Quantitative Proteome Analysis Using Isobaric Peptide Termini Labeling (IPTL)

  • Magnus Ø. Arntzen
  • Christian J. Koehler
  • Achim Treumann
  • Bernd Thiede
Part of the Methods in Molecular Biology book series (MIMB, volume 753)


The quantitative comparison of proteome level changes across biological samples has become an essential feature in proteomics that remains challenging. We have recently introduced isobaric peptide termini labeling (IPTL), a novel strategy for isobaric quantification based on the derivatization of peptide termini with complementary isotopically labeled reagents. Unlike non-isobaric quantification methods, sample complexity at the MS level is not increased, providing improved sensitivity and protein coverage. The distinguishing feature of IPTL when comparing it to more established isobaric labeling methods (iTRAQ and TMT) is the presence of quantification signatures in all sequence-determining ions in MS/MS spectra, not only in the low mass reporter ion region. This makes IPTL a quantification method that is accessible to mass spectrometers with limited capabilities in the low mass range. Also, the presence of several quantification points in each MS/MS spectrum increases the robustness of the quantification procedure.

Key words

Chemical labeling isobaric labeling IsobariQ IPTL iTRAQ mass spectrometry quantitative proteomics TMT 



IPTL was supported by the National Program for Research in Functional Genomics in Norway (FUGE, project no. 183418/S10) of the Norwegian Research Council, MLSUiO and FUGE-Øst to BT.


  1. 1.
    Ong, S. E., and Mann, M. (2005) Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 1, 252–262.PubMedCrossRefGoogle Scholar
  2. 2.
    Thompson, A., Schafer, J., Kuhn, K., Kienle, S., Schwarz, J., Schmidt, G., et al. (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 75, 1895–1904.PubMedCrossRefGoogle Scholar
  3. 3.
    Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., et al. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics 3, 1154–1169.PubMedCrossRefGoogle Scholar
  4. 4.
    Choe, L., D’Ascenzo, M., Relkin, D., Ross, P., Williamson, B., Guertin, S. et al. (2007) 8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment of Alzheimer’s disease. Proteomics 7, 3651–3660.PubMedCrossRefGoogle Scholar
  5. 5.
    Koehler, C. J., Strozynski, M., Kozielski, F., Treumann, A., and Thiede, B. (2009) Isobaric peptide termini labeling for MS/MS-based quantitative proteomics. J. Proteome. Res. 8, 4333–4341.PubMedCrossRefGoogle Scholar
  6. 6.
    Webster, J., and Oxley, D. (2005) Peptide mass fingerprinting: protein identification using MALDI-TOF mass spectrometry. Methods Mol. Biol. 310, 227–240.PubMedCrossRefGoogle Scholar
  7. 7.
    Arntzen, M.Ø., Koehler, C.J., Barsnes, F.S., Berven, F.S., Treumann, A., and Thiede, B. (2011) IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT. J. Proteome Res. 10, 913–920.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Magnus Ø. Arntzen
    • 1
    • 2
    • 3
  • Christian J. Koehler
    • 1
  • Achim Treumann
    • 4
  • Bernd Thiede
    • 1
  1. 1.The Biotechnology Centre of Oslo, University of OsloOsloNorway
  2. 2.Institute of Immunology, Rikshospitalet HF, University of OsloOsloNorway
  3. 3.Department of Chemistry, Biotechnology and Food ScienceNorwegian University of Life SciencesÅsNorway
  4. 4.NEPAF Proteome Analysis FacilityNewcastleUK

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