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iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer.

Timothy J Griffin1, Hongwei Xie, Sricharan Bandhakavi

  • 1Department of Biochemistry, Molecular Biology, and Biophysics, Center for Mass Spectrometry and Proteomics, University of Minnesota, Minneapolis, Minnesota 55455, USA. tgriffin@umn.edu

Journal of Proteome Research
|October 2, 2007
PubMed
Summary

Optimized linear ion trap (LTQ) instruments with pulsed Q dissociation (PQD) can effectively analyze iTRAQ-labeled peptides for quantitative proteomics. Software for summing reporter ions enhances accuracy, making LTQ-PQD a viable option.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Analytical Chemistry

Background:

  • Linear ion trap (LTQ) instruments offer high sensitivity for proteomics but struggle with low mass peptide fragments.
  • This limitation hinders their use with isobaric tags for relative and absolute quantitation (iTRAQ) reagent-labeled samples.
  • The effectiveness of LTQ's pulsed Q dissociation (PQD) for iTRAQ peptides is uncertain.

Purpose of the Study:

  • To evaluate and optimize the use of LTQ-PQD for quantitative proteomic analysis of iTRAQ-labeled peptides.
  • To develop and validate a software solution for improving quantification accuracy.
  • To provide guidelines for successful quantitative proteomic studies using this methodology.

Main Methods:

  • Standard peptide mixtures were analyzed using an LTQ instrument with optimized PQD settings.
  • Collision energy, microscan acquisition, and repeat count were systematically tuned.
  • A novel software tool was developed to sum reporter ion intensities for abundance ratio calculation.
  • Results were compared against analysis performed on a Qstar instrument.

Main Results:

  • Careful tuning of relative collision energy is crucial for effective iTRAQ peptide fragmentation.
  • Increased microscan acquisition and repeat count improved quantification accuracy at the cost of slightly reduced peptide identification.
  • The developed software accurately calculated abundance ratios by summing reporter ion intensities.
  • Optimized LTQ-PQD analysis with the software showed strong correlation with Qstar instrument results.

Conclusions:

  • LTQ-PQD is an effective method for quantitative proteomic analysis of iTRAQ-labeled peptides.
  • Optimized instrument settings and dedicated software are key to achieving high accuracy.
  • This study provides practical guidelines for implementing successful quantitative proteomic workflows.