HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Supplemental Data All Versions of this Article: M800068-MCP200v1 7/10/1983    most recent Submit a response Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Request Permissions Glossary Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Han, C.-L. Articles by Chen, Y.-J. Search for Related Content PubMed PubMed Citation Articles by Han, C.-L. Articles by Chen, Y.-J. Related Collections Related Webpages Social Bookmarking                      What's this?

F1000 Biology *Recommended* - FREE!

Molecular & Cellular Proteomics 7:1983-1997, 2008.
© 2008 by The American Society for Biochemistry and Molecular Biology, Inc.

---

Research

A Multiplexed Quantitative Strategy for Membrane Proteomics

Opportunities for Mining Therapeutic Targets for Autosomal Dominant Polycystic Kidney Disease^*,S

Chia-Li Han, Chih-Wei Chien, Wen-Cheng Chen^¶, Yet-Ran Chen^||, Chien-Peng Wu^||, Hung Li^** and Yu-Ju Chen^,

From the Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan, Graduate Institute of Medical Biotechnology, Chang Gung University, Tao-Yuan 333, Taiwan, ^¶ Institute of Biochemistry, National Yang-Ming University, Taipei 112, Taiwan, ^|| Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202, Taiwan, and ^** Institute of Molecular Biology and Institute of Chemistry and Genomic Research Center, Academia Sinica, Taipei 115, Taiwan

Toward multiplexed, comprehensive, and robust quantitation of the membrane proteome, we report a strategy combining gel-assisted digestion, iTRAQ (isobaric tags for relative and absolute quantitation) labeling, and LC-MS/MS. Quantitation of four independently purified membrane fractions from HeLa cells gave high accuracy (<8% error) and precision (<12% relative S.D.), demonstrating a high degree of consistency and reproducibility of this quantitation platform. Under stringent identification criteria (false discovery rate = 0%), the strategy efficiently quantified membrane proteins; as many as 520 proteins (91%) were membrane proteins, each quantified based on an average of 14.1 peptides per integral membrane protein. In addition to significant improvements in signal intensity for most quantified proteins, most remarkably, topological analysis revealed that the biggest improvement was achieved in detection of transmembrane peptides from integral membrane proteins with up to 19 transmembrane helices. To the best of our knowledge, this level of coverage exceeds that achieved previously using MS and provides superior quantitation accuracy compared with other methods. We applied this approach to the first proteomics delineation of phenotypic expression in a mouse model of autosomal dominant polycystic kidney disease (ADPKD). By characterizing kidney cell plasma membrane from wild-type versus PKD1 knock-out mice, 791 proteins were quantified, and 67 and 37 proteins showed 2-fold up-regulation and down-regulation, respectively. Some of these differentially expressed membrane proteins are involved in the mechanisms underlying major abnormalities in ADPKD, including epithelial cell proliferation and apoptosis, cell-cell and cell-matrix interactions, ion and fluid secretion, and membrane protein polarity. Among these proteins, targeting therapeutics to certain transporters/receptors, such as epidermal growth factor receptor, has proven effective in preclinical studies of ADPKD; others are known drug targets in various diseases. Our method demonstrates how comparative membrane proteomics can provide insight into the molecular mechanisms underlying ADPKD and the identification of potential drug targets, which may lead to new therapeutic opportunities to prevent or retard the disease.

CiteULike    Complore    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

Related Webpages: