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Originally published In Press as doi:10.1074/mcp.M400129-MCP200 on September 22, 2004.
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Molecular & Cellular Proteomics 3:1154-1169, 2004.
© 2004 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*,S

Philip L. Ross{ddagger}, Yulin N. Huang{ddagger}, Jason N. Marchese{ddagger}, Brian Williamson{ddagger}, Kenneth Parker{ddagger}, Stephen Hattan{ddagger}, Nikita Khainovski{ddagger}, Sasi Pillai{ddagger}, Subhakar Dey{ddagger}, Scott Daniels{ddagger}, Subhasish Purkayastha{ddagger}, Peter Juhasz{ddagger}, Stephen Martin{ddagger}, Michael Bartlet-Jones§, Feng He, Allan Jacobson and Darryl J. Pappin{ddagger},|,**

From {ddagger} Applied Biosystems, Framingham, MA 01701; § Cancer Research UK, London WC2A 3PX, United Kingdom; Department of Molecular Genetics and Microbiology, University of Massachusetts, Medical School, Worcester, MA 01655; and | Section of Proteomics, Imperial College, Hammersmith Campus, London W12 ONN, United Kingdom

We describe here a multiplexed protein quantitation strategy that provides relative and absolute measurements of proteins in complex mixtures. At the core of this methodology is a multiplexed set of isobaric reagents that yield amine-derivatized peptides. The derivatized peptides are indistinguishable in MS, but exhibit intense low-mass MS/MS signature ions that support quantitation. In this study, we have examined the global protein expression of a wild-type yeast strain and the isogenic upf1{Delta} and xrn1{Delta} mutant strains that are defective in the nonsense-mediated mRNA decay and the general 5' to 3' decay pathways, respectively. We also demonstrate the use of 4-fold multiplexing to enable relative protein measurements simultaneously with determination of absolute levels of a target protein using synthetic isobaric peptide standards. We find that inactivation of Upf1p and Xrn1p causes common as well as unique effects on protein expression.

** To whom correspondence should be addressed: Applied Biosystems, 500 Old Connecticut Path, Framingham, MA 01701. Tel.: 508-383-7484; Fax: 508-383-7813; E-mail: pappindj{at}appliedbiosystems.com


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Y. Chen, L.-Y. Choong, Q. Lin, R. Philp, C.-H. Wong, B.-K. Ang, Y.-L. Tan, M.-C.-S. Loh, C.-L. Hew, N. Shah, et al.
Differential Expression of Novel Tyrosine Kinase Substrates during Breast Cancer Development
Mol. Cell. Proteomics, December 1, 2007; 6(12): 2072 - 2087.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
H. Keshishian, T. Addona, M. Burgess, E. Kuhn, and S. A. Carr
Quantitative, Multiplexed Assays for Low Abundance Proteins in Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution
Mol. Cell. Proteomics, December 1, 2007; 6(12): 2212 - 2229.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
R. Ahrends, S. Pieper, A. Kuhn, H. Weisshoff, M. Hamester, T. Lindemann, C. Scheler, K. Lehmann, K. Taubner, and M. W. Linscheid
A Metal-coded Affinity Tag Approach to Quantitative Proteomics
Mol. Cell. Proteomics, November 1, 2007; 6(11): 1907 - 1916.
[Abstract] [Full Text] [PDF]

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 Molecular Cancer TherapeuticsHome page
L.-Y. Choong, S. Lim, M. C.-S. Loh, X. Man, Y. Chen, W. Toy, M. Pan, C.-S. Chen, A. Poonepalli, M. P. Hande, et al.
Progressive loss of epidermal growth factor receptor in a subpopulation of breast cancers: implications in target-directed therapeutics
Mol. Cancer Ther., November 1, 2007; 6(11): 2828 - 2842.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
J. J. Thelen and S. C. Peck
Quantitative Proteomics in Plants: Choices in Abundance
PLANT CELL, November 1, 2007; 19(11): 3339 - 3346.
[Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
S. Pan, M. Shi, J. Jin, R. L. Albin, A. Lieberman, M. Gearing, B. Lin, C. Pan, X. Yan, D. T. Kashima, et al.
Proteomics Identification of Proteins in Human Cortex Using Multidimensional Separations and MALDI Tandem Mass Spectrometer
Mol. Cell. Proteomics, October 1, 2007; 6(10): 1818 - 1823.
[Abstract] [Full Text] [PDF]

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 Genome ResHome page
A. K. Schmid, D. J. Reiss, A. Kaur, M. Pan, N. King, P. T. Van, L. Hohmann, D. B. Martin, and N. S. Baliga
The anatomy of microbial cell state transitions in response to oxygen
Genome Res., October 1, 2007; 17(10): 1399 - 1413.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
Z. Li, Q. Lin, J. Chen, J. L. Wu, T. K. Lim, S. S. Loh, X. Tang, and C.-L. Hew
Shotgun Identification of the Structural Proteome of Shrimp White Spot Syndrome Virus and iTRAQ Differentiation of Envelope and Nucleocapsid Subproteomes
Mol. Cell. Proteomics, September 1, 2007; 6(9): 1609 - 1620.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
P. R. Cutillas and B. Vanhaesebroeck
Quantitative Profile of Five Murine Core Proteomes Using Label-free Functional Proteomics
Mol. Cell. Proteomics, September 1, 2007; 6(9): 1560 - 1573.
[Abstract] [Full Text] [PDF]

