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

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.