proBAMconvert: A Conversion Tool for proBAM/proBed | Zendy

Volodimir Olexiouk | Zendy; Gerben Menschaert | Zendy

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proBAMconvert: A Conversion Tool for proBAM/proBed

Author(s) -

Volodimir Olexiouk,

Gerben Menschaert

Publication year - 2017

Publication title -

journal of proteome research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 1.644

H-Index - 161

eISSN - 1535-3907

pISSN - 1535-3893

DOI - 10.1021/acs.jproteome.7b00132

Subject(s) - proteogenomics , computer science , interface (matter) , identification (biology) , context (archaeology) , documentation , file format , user interface , proteomics , computational biology , genomics , database , genome , operating system , chemistry , biology , paleontology , biochemistry , botany , bubble , maximum bubble pressure method , gene

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 http://probam.biobix.be .

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