Display options
Cite
Côté RG, Griss J, Dianes JA, 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. Mol Cell Proteomics. 2012;11(12):1682-9doi: 10.1074/mcp.O112.021543.
Côté, R. G., Griss, J., Dianes, J. A., Wang, R., Wright, J. C., van den Toorn, H. W., van Breukelen, B., Heck, A. J., Hulstaert, N., Martens, L., Reisinger, F., Csordas, A., Ovelleiro, D., Perez-Rivevol, Y., Barsnes, H., Hermjakob, H., & Vizcaíno, J. A. (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 : MCP, 11(12), 1682-9. https://doi.org/10.1074/mcp.O112.021543
Côté, Richard G, 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 : MCP vol. 11,12 (2012): 1682-9. doi: https://doi.org/10.1074/mcp.O112.021543
Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, Vizcaíno JA. The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Mol Cell Proteomics. 2012 Dec;11(12):1682-9. doi: 10.1074/mcp.O112.021543. Epub 2012 Sep 04. PMID: 22949509; PMCID: PMC3518121.
Copy Download .nbib Format: NLM
Share it on

Mol Cell Proteomics. 2012 Dec;11(12):1682-9. doi: 10.1074/mcp.O112.021543. Epub 2012 Sep 04.

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 : MCP

Richard G Côté, Johannes Griss, José A Dianes, Rui Wang, James C Wright, Henk W P van den Toorn, Bas van Breukelen, Albert J R Heck, Niels Hulstaert, Lennart Martens, Florian Reisinger, Attila Csordas, David Ovelleiro, Yasset Perez-Rivevol, Harald Barsnes, Henning Hermjakob, Juan Antonio Vizcaíno

Affiliations

  1. Proteomics Services Team, EMBL Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

PMID: 22949509 PMCID: PMC3518121 DOI: 10.1074/mcp.O112.021543

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 MS-proteomics data repositories.

References

  1. Nat Biotechnol. 2009 Jul;27(7):579 - PubMed
  2. Proteomics. 2010 Apr;10(7):1522-4 - PubMed
  3. J Proteome Res. 2009 Jun;8(6):3037-43 - PubMed
  4. Nucleic Acids Res. 2010 Jan;38(Database issue):D736-42 - PubMed
  5. Proteomics. 2012 Mar;12(6):795-8 - PubMed
  6. Proteomics. 2007 Oct;7(19):3436-40 - PubMed
  7. Nat Biotechnol. 2008 Aug;26(8):864-6 - PubMed
  8. Expert Rev Proteomics. 2006 Feb;3(1):1-3 - PubMed
  9. Database (Oxford). 2012 Mar 20;2012:bas004 - PubMed
  10. Nat Biotechnol. 2012 Feb 08;30(2):135-7 - PubMed
  11. Proteomics. 2010 Apr;10(7):1332-5 - PubMed
  12. Proteomics. 2009 Nov;9(22):5112-9 - PubMed
  13. Proteomics. 2012 Mar;12(6):790-4 - PubMed
  14. Nat Biotechnol. 2009 Jul;27(7):598-9 - PubMed
  15. Mol Cell Proteomics. 2005 Oct;4(10):1419-40 - PubMed
  16. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W155-60 - PubMed
  17. J Proteome Res. 2011 Aug 5;10(8):3840-3 - PubMed
  18. Proteomics. 2009 Sep;9(18):4276-83 - PubMed
  19. Mol Cell Proteomics. 2011 Jan;10(1):R110.000133 - PubMed
  20. BMC Bioinformatics. 2010 Jan 17;11:34 - PubMed
  21. Mol Cell Proteomics. 2012 Jul;11(7):M111.014381 - PubMed
  22. EMBO Rep. 2008 May;9(5):429-34 - PubMed

Substances

MeSH terms

Publication Types

Grant support