CAPER 2.0: an interactive, configurable, and extensible workflow-based platform to analyze data sets from the...

Area of Science:

• Proteomics
• Bioinformatics
• Genomics

Background:

• The Chromosome-centric Human Proteome Project (C-HPP) aims to comprehensively map and annotate the human proteome.
• Increasing volumes of proteomic data necessitate advanced bioinformatics tools for effective analysis and knowledge extraction.

Purpose of the Study:

• To address the data analysis challenges in the C-HPP, this study introduces CAPER 2.0.
• CAPER 2.0 is an interactive, configurable, and extensible platform designed for C-HPP data analysis and visualization.

Main Methods:

• The study presents CAPER 2.0, an updated proteome browser.
• CAPER 2.0 features a workflow system for creating, editing, running, and sharing analysis pipelines.
• It includes visualization tools like track-view and heatmap-view.

Main Results:

• CAPER 2.0 provides a powerful toolbox for C-HPP data analysis.
• The platform facilitates customized and reproducible proteomic data analysis.
• Four specific workflows demonstrate its utility: finding missing proteins, genome annotation, integrating peptide data with ENCODE datasets, and functional protein annotation.

Conclusions:

• CAPER 2.0 enhances the ability to analyze and visualize C-HPP proteomic data.
• The platform empowers users to conduct their own complex proteomic data analyses.
• CAPER 2.0 supports the ongoing goals of the C-HPP for comprehensive human proteome mapping.