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proBAMconvert: A Conversion Tool for proBAM/proBed.

Volodimir Olexiouk1, Gerben Menschaert1

  • 1Lab of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University , 9000 Ghent, Belgium.

Journal of Proteome Research
|June 3, 2017
PubMed
Summary
This summary is machine-generated.

New proBAM and proBed formats enhance genomics and proteomics integration for proteogenomics. The proBAMconvert tool simplifies converting mass spectrometry data to these formats, aiding analysis.

Keywords:
bioinformaticsconversion toolproBAMproBedproteogenomics

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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.