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iTRAQPak: an R based analysis and visualization package for 8-plex isobaric protein expression data.

Mark D'Ascenzo1, Leila Choe, Kelvin H Lee

  • 1Plant Molecular Biology, Penn State University, USA.

Briefings in Functional Genomics & Proteomics
|February 15, 2008
PubMed
Summary
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High throughput proteomics uses mass spectrometry for quantitative protein analysis. We present iTRAQPak, a free R software package for analyzing 8-plex iTRAQ data from Alzheimer's disease cerebrospinal fluid samples.

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • High-throughput proteomics relies on mass spectrometry for quantitative protein expression analysis.
  • Isobaric tagging techniques, such as iTRAQ (isobaric tags for relative and absolute quantitation), allow for multiplexed analysis of up to eight protein samples.
  • Understanding protein expression dynamics is crucial in disease research.

Purpose of the Study:

  • To introduce iTRAQPak, a novel, free software package for analyzing 8-plex iTRAQ data.
  • To provide a user-friendly tool within the R statistical environment for proteomic data analysis.
  • To demonstrate the utility of iTRAQPak using real-world Alzheimer's disease research data.

Main Methods:

  • Development of iTRAQPak, a software package in the R statistical and visualization environment.

Related Experiment Videos

  • Application of iTRAQPak to analyze 8-plex iTRAQ quantitative proteomic data.
  • Utilizing cerebrospinal fluid samples from Alzheimer's disease subjects in a Phase I drug trial for validation.

    • Main Results:

    • iTRAQPak successfully analyzes 8-plex iTRAQ protein expression data.
    • The software package is demonstrated to be effective for complex proteomic analyses.
    • The analysis provides insights into protein expression in Alzheimer's disease.

    Conclusions:

    • iTRAQPak is a valuable free software tool for researchers in high-throughput proteomics.
    • The package facilitates the quantitative analysis of 8-plex iTRAQ data, aiding in the study of protein expression dynamics.
    • This tool can be applied to various research areas, including neurodegenerative diseases like Alzheimer's.