Abstract
Isotope labeling combined with LC-MS/MS provides a robust platform for quantitative proteomics. Protein quantitation based on mass spectral data falls into two categories: one determined by MS/MS scans, e.g., iTRAQ-labeling quantitation, and the other by MS scans, e.g., quantitation using SILAC, ICAT, or 18O labeling. In large-scale LC-MS proteomic experiments, tens of thousands of MS and MS/MS spectra are generated and need to be analyzed. Data noise further complicates the data analysis. In this chapter, we present two automated tools, called Multi-Q and MaXIC-Q, for MS/MS- and MS-based quantitation analysis. They are designed as generic platforms that can accommodate search results from SEQUEST and Mascot, as well as mzXML files converted from raw files produced by various mass spectrometers. Toward accurate quantitation analysis, Multi-Q determines detection limits of the user’s instrument to filter out outliers and MaXIC-Q adopts stringent validation on our constructed projected ion mass spectra to ensure correct data for quantitation.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Griffin, T. J., Goodlett, D. R., and Aebersold, R. (2001) Advances in proteome analysis by mass spectrometry. Curr. Opin. Biotechnol. 12, 607-612.
Domon, B., and Aebersold, R. (2006) Mass spectrometry and protein analysis. Science 312, 212-217.
Nesvizhskii, A. I., and Aebersold, R. (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics 4, 1419-1440.
Washburn, M. P., Wolters, D., and Yates, J. R., III. (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247.
Tao, W. A., and Aebersold, R. (2003) Advances in quantitative proteomics via stable isotope tagging and mass spectrometry. Curr. Opin. Biotechnol. 14, 110-118.
Semmes, O. J., Malik, G., and Ward, M. (2006) Application of mass spectrometry to the discovery of biomarkers for detection of prostate cancer. J. Cell. Biochem. 98, 496-503.
Thompson, A., Schäfer, J., Kuhn, K., Kienle, S., Schwarz, J., Schmidt, G., Neumann, T., and Hamon, C. (2003). Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 75, 1895-1904.
Ong, S. E., and Mann, M. (2005) Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 1, 252-262.
Islinger, M., Li, K. W., Loos, M., Lueers, G., and Voelkl, A. (2006) ITRAQ-quantification as an analytical tool to describe proteome changes in rat liver peroxisomes after bezafibrate treatment. Mol. Cell. Proteomics 5, S186.
Jabs, W., Lubeck, M., Schweiger-Hufnagel, U., Suckau, D., and Hahner, S. (2006) A comparative study of iTRAQ- and ICPL-based protein quantification. Mol. Cell. Proteomics 5, S248.
Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999.
Yao, X., Freas, A., Ramirez, J., Demirev, P. A., and Fenselau, C. (2001) Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal. Chem. 73, 2836-2842.
Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., and Mann, M. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386.
Ong, S. E., Kratchmarova, I., and Mann, M. (2003) Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J. Proteome Res. 2, 173-181.
Ong, S. E., and Mann, M. (2006) A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat. Protoc. 1, 2650-2660.
Ong, S. E., and Mann, M. (2007) Stable isotope labeling by amino acids in cell culture for quantitative proteomics. In: Quantitative Proteomics by Mass Spectrometry, Sechi, S., ed., Methods Mol. Biol. 359, 37-52.
Callister, S. J., Barry R. C., Adkins, J. N., Johnson, E. T., Qian, W., Webb-Robertson B. M., Smith R. D., and Lipton M. S. (2006) Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. J. Proteome Res. 5 , 277-286.
Shadforth, I. P., Dunkley, T. P., Lilley, K. S., and Bessant, C. (2005) i-Tracker: for quantitative proteomics using iTRAQ. BMC Genomics 6, 145.
Han, D. K., Eng, J., Zhou, H., and Aebersold, R. (2001) Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19, 946-951.
Li, X. J., Zhang, H., Ranish, J. A., and Aebersold, R. (2003) Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal. Chem. 75, 6648-6657.
MacCoss, M. J., Wu, C. C., Liu, H., Sadygov, R., and Yates, J. R., III. (2003) A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal. Chem. 75, 6912-6921.
Lin, W. T., Hung, W. N., Yian, Y. H., Wu, K. P., Han, C. L., Chen, Y. R., Chen, Y. J., Sung, T. Y., and Hsu, W. L. (2006) Multi-Q: a fully automated tool for multiplexed protein quantitation. J. Proteome Res. 5, 2328-2338.
Yu, C. Y., Tsui, Y. H., Yian, Y. H., Sung, T. Y., and Hsu, W. L. (2007) The Multi-Q web server for multiplexed protein quantitation. Nucleic Acids Res. 35, W707-W712.
Tsou, C. C, Tsui, Y. H., Yian, Y. H., Chen, Y. J., Yang, H. Y., Yu, C. Y., Lynn, K. S., Chen, Y. J., Sung, T. Y., and Hsu, W. L. (2009) MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC-MS. Nucleic Acids Res. 37, suppl_2 W661-W669.
Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392.
Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658.
Weisstein, Eric W. “Moving Average.” From MathWorld - A Wolfram Web Resource. http://mathworld.wolfram.com/MovingAverage.html
Golub, G. H., Van Loan, C.F. (1996) Matrix Computations. 3rd edition, The Johns Hopkins University Press: USA.
Savitzky, A, and Marcel J.E. Golay (1964) Smoothing and differentiation of data by simplified least squares procedures. Anal. Chem. 36, 1627-1639.
De Boor, C. (1978) A Practical Guide to Splines, 1st ed., pp. 114-115, Springer Verlag, NY.
Lau, K. W., Jones, A. R., Swainston, N., Siepen, J.A., and Hubbard, S. J. (2007) Capture and analysis of quantitative proteomic data. Proteomics 7, 2787-2799.
Muller, L. N., Brusniak, M.Y., Mani, D. R., and Aebersold, R. (2008). An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J. Proteome Res. 7, 51-61.
MacCoss, M. J., Toth, M. J., Matthews, D. E. (2001) Evaluation and optimization of ion-current ratio measurements by selected-ion-monitoring mass spectrometry. Anal. Chem. 73, 2976-2984.
Aggarwal, K., Choe, L. H., Lee, K. H. (2005) Quantitative analysis of protein expression using amine-specific isobaric tags in Escherichia coli cells expressing rhsA elements. Proteomics 5, 2297-2308.
Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., Speed, T. P. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30, e15.
Ravin, N. V., and Ravin, V. K. (1999) Use of a linear multicopy vector based on the mini-replicon of temperate coliphage N15 for cloning DNA with abnormal secondary structures. Nucleic Acids Res. 27, e13.
Acknowledgments
The authors gratefully acknowledge the financial support from the thematic program of Academia Sinica under Grant AS94B003 and AS95ASIA02 and the National Science Council of Taiwan under Grant NSC 95-3114-P-002-005-Y. We would also like to thank our collaborator Dr. Yu-Ju Chen’s lab in the Institute of Chemistry, Academia Sinica. Without their help and encouragement, this research would not have been possible.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Hsu, WL., Sung, TY. (2010). Automated Generic Analysis Tools for Protein Quantitation Using Stable Isotope Labeling. In: Hubbard, S., Jones, A. (eds) Proteome Bioinformatics. Methods in Molecular Biology™, vol 604. Humana Press. https://doi.org/10.1007/978-1-60761-444-9_17
Download citation
DOI: https://doi.org/10.1007/978-1-60761-444-9_17
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60761-443-2
Online ISBN: 978-1-60761-444-9
eBook Packages: Springer Protocols