PRIDE Toolsuite

PRIDE Toolsuite provides programmatic access to and manipulation of proteomics datasets in the PRIDE (PRoteomics IDEntifications) repository to support mass spectrometry proteomics analysis and proteogenomics integration.

Key Features:

• Data interaction: Programmatic access to and manipulation of proteomics datasets archived in PRIDE.
• Integration with standards: Support for proBAM and proBed, which adapt SAM/BAM and BED formats for proteomics and proteogenomics.
• Compatibility with genomic tooling: Enables reuse of SAMtools and Bedtools and supports visualization in genome browsers.
• File generation and conversion: Tools for generating and converting files to proBAM and proBed and for downstream analyses that leverage encoded proteomics information.

Scientific Applications:

• Proteogenomics workflows: Enables interoperability between mass spectrometry proteomics and genomics/transcriptomics data to support proteogenomics analyses.
• Cross-omics integration: Facilitates integrated interpretation across proteomics, genomics, and transcriptomics using proBAM/proBed formats and genome browser visualization.
• Visualization in genomic context: Supports display of proteomics-derived mappings and annotations in multiple genome browsers.

Methodology:

Programmatic interaction, analysis, and visualization of PRIDE data; generation and conversion to proBAM and proBed formats; reuse of SAMtools and Bedtools; output compatible with genome browsers.