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 BioinformaticsHome page
D. Zhu, Y. Li, and H. Li
Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data
Bioinformatics, September 1, 2007; 23(17): 2298 - 2305.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
C. W. Turck, A. M. Falick, J. A. Kowalak, W. S. Lane, K. S. Lilley, B. S. Phinney, S. T. Weintraub, H. E. Witkowska, and N. A. Yates
The Association of Biomolecular Resource Facilities Proteomics Research Group 2006 Study: Relative Protein Quantitation
Mol. Cell. Proteomics, August 1, 2007; 6(8): 1291 - 1298.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
C.-Y. Yu, Y.-H. Tsui, Y.-H. Yian, T.-Y. Sung, and W.-L. Hsu
The Multi-Q web server for multiplexed protein quantitation
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W707 - W712.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
A. Ramos-Fernandez, D. Lopez-Ferrer, and J. Vazquez
Improved Method for Differential Expression Proteomics Using Trypsin-catalyzed 18O Labeling with a Correction for Labeling Efficiency
Mol. Cell. Proteomics, July 1, 2007; 6(7): 1274 - 1286.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
C. S. Lane, Y. Wang, R. Betts, W. J. Griffiths, and L. H. Patterson
Comparative Cytochrome P450 Proteomics in the Livers of Immunodeficient Mice Using 18O Stable Isotope Labeling
Mol. Cell. Proteomics, June 1, 2007; 6(6): 953 - 962.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
M. Heller, E. Schlappritzi, D. Stalder, J.-M. Nuoffer, and A. Haeberli
Compositional Protein Analysis of High Density Lipoproteins in Hypercholesterolemia by Shotgun LC-MS/MS and Probabilistic Peptide Scoring
Mol. Cell. Proteomics, June 1, 2007; 6(6): 1059 - 1072.
[Abstract] [Full Text] [PDF]

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 J. Bacteriol.Home page
M. Jiang, S. M. Sullivan, A. K. Walker, J. R. Strahler, P. C. Andrews, and J. R. Maddock
Identification of Novel Escherichia coli Ribosome-Associated Proteins Using Isobaric Tags and Multidimensional Protein Identification Techniques
J. Bacteriol., May 1, 2007; 189(9): 3434 - 3444.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
J. P. C. Vissers, J. I. Langridge, and J. M. F. G. Aerts
Analysis and Quantification of Diagnostic Serum Markers and Protein Signatures for Gaucher Disease
Mol. Cell. Proteomics, May 1, 2007; 6(5): 755 - 766.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
E. L. Huttlin, A. D. Hegeman, A. C. Harms, and M. R. Sussman
Comparison of Full Versus Partial Metabolic Labeling for Quantitative Proteomics Analysis in Arabidopsis thaliana
Mol. Cell. Proteomics, May 1, 2007; 6(5): 860 - 881.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
R. A. Dean and C. M. Overall
Proteomics Discovery of Metalloproteinase Substrates in the Cellular Context by iTRAQTM Labeling Reveals a Diverse MMP-2 Substrate Degradome
Mol. Cell. Proteomics, April 1, 2007; 6(4): 611 - 623.
[Abstract] [Full Text] [PDF]

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 Proc. Natl. Acad. Sci. USAHome page
D. F. Moore, O. V. Krokhin, R. C. Beavis, M. Ries, C. Robinson, E. Goldin, R. O. Brady, J. A. Wilkins, and R. Schiffmann
Proteomics of specific treatment-related alterations in Fabry disease: A strategy to identify biological abnormalities
PNAS, February 20, 2007; 104(8): 2873 - 2878.
[Abstract] [Full Text] [PDF]

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 J. Bacteriol.Home page
T. J. Radosevich, T. A. Reinhardt, J. D. Lippolis, J. P. Bannantine, and J. R. Stabel
Proteome and Differential Expression Analysis of Membrane and Cytosolic Proteins from Mycobacterium avium subsp. paratuberculosis Strains K-10 and 187
J. Bacteriol., February 1, 2007; 189(3): 1109 - 1117.
[Abstract] [Full Text] [PDF]

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 Mol. Cell. ProteomicsHome page
C. J. Mason, T. M. Therneau, J. E. Eckel-Passow, K. L. Johnson, A. L. Oberg, J. E. Olson, K. S. Nair, D. C. Muddiman, and H. R. Bergen III
A Method for Automatically Interpreting Mass Spectra of 18O-Labeled Isotopic Clusters
Mol. Cell. Proteomics, February 1, 2007; 6(2): 305 - 318.
[Abstract] [Full Text] [PDF]


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