Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

Area of Science:

• Proteomics
• Bioinformatics
• Computational Biology

Background:

• Genomics technologies have advanced rapidly, democratizing genotype determination.
• Proteomics technologies are emerging, enabling cellular phenotype and molecular event determination.
• Mass spectrometry (MS) is a core proteomic technology for protein analysis, including sequence, interactions, and post-translational modifications (PTMs).

Purpose of the Study:

• To review the Trans-Proteomics Pipeline (TPP) workflow for quantitative MS proteomics.
• To highlight TPP's capabilities, including its tools, modes of operation (desktop to cloud), and new features.
• To discuss common challenges in MS/MS data analysis and future TPP developments.

Main Methods:

• Review of the Trans-Proteomics Pipeline (TPP) architecture and functionalities.
• Description of TPP's support for major operating systems and instrument vendors using open data formats.
• Explanation of TPP's application in various computational environments, from local desktops to cloud platforms.

Main Results:

• The TPP provides a standardized, open-source data processing pipeline for reproducible, large-scale quantitative MS proteomics.
• New features in TPP include enhanced data visualization capabilities.
• The review identifies common pitfalls in MS/MS dataset analysis and outlines upcoming TPP enhancements.

Conclusions:

• The TPP is a comprehensive and versatile tool for quantitative proteomics, supporting reproducible research.
• Its adaptability across different computing environments and ongoing development make it a valuable asset for the proteomics community.
• Addressing common data analysis challenges and incorporating new features will further enhance TPP's utility.