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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

Côté, Richard G.; Griss, Johannes; Dianes, José A.; Wang, Rui; Wright, James C.; van den Toorn, Henk W.P.; van Breukelen, Bas; Heck, Albert J. R.; Hulstaert, Niels; Martens, Lennart; Reisinger, Florian; Csordas, Attila; Ovelleiro, David; Perez-Rivevol, Yasset; Barsnes, Harald; Hermjakob, Henning; Vizcaíno, Juan Antonio
Peer reviewed, Journal article
Published version
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https://hdl.handle.net/1956/16687
Utgivelsesdato
2012-12
Metadata
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Samlinger
  • Department of Biomedicine [609]
Originalversjon
https://doi.org/10.1074/mcp.o112.021543
Sammendrag
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.
Utgiver
ASBMB
Tidsskrift
Molecular & Cellular Proteomics
Opphavsrett
Copyright 2012 by The American Society for Biochemistry and Molecular Biology, Inc.

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