proBAMconvert specifications


Unique identifier OMICS_19076
Name proBAMconvert
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format mzIdentML8, pepXML and mzTab
Output format proBAM, proBed
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Gerben Menschaert
  • person_outline Volodimir Olexiouk

Additional information

Publication for proBAMconvert

proBAMconvert citations


The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

Genome Biol
PMCID: 5793360
PMID: 29386051
DOI: 10.1186/s13059-017-1377-x

[…] mics data interpretation, protein and gene inference, count-based quantification, and data integration. It also provides a function to generate a peptide-based proBAM file coming from a PSM-based one.ProBAMconvert is another intuitive tool that enables the conversion from mzIdentML, mzTab, and pepXML (another popular proteomics open format) [] to both peptide- or PSM-based proBAM and proBed (http: […]


Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

J Proteome Res
PMCID: 5715286
PMID: 28849660
DOI: 10.1021/acs.jproteome.7b00370

[…] among other formats, several tools have also recently been developed. ms-data-core-api and PGConverter ( write to proBed, proBAMr writes to proBAM, and proBAMconvert ( writes to both formats. PGConverter also contains a validation module. proBAMtools is available for further downstream analysis of proBAM files.A systematic app […]

proBAMconvert institution(s)
Lab of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling; Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
proBAMconvert funding source(s)
Postdoctoral Fellow of the Research Foundation – Flanders (FWO-Vlaanderen) [12A7813N] and research grant from the Research Foundation - Flanders (FWO-Vlaanderen) [G0D3114N].

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