CAPER 3.0: A Scalable Cloud-Based System for Data-Intensive Analysis of Chromosome-Centric Human Proteome Project...

Area of Science:

• Proteomics
• Bioinformatics
• Computational Biology

Background:

• The Chromosome-centric Human Proteome Project (C-HPP) aims to systematically catalog all human proteins.
• Analyzing the large volume of MS/MS data generated by C-HPP presents significant computational challenges, particularly for smaller research labs.
• Existing tools may lack the scalability and user-friendliness required for intensive proteomic data analysis.

Purpose of the Study:

• To develop and present CAPER 3.0, an enhanced, scalable, cloud-based system for data-intensive analysis of C-HPP datasets.
• To provide a user-friendly platform that facilitates MS/MS-based peptide identification and analysis for the proteomic community.
• To enable researchers, including those without programming expertise, to perform complex proteomic data analyses.

Main Methods:

• Development of CAPER 3.0, a cloud-based system leveraging cloud computing for MS/MS data analysis.
• Implementation of a graphical user interface (GUI) for data transfer, job configuration, progress tracking, and result visualization.
• Utilization of both public and private cloud infrastructure to enhance data analysis flexibility.
• Application of CAPER 3.0 to address specific data-intensive challenges such as novel peptide detection, SAV identification, and exon-skipping event analysis.

Main Results:

• CAPER 3.0 successfully facilitates MS/MS-based peptide identification using scalable cloud technology.
• The system's GUI simplifies complex data management and analysis workflows, making it accessible to users with limited computational expertise.
• Demonstrated utility of CAPER 3.0 in solving four distinct data-intensive proteomic problems, including novel peptide detection and variant identification.
• CAPER 3.0 supports analysis using both public and private cloud environments, offering flexibility for diverse laboratory needs.

Conclusions:

• CAPER 3.0 is a powerful, scalable, and user-friendly cloud-based system designed to meet the data-intensive analysis demands of the C-HPP.
• The system democratizes advanced proteomic data analysis, empowering researchers lacking specialized computational infrastructure.
• CAPER 3.0 effectively addresses key challenges in proteomic data analysis, contributing to the advancement of the C-HPP and broader proteomic research.