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Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.

Hui-Yin Chang1,2, Yamei Deng1, Ruohong Li1

  • 1Department of Pathology, University of Michigan, Ann Arbor, MI, USA.

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TMT-Integrator, a new bioinformatics tool, enhances quantitative proteomics by providing integrated reports from TMT and iTRAQ experiments. It demonstrates superior performance in protein and phosphosite quantification compared to existing methods.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Mass Spectrometry

Background:

  • Isobaric mass tags like iTRAQ and TMT are essential for multiplex quantitative proteomics.
  • Processing quantitative results from these experiments requires sophisticated bioinformatics tools.

Purpose of the Study:

  • To introduce TMT-Integrator, a novel bioinformatics tool for processing TMT and iTRAQ quantitative proteomics data.
  • To offer integrative analysis reports at multiple biological levels (gene, protein, peptide, PTM sites).

Main Methods:

  • TMT-Integrator was integrated into the FragPipe computational platform.
  • The performance of the FragPipe/TMT-Integrator pipeline was benchmarked against MaxQuant and Proteome Discoverer.
  • Analysis utilized five diverse TMT datasets, including spike-in, clinical, and advanced reagent experiments.

Main Results:

  • FragPipe/TMT-Integrator quantified more proteins in E. coli and ccRCC whole proteome datasets.
  • More phosphorylated sites were identified in the ccRCC phosphoproteome dataset using this pipeline.
  • The FragPipe/TMT-Integrator pipeline demonstrated more robust quantification performance.

Conclusions:

  • TMT-Integrator is a valuable component for TMT and iTRAQ data analysis workflows.
  • The FragPipe/TMT-Integrator pipeline offers enhanced performance in protein and phosphosite quantification.
  • This tool provides comprehensive and robust analysis for multiplex quantitative proteomics.