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Related Experiment Video

Updated: Jun 4, 2026

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
14:51

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

iTRAQ protein quantification: a quality-controlled workflow.

Julia M Burkhart1, Marc Vaudel, René P Zahedi

  • 1Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany.

Proteomics
|February 18, 2011
PubMed
Summary
This summary is machine-generated.

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This study introduces a quality control workflow for isobaric tag for relative and absolute quantitation (iTRAQ) to ensure accurate peptide and protein quantification. It provides methods to assess iTRAQ effectiveness and improve protein ratio reliability.

Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Reporter ion-based methods are crucial for peptide and protein quantification.
  • Tandem Mass Tag (TMT) and iTRAQ are widely adopted labeling techniques in proteomics.
  • Current application of these methods often lacks rigorous quality control, potentially leading to unreliable results.

Purpose of the Study:

  • To develop a comprehensive, step-by-step quality control (QC) strategy for the iTRAQ workflow.
  • To establish metrics and techniques for evaluating the effectiveness of iTRAQ quantification.
  • To introduce a novel method for enhancing the reliability of protein ratio estimation.

Main Methods:

  • Implementation of a detailed QC protocol covering sample preparation to data analysis.

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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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Last Updated: Jun 4, 2026

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
14:51

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

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

  • Development of specific metrics to assess iTRAQ performance at each workflow stage.
  • Introduction of a new algorithm for improved protein ratio calculation.

    • Main Results:

    • The proposed QC workflow identifies potential limitations in iTRAQ experiments.
    • Established metrics provide objective measures of iTRAQ quantification accuracy.
    • The novel method demonstrates enhanced reliability in estimating protein ratios.

    Conclusions:

    • A robust iTRAQ QC workflow is essential for trustworthy proteomic data.
    • Implementing these QC steps mitigates risks associated with iTRAQ limitations.
    • The study offers a pathway to more dependable protein quantification using iTRAQ.