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Related Experiment Video

Updated: Jun 6, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT.

Magnus Ø Arntzen1, Christian J Koehler, Harald Barsnes

  • 1The Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway.

Journal of Proteome Research
|November 12, 2010
PubMed
Summary
This summary is machine-generated.

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New software, IsobariQ, enables precise proteome quantification using isobaric peptide termini labeling (IPTL) and reporter ion techniques like TMT. It addresses data variance issues for more reliable results in proteomics research.

Area of Science:

  • Proteomics
  • Quantitative Mass Spectrometry
  • Bioinformatics

Background:

  • Isobaric peptide labeling is crucial for relative proteome quantification.
  • Existing methods like iTRAQ and TMT rely on reporter ions, while Isobaric Peptide Termini Labeling (IPTL) offers richer spectral data.
  • The complexity of IPTL data necessitates specialized software for accurate quantification.

Purpose of the Study:

  • To develop novel software, IsobariQ, for extracting quantitative information from MS/MS spectra generated by IPTL.
  • To integrate support for established reporter ion techniques (iTRAQ, TMT) within the same software.
  • To incorporate advanced statistical methods for handling variance heterogeneity in proteomics data.

Main Methods:

  • Development of the IsobariQ software tool.

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Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
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Last Updated: Jun 6, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

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  • Implementation of algorithms for analyzing MS/MS spectra from IPTL and reporter ion labeling.
  • Integration of the R statistical package and Variance Stabilizing Normalization (VSN) algorithms.
  • Validation using experimental datasets from 6-plex TMT and IPTL labeling.

    • Main Results:

    • IsobariQ successfully extracts quantitative information from complex MS/MS spectra.
    • The software supports both IPTL and reporter ion-based quantification methods.
    • Variance stabilizing normalization is effectively applied to address data heterogeneity.
    • Demonstrated identification of protease cleavage substrates, such as caspase targets in apoptosis.

    Conclusions:

    • IsobariQ provides a robust platform for quantitative proteomics using diverse isobaric labeling strategies.
    • The software enhances data reliability by addressing variance heterogeneity.
    • IsobariQ facilitates the identification of biologically relevant protein modifications and interactions.