PRIDE Converter - Efficient Database Deposition of Mass Spectrometry Data

在分子生物学的快速发展中，公开生物数据一直是至关重要的。然而，令人遗憾的是，与基因组学和转录组学等其他学科相比，公共领域知识库中的蛋白质组学数据量仍然相当低。蛋白质组学数据最著名的公共储存库之一是蛋白质组学鉴定数据库(Pride，http://www.ebi.ac.uk)at the EBI，位于剑桥。目前，蛋白质组学期刊越来越多地要求将MS数据公开存放到公共储存库，特别是要求Pride支持相关手稿的出版。与此同时，资助机构(如英国的BBRSR和Wellcome Trust)显然支持这一趋势，以此作为最大化所提供资金价值的一种方式。然而，实际上，如果不能向研究界提供能够有效获取技术和生物元数据的可靠和“用户友好”的提交工具，这一公共数据共享政策就不可能取得成功。提交工具Pride Converter(http://code.google.com/p/pride-converter))就是考虑到这一思想而开发的。它是一个开源的、独立于平台的软件，它的成功在很大程度上要归功于其易于使用的图形用户界面(GUI)组件。Pride Converter是目前为止这类工具中最全面和最受欢迎的工具，因为它使MS数据的提交变得更加容易和直接。它绝对是过去两年骄傲数据内容大幅增长的关键因素，并成为大多数研究人员事实上的骄傲提交工具。从2009年1月到2010年9月，Pride通过Pride Converter收到了243份数据证词，包括超过6360万个质谱图。这里提出的重新开发是基于Pride策展人在与数据储存者直接交换时收集的用户反馈，以及与期刊编辑的讨论，以及最近制定的社区质谱仪标准。除了技术目标a-b(见《技术总结》)之外，我们迫切需要实现对当前社区数据标准的支持。最近发表了用于表示质谱图的mzML，它取代了目前由Pride Converter支持的mzData。用于表示蛋白质和多肽标识的mzIdentML最近已经发布，并且已经被Mascot 2.3和其他工具支持。该提案的主要目标c)是在Pride Converter中实现完全的mzML/mzIdentML支持。除了数据表示标准外，HuPo蛋白质组学标准倡议还发布了一系列“最低要求”文件，描述了蛋白质组学实验应报告的元数据项目。目前，是否遵守这些最低要求文档并未通过PROCE转换器的验证。关键目标d)是实施这种验证，但也要通过为重复提交过程提供模板机制来有效地遵守这些要求。这将使数据的再利用更加可行，并将允许对数据进行更可靠的全球重新分析(荟萃分析研究)。在目前的形式下，Pride Converter仅为定量MS技术提供基本支持，而定量MS技术正迅速成为标准的蛋白质组学方法。主要目标e)旨在实现对定量蛋白质组学工具的轻量级Pride Converter支持。最终目标f)是蛋白质推断的标准化。目前，蛋白质组学搜索工具通常从一系列相同的蛋白质中选择一种用于给定的多肽集。我们将在不同的搜索工具之间尽可能地标准化这一过程，以确保蛋白质组学数据的最佳可比性。

Public availability of biological data has been of paramount importance in the rapid development of molecular biology. However, the amount of proteomics data in public domain repositories is regrettably still quite low in comparison with other disciplines like genomics and transcriptomics. One of the most prominent public repositories for proteomics data is the PRoteomics IDEntifications database (PRIDE, http://www.ebi.ac.uk) at the EBI, in Cambridge. At present proteomics journals are increasingly mandating public deposition of MS data to public repositories in general, and to PRIDE in particular, to support the publication of related manuscripts. At the same time, funding agencies (such as BBRSR and the Wellcome Trust in the UK) are clearly supporting this trend as a way to maximize the value of the funds provided. However, in practical terms, this public data-sharing policy cannot succeed if no reliable and 'user-friendly' submission tools, that can efficiently capture the technical and biological metadata, are provided to the research community. The submission tool PRIDE Converter (http://code.google.com/p/pride-converter) was developed with that idea in mind. It is an open source, platform independent software and a big part of its success can be attributed to its easy-to-use graphical user interface (GUI) component. PRIDE Converter is currently by far the most comprehensive and popular tool of this kind, since it made the submission of MS data a much easier and more straightforward process. It has definitely been the key factor in the huge growth in data contents in PRIDE for the last two years and has become the de facto submission tool for PRIDE for most researchers. From Jan 2009 to Sept 2010, PRIDE has received 243 data depositions, comprising more than 63.6 million mass spectra, through PRIDE Converter. The redevelopment proposed here is based on user feedback gathered by PRIDE curators in direct exchange with data depositors, as well as on discussions with journal editors, and recent development of community standards for mass spectrometry (MS). Beyond the technical objectives a-b (see 'Technical Summary'), we urgently need to implement support for current community data standards. mzML for the representation of mass spectra has recently been published and supersedes mzData, currently supported by PRIDE Converter. mzIdentML for the representation of protein and peptide identifications has recently been released and is already supported by Mascot 2.3 and other tools. Key objective c) of this proposal is to implement full mzML/mzIdentML support in PRIDE Converter. In addition to standards for data representation, the HUPO Proteomics Standards Initiative has published a series of 'Minimum Requirements' documents, describing the metadata items which should be reported for proteomics experiments. Currently, adherence to these Minimum requirements documents is not validated by the PRIDE Converter. Key objective d) is to implement such validation, but also to make adherence to these requirements efficient by providing a template mechanism for repetitive submission processes. This will make the reuse of the data more feasible and will allow perform more reliable global re-analysis of data (meta-analysis studies). In its current form, the PRIDE Converter provides only rudimentary support for quantitative MS technologies, which are quickly becoming the standard proteomics approach. Key objective e) aims to implement light weight PRIDE Converter support for quantitative proteomics tools. The final objective f) is the standardisation of protein inference. Currently, proteomics search tools usually select one of a range of equivalent protein choices for a given peptide set. We will standardise this process as much as possible between different search tools, to ensure optimised comparability of proteomics data.