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jmzTab: a java interface to the mzTab data standard.

Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, VizcaĆ­no JA - Proteomics (2014)

Bottom Line: mzTab is the most recent standard format developed by the Proteomics Standards Initiative. mzTab is a flexible tab-delimited file that can capture identification and quantification results coming from MS-based proteomics and metabolomics approaches.The second key feature of the jmzTab model is that it provides a flexible framework to maintain the logical integrity between the metadata and the table-based sections in the mzTab files.In this article, as two example implementations, we also describe two stand-alone tools that can be used to validate mzTab files and to convert PRIDE XML files to mzTab.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Computer Science and Technology, Hubei University of Education, Wuhan, China.

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Screenshots of the mzTabGUI tool. (A) Example of validation report. Six error messages are output in the console panel. (B) Example of conversion of one PRIDE XML file to mzTab.
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fig02: Screenshots of the mzTabGUI tool. (A) Example of validation report. Six error messages are output in the console panel. (B) Example of conversion of one PRIDE XML file to mzTab.

Mentions: mzTabGUI, a desktop application which provides mzTab validation functionality and conversion from PRIDE XML files to mzTab, in two different tabs (Fig.2). After the conversion, the tool additionally performs an automatic validation of the mzTab file.


jmzTab: a java interface to the mzTab data standard.

Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, VizcaĆ­no JA - Proteomics (2014)

Screenshots of the mzTabGUI tool. (A) Example of validation report. Six error messages are output in the console panel. (B) Example of conversion of one PRIDE XML file to mzTab.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230411&req=5

fig02: Screenshots of the mzTabGUI tool. (A) Example of validation report. Six error messages are output in the console panel. (B) Example of conversion of one PRIDE XML file to mzTab.
Mentions: mzTabGUI, a desktop application which provides mzTab validation functionality and conversion from PRIDE XML files to mzTab, in two different tabs (Fig.2). After the conversion, the tool additionally performs an automatic validation of the mzTab file.

Bottom Line: mzTab is the most recent standard format developed by the Proteomics Standards Initiative. mzTab is a flexible tab-delimited file that can capture identification and quantification results coming from MS-based proteomics and metabolomics approaches.The second key feature of the jmzTab model is that it provides a flexible framework to maintain the logical integrity between the metadata and the table-based sections in the mzTab files.In this article, as two example implementations, we also describe two stand-alone tools that can be used to validate mzTab files and to convert PRIDE XML files to mzTab.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Computer Science and Technology, Hubei University of Education, Wuhan, China.

Show MeSH