Proteogenomics Dashboard for the Human Proteome Project

Area of Science:

• Proteomics
• Genomics
• Bioinformatics

Background:

• The Spanish Human Proteome Project (SpHPP) consortium aims to map the entire human proteome.
• Genomics projects like ENCODE provide valuable data on human cell lines.
• Integrating multi-omics data is crucial for comprehensive proteome analysis.

Purpose of the Study:

• To develop a novel proteomics-based dashboard, dasHPPboard, for the SpHPP.
• To facilitate the mapping of the human proteome by integrating diverse experimental data.
• To provide a resource for identifying missing proteins and understanding gene expression.

Main Methods:

• Collected and processed shotgun and selected reaction monitoring proteomics data.
• Integrated transcriptomics data from ENCODE and Human Body Map (HBM) projects.
• Developed peptide databases using single nucleotide variants and RNA-Seq data for enhanced protein identification.

Main Results:

• The dasHPPboard visualizes and shares integrated proteomic and transcriptomic data.
• Identified gene expression patterns in cell lines and tissues, focusing on proteins with limited proteomic evidence.
• Enabled sample-specific protein identification using custom peptide databases.

Conclusions:

• The dasHPPboard serves as a valuable resource for proteogenomics analyses.
• Facilitates the discovery and characterization of the human proteome.
• Promotes data sharing and visualization for the HPP community.