access via your institution ACCESS

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3205–3216 (2002). Article  CAS  Google Scholar  Download references ACKNOWLEDGEMENTS We thank S. Hahn for the gift of rTBP and antibodies to TBP, TFIIB and SRB4, A. Nesvizhskii for help with

data analysis and J. Aitchison, M. Wright and B. Wollscheid for comments on the manuscript. This work was supported by grants from the US National Cancer Institute and US National

Institutes of Health Research Resource Center, by federal funds from the National Heart, Lung, and Blood Institute of the National Institutes of Health and by a postdoctoral fellowship from

the National Institutes of Health to J.A.R. Partial funding for this work came through a gift from Merck and Co. to the Institute for Systems Biology. AUTHOR INFORMATION Author notes *

Samuel O. Purvine Present address: Biatech, 19310 North Creek Parkway, Suite 115, Bothell, Washington, 98011, USA AUTHORS AND AFFILIATIONS * Institute for Systems Biology, 1441 North 34th

Street, Seattle, 98103-8904, Washington, USA Jeffrey A. Ranish, Eugene C. Yi, Deena M. Leslie, David R. Goodlett, Jimmy Eng & Ruedi Aebersold Authors * Jeffrey A. Ranish View author

publications You can also search for this author inPubMed Google Scholar * Eugene C. Yi View author publications You can also search for this author inPubMed Google Scholar * Deena M. Leslie

View author publications You can also search for this author inPubMed Google Scholar * Samuel O. Purvine View author publications You can also search for this author inPubMed Google Scholar

* David R. Goodlett View author publications You can also search for this author inPubMed Google Scholar * Jimmy Eng View author publications You can also search for this author inPubMed 

Google Scholar * Ruedi Aebersold View author publications You can also search for this author inPubMed Google Scholar CORRESPONDING AUTHOR Correspondence to Ruedi Aebersold. ETHICS

DECLARATIONS COMPETING INTERESTS The authors declare no competing financial interests. SUPPLEMENTARY INFORMATION SUPPLEMENTARY FIG. 1 SUPPLEMENTARY TABLE 1 SUPPLEMENTARY TABLE 2 RIGHTS AND

PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Ranish, J., Yi, E., Leslie, D. _et al._ The study of macromolecular complexes by quantitative proteomics. _Nat

Genet_ 33, 349–355 (2003). https://doi.org/10.1038/ng1101 Download citation * Received: 07 October 2002 * Accepted: 19 January 2003 * Published: 18 February 2003 * Issue Date: March 2003 *

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