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J Proteome Res. 2017 Jul 7;16(7):2639-2644. doi: 10.1021/acs.jproteome.7b00132. Epub 2017 Jun 9.

proBAMconvert: A Conversion Tool for proBAM/proBed.

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


The introduction of new standard formats, proBAM and proBed, improves the integration of genomics and proteomics information, thus aiding proteogenomics applications. These novel formats enable peptide spectrum matches (PSM) to be stored, inspected, and analyzed within the context of the genome. However, an easy-to-use and transparent tool to convert mass spectrometry identification files to these new formats is indispensable. proBAMconvert enables the conversion of common identification file formats (mzIdentML, mzTab, and pepXML) to proBAM/proBed using an intuitive interface. Furthermore, ProBAMconvert enables information to be output both at the PSM and peptide levels and has a command line interface next to the graphical user interface. Detailed documentation and a completely worked-out tutorial is available at .


bioinformatics; conversion tool; proBAM; proBed; proteogenomics

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