Introduction

Isobaric peptide labeling plays an important role in relative quantitative comparisons of proteomes. Isobaric labeling techniques utilize MS/MS spectra for relative quantification, which can be either based on the relative intensities of reporter ions in the low mass region (iTRAQ and TMT) or on the relative intensities of quantification signatures throughout the spectrum due to isobaric peptide termini labeling (IPTL). Due to the increased quantitative information found in MS/MS fragment spectra generated by the recently developed IPTL approach, new software was required to extract the quantitative information. IsobariQ was specifically developed for this purpose; however, support for the reporter ion techniques iTRAQ and TMT is also included. In addition, to address recently emphasized issues about heterogeneity of variance in proteomics data sets, IsobariQ employs the statistical software package R and variance stabilizing normalization (VSN) algorithms available therein. Finally, the functionality of IsobariQ is validated with data sets of experiments using 6-plex TMT and IPTL. Notably, protein substrates resulting from cleavage by proteases can be identified as shown for caspase targets in apoptosis.

Publications

  1. IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT.
    Cite this
    Arntzen MØ, Koehler CJ, Barsnes H, Berven FS, Treumann A, Thiede B, 2011-02-01 - Journal of proteome research

Credits

  1. Magnus Ø Arntzen
    Developer

  2. Christian J Koehler
    Developer

  3. Harald Barsnes
    Developer

  4. Frode S Berven
    Developer

  5. Achim Treumann
    Developer

  6. Bernd Thiede
    Investigator

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Summary
AccessionBT003512
Tool TypeApplication
Category
PlatformsWindows
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByBernd Thiede