ProCon (Proteomics Conversion Tool)

ProCon converts proteomics identification data from proprietary outputs into mzIdentML and PRIDE XML, the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) standard formats, to enable standardized submission to public repositories and reuse of experimental data.

Key Features:

• Implementation: Implemented in Java.
• Standardization Support: Conforms to the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) by exporting data to mzIdentML and PRIDE XML.
• Input Compatibility: Accepts Sequest™/Comet .out files, ProteomeDiscoverer® 1.x (versions 1.1 to 1.4) outputs, and LIMS exports from ProteinScape® 1.3 and 2.1.
• Repository Compatibility: Generates outputs aligned with public repository submission requirements that mandate HUPO-PSI formats.

Scientific Applications:

• Data deposition: Enables deposition of proteomics identification datasets into public repositories via mzIdentML and PRIDE XML export.
• Reproducibility and transparency: Converts proprietary search results into standardized formats to support reproducibility and transparent reporting of proteomics experiments.
• Data reuse and archival: Facilitates long-term storage, sharing, and reuse of experimental proteomics identification data across tools and repositories.

Methodology:

The tool operates by reading input files from various proteomics software outputs and systematically transforming them into the mzIdentML or PRIDE XML format.