The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
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DOI：
10.1074/mcp.o112.021543
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发表时间：
2012-12
期刊：
影响因子：
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通讯作者：
Vizcaíno JA
中科院分区：
文献类型：
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作者：
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
最初的 PRIDE Converter 工具极大地简化了将基于质谱 (MS) 的蛋白质组数据提交到 PRIDE 数据库的过程。然而，经过大量用户反馈后，人们注意到该工具存在一些局限性，无法满足现在变得司空见惯的一些用户需求。这促使我们设计和实现一套全新的工具，该工具将建立在原始 PRIDE Converter 的成功基础上，并允许用户生成可提交的、注释良好的 PRIDE XML 文件。 PRIDE Converter 2工具套件允许用户将搜索结果文件转换为PRIDE XML（执行向PRIDE数据库提交所需的格式），生成可用作提交定量和基于凝胶的MS数据的基础的mzTab骨架文件，并通过滤除污染物和空光谱或将多个PRIDE XML文件合并在一起来对PRIDE XML文件进行后处理。所有工具都具有图形用户界面，提供基于对话框的、用户友好的方式来转换和准备文件以供提交，以及命令行界面，可用于将工具集成到现有或新颖的管道中，供批处理和高级用户使用。因此，PRIDE Converter 2 工具套件将成为 PRIDE 以及 MS 蛋白质组数据存储库 ProteomeXchange 联盟提交过程的基石。
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.