IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments.

Area of Science:

• Biomedical Research
• Bioinformatics
• Proteomics

Background:

• Reproducibility is a significant challenge in biomedical research.
• Complex bioinformatic workflows in proteomics often involve numerous software tools and parameters, making methods sections insufficient for complete reproduction.
• Ensuring tool interoperability requires extensive parameter definition and data manipulation.

Purpose of the Study:

• To present IsoProt, a comprehensive and reproducible bioinformatic workflow for quantitative proteomics.
• To address the limitations of current methods sections in fully describing and enabling the reproduction of proteomics data analysis.
• To provide a user-friendly solution for analyzing isobarically labeled proteomics data.

Main Methods:

• IsoProt is deployed on a portable container environment for consistent execution.
• The workflow exclusively utilizes open-source tools.
• It features an interactive browser interface for easy configuration and execution of analysis steps.

Main Results:

• IsoProt provides a complete record of performed analyses, including R code for statistical analysis, downloadable as an HTML document.
• The workflow ensures identical results regardless of the computer platform.
• It facilitates the reproducible analysis of quantitative proteomics data.

Conclusions:

• IsoProt significantly improves the reproducibility of quantitative proteomics data analysis.
• The containerized, open-source approach ensures consistent and reliable results.
• This workflow enhances the transparency and reliability of biomedical research findings.