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The PRoteomics IDEntification (PRIDE) converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium

(2012) MOLECULAR & CELLULAR PROTEOMICS. 11(12). p.1682-1689
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Abstract
The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user feedback, it was noted that the tool had some limitations and could not handle several user requirements that were now becoming commonplace. This prompted us to design and implement a whole new suite of tools that would build on the successes of the original PRIDE Converter and allow users to generate submission-ready, well-annotated PRIDE XML files. The PRIDE Converter 2 tool suite allows users to convert search result files into PRIDE XML (the format needed for performing submissions to the PRIDE database), generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra, or by merging several PRIDE XML files together. All the tools have both a graphical user interface that provides a dialog-based, user-friendly way to convert and prepare files for submission, as well as a command-line interface that can be used to integrate the tools into existing or novel pipelines, for batch processing and power users. The PRIDE Converter 2 tool suite will thus become a cornerstone in the submission process to PRIDE and, by extension, to the ProteomeXchange consortium of MSproteomics data repositories.
Keywords
VISUALIZE, STANDARD, KeyWords Plus: ONTOLOGY LOOKUP SERVICE, API, PARSER, LIBRARY

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MLA
Côté, Richard G, Johannes Griss, José A Dianes, et al. “The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium.” MOLECULAR & CELLULAR PROTEOMICS 11.12 (2012): 1682–1689. Print.
APA
Côté, R. G., Griss, J., Dianes, J. A., Wang, R., Wright, J. C., van den Toorn, H. W., van Breukelen, B., et al. (2012). The PRoteomics IDEntification (PRIDE) converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. MOLECULAR & CELLULAR PROTEOMICS, 11(12), 1682–1689.
Chicago author-date
Côté, Richard G, Johannes Griss, José A Dianes, Rui Wang, James C Wright, Henk WP van den Toorn, Bas van Breukelen, et al. 2012. “The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium.” Molecular & Cellular Proteomics 11 (12): 1682–1689.
Chicago author-date (all authors)
Côté, Richard G, Johannes Griss, José A Dianes, Rui Wang, James C Wright, Henk WP van den Toorn, Bas van Breukelen, Albert JR Heck, Niels Hulstaert, Lennart Martens, Florian Reisinger, Attila Csordas, David Ovelleiro, Yasset Perez-Rivevol, Harald Barsnes, Henning Hermjakob, and Juan Antonio Vizcaíno. 2012. “The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium.” Molecular & Cellular Proteomics 11 (12): 1682–1689.
Vancouver
1.
Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, et al. The PRoteomics IDEntification (PRIDE) converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. MOLECULAR & CELLULAR PROTEOMICS. 2012;11(12):1682–9.
IEEE
[1]
R. G. Côté et al., “The PRoteomics IDEntification (PRIDE) converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium,” MOLECULAR & CELLULAR PROTEOMICS, vol. 11, no. 12, pp. 1682–1689, 2012.
@article{3183768,
  abstract     = {{The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user feedback, it was noted that the tool had some limitations and could not handle several user requirements that were now becoming commonplace. This prompted us to design and implement a whole new suite of tools that would build on the successes of the original PRIDE Converter and allow users to generate submission-ready, well-annotated PRIDE XML files. The PRIDE Converter 2 tool suite allows users to convert search result files into PRIDE XML (the format needed for performing submissions to the PRIDE database), generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra, or by merging several PRIDE XML files together. All the tools have both a graphical user interface that provides a dialog-based, user-friendly way to convert and prepare files for submission, as well as a command-line interface that can be used to integrate the tools into existing or novel pipelines, for batch processing and power users. The PRIDE Converter 2 tool suite will thus become a cornerstone in the submission process to PRIDE and, by extension, to the ProteomeXchange consortium of MSproteomics data repositories.}},
  author       = {{Côté, Richard G and Griss, Johannes and Dianes, José A and Wang, Rui and Wright, James C and van den Toorn, Henk WP and van Breukelen, Bas and Heck, Albert JR and Hulstaert, Niels and Martens, Lennart and Reisinger, Florian and Csordas, Attila and Ovelleiro, David and Perez-Rivevol, Yasset and Barsnes, Harald and Hermjakob, Henning and Vizcaíno, Juan Antonio}},
  issn         = {{1535-9476}},
  journal      = {{MOLECULAR & CELLULAR PROTEOMICS}},
  keywords     = {{VISUALIZE,STANDARD,KeyWords Plus: ONTOLOGY LOOKUP SERVICE,API,PARSER,LIBRARY}},
  language     = {{eng}},
  number       = {{12}},
  pages        = {{1682--1689}},
  title        = {{The PRoteomics IDEntification (PRIDE) converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium}},
  url          = {{http://dx.doi.org/10.1074/mcp.O112.021543}},
  volume       = {{11}},
  year         = {{2012}},
}

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