proBAMconvert: A Conversion Tool for proBAM/proBed.

Area of Science:

• Proteogenomics
• Genomics
• Proteomics
• Mass Spectrometry Data Analysis

Background:

• Integrating genomics and proteomics data is crucial for advanced biological insights.
• Standardized formats are needed to facilitate data sharing and analysis in proteogenomics.
• Existing workflows lack efficient tools for converting mass spectrometry identification data into integrated formats.

Purpose of the Study:

• To introduce novel proBAM and proBed formats for improved integration of genomics and proteomics data.
• To develop a user-friendly tool, proBAMconvert, for converting mass spectrometry identification files to proBAM/proBed formats.
• To facilitate the storage, inspection, and analysis of peptide spectrum matches (PSM) within a genomic context.

Main Methods:

• Development of the proBAMconvert software with both graphical and command-line interfaces.
• Implementation of conversion capabilities for common identification file formats: mzIdentML, mzTab, and pepXML.
• Support for outputting information at both PSM and peptide levels.

Main Results:

• Successful creation of proBAM and proBed formats for enhanced data integration.
• ProBAMconvert effectively converts mzIdentML, mzTab, and pepXML files to proBAM/proBed.
• The tool provides flexible output options at PSM and peptide levels.
• Comprehensive documentation and a tutorial are available to support users.

Conclusions:

• The proBAM and proBed formats represent a significant advancement in integrating genomics and proteomics data.
• ProBAMconvert offers a vital, accessible solution for data conversion in proteogenomics research.
• The tool's versatility and ease of use will accelerate proteogenomics applications and data analysis.