ICPL Labeling Strategies for Proteome Research

  • Friedrich LottspeichEmail author
  • Josef Kellermann
Part of the Methods in Molecular Biology book series (MIMB, volume 753)


Stable isotope labeling in combination with mass spectrometry has emerged as a powerful tool to identify and quantify thousands of proteins within complex protein mixtures. Isotope-coded protein label (ICPL) is capable of high-throughput quantitative proteome profiling on a global scale. Since ICPL is based on stable isotope tagging at the free amino groups of intact proteins, it is applicable to any protein sample, including extracts from tissues or body fluids. After labeling of up to four different proteome states, the samples can be combined and the complexity reduced by any separation method currently employed in protein chemistry. After enzymatic cleavage of the protein fractions the ratios of peptides in the different proteome states can be calculated by simple MS-based mass spectrometric analyses. Only peptides that exhibit regulations in the different proteome states are further investigated for identification by tandem-mass spectrometry. The quantification of multiplexed ICPL experiments is greatly facilitated by the recently published ICPLQuant software, which was especially designed to cover the whole ICPL workflow. The method shows highly accurate and reproducible quantification of proteins, yields high sequence coverage, and is indispensable for the comprehensive detection of posttranslational modifications and protein isoforms.

Key words

ICPL isotope-coded protein label ICPLQuant quantitative proteomics post-metabolic labeling 


  1. 1.
    Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., Purkayastha, S., Juhasz, P., Martin, S., Bartlet-Jones, M., He, F., Jacobson, A., and Pappin, D. J. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Molecular & Cellular Proteomics 3(12), 1154–1169CrossRefGoogle Scholar
  2. 2.
    Kellermann, J. Sample Preparation for Differential Proteome Analysis: Labeling Technologies for Mass Spectrometry. In: Proteomics Sample Preparation. von Hagen, J. (ed.), pp. 105–118 (Wiley-VCH, Weinheim, 2008)Google Scholar
  3. 3.
    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. Molecular & Cellular Proteomics 1(5), 376–386CrossRefGoogle Scholar
  4. 4.
    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. Nature Biotechnology 17, 994–999PubMedCrossRefGoogle Scholar
  5. 5.
    Schmidt, A., Kellermann, J., and Lottspeich, F. (2005) A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5, 4–15PubMedCrossRefGoogle Scholar
  6. 6.
    Brunner, A., Keidel, E., Dosch, D., Kellermann, J., and Lottspeich F. (2010) ICPLQuant – a software for non-isobaric isotopic labeling proteomics. Proteomics 10, 315–323PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Max Planck Institute of Biochemistry, Protein AnalysisMartinsriedGermany

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