Advancing data and metadata standards for proteomics mass spectra

项目摘要 基于质谱学的蛋白质组学是目前应用最广泛的蛋白质组学分析技术 复杂的蛋白质混合物。它有能力检测和量化数千种蛋白质的丰度和 他们的变体，翻译后的修饰，以及每个实验的相互作用。有一套强大的开放的、 用于编码来自MS蛋白质组学分析的大多数阶段的数据和元数据的标准化数据格式， 由蛋白质组学标准倡议(PSI)开发。然而，目前还没有一个标准化的 一种普遍引用在分析中使用或作为证据的光谱的机制 已公布的索赔。此外，尽管光谱匹配的显著优势得到了广泛认可 方法，一个经批准的PSI标准，用于存储和交换以下形式的参考光谱 光谱库仍然明显缺乏。在这里，我们建议在数据标准方面进行重大改进 随着蛋白质组学质谱学三个相互关联的标准的发展。 首先，为了解决在整个资源中识别和访问特定频谱的困难 ，我们将制定一个通用的频谱识别器标准，可以广泛用于参考、定位和 访问特定的频谱。第二，以PSI在开发官方标准方面的丰富经验为基础 对于广泛使用的光谱格式，我们将彻底改革现有的一套粗略光谱库格式，并开发一个 新的标准化和全面的光谱库格式，将有效地存储、使用和 参考光谱的交换。第三，我们将开发一个标准的应用程序编程接口 将标准部署到整个社区，使用户和自动化软件能够查询和 交换有关光谱、多肽和蛋白质的信息。 这些标准将根据PSI自成立以来开发的有效方法来制定 成立于2002年。这意味着我们将召集来自世界各地的重要利益攸关方 共同制定标准，创建规范文档和示例。这些规范文档 然后经过正式的PSI文件过程，这使每个拟议的标准都经历了三轮 迭代审查和细化。然后我们将开发开放源码软件，使其能够使用这些 多种编程语言的标准，以促进广泛使用。最后，我们将实施 这些标准通过这些软件库获得了三个最大的ProteomeXchange蛋白质组学数据 存储库，这将确保高可见性。这三个相互关联的标准的发展将 实现蛋白质组学领域的实质性进展，并很有可能延伸到基于MS的代谢组学 也是。

Project Summary Mass spectrometry (MS) based proteomics is currently the most widely used technology for the analysis of complex protein mixtures. It has the ability to detect and quantify the abundance of thousands of proteins and their variants, post-translational modifications, and interactions per experiment. There is a robust set of open, standardized data formats for encoding data and metadata from most stages of MS proteomics analysis, developed by the Proteomics Standards Initiative (PSI). However, there is not currently a standardized mechanism for universally referencing a spectrum that is used in an analysis or held up as evidence for a published claim. Further, despite the widely recognized significant advantages of spectrum matching approaches, an approved PSI standard for the storage and exchange of reference spectra in the form of spectral libraries is still glaringly absent. Here we propose a major advancement in data standards for proteomics mass spectra with the development of three interrelated standards. First, in order to solve the difficulty in identifying and accessing a specific spectrum in resources throughout the world, we will develop a universal spectrum identifier standard that can be widely used to reference, locate and access a specific spectrum. Second, building on PSI's extensive experience in developing official standard formats that are widely used, we will overhaul the current set of crude spectral library formats and develop a new standardized and comprehensive spectral library format that will be effective for the storage, use, and exchange of reference spectra. Third, we will develop a standard application programming interface that deploys the standards to the whole community by enabling users and automated software to query and exchange information about spectra, peptides, and proteins. These standards will be developed according the effective methodologies that the PSI has developed since its inception in 2002. This means that we will assemble the important stakeholders from all over the world to jointly develop the standards, create specification documents and examples. These specification documents then undergo the official PSI document process, which subjects each proposed standard to three rounds of iterative review and refinement. We will then develop open-source software that enables the use of these standards in multiple programming languages in order to promote widespread usage. Finally we will implement these standards via these software libraries at the three largest ProteomeXchange proteomics data repositories, which will ensure high visibility. The development of these three interrelated standards will achieve a substantial advance for the field of proteomics MS, and may well extend to MS-based metabolomics as well.