Advancing data and metadata standards for proteomics mass spectra

项目摘要 基于质谱（MS）的蛋白质组学是目前最广泛使用的用于蛋白质组学分析的技术。 复杂的蛋白质混合物。它有能力检测和量化数以千计的蛋白质的丰度， 它们的变体、翻译后修饰和每个实验的相互作用。有一套强大的开放， 标准化数据格式，用于对来自MS蛋白质组学分析的大多数阶段的数据和元数据进行编码， 由蛋白质组学标准倡议组织（PSI）开发。然而，目前还没有标准化的 一种普遍引用光谱的机制，该光谱用于分析或作为证据， 公布的声明。此外，尽管光谱匹配具有广泛公认的显著优点， 方法，一个批准的PSI标准的存储和交换的形式参考光谱 令人遗憾的是，光谱库仍然不存在。在这里，我们提出了一个数据标准的重大进步， 蛋白质组学质谱与三个相互关联的标准的发展。 首先，为了解决在整个频谱资源中识别和接入特定频谱的困难， 我们将制定一个通用的频谱标识符标准，可广泛用于参考、定位和 接入特定的频谱。第二，基于PSI在制定官方标准方面的丰富经验 格式，我们将彻底改革目前的一套原油光谱库格式，并制定一个 新的标准化和全面的光谱库格式，将有效的存储，使用， 交换参考光谱。第三，我们将开发一个标准的应用程序编程接口， 通过使用户和自动化软件能够查询和 交换有关光谱、肽和蛋白质的信息。 这些标准将根据防扩散安全倡议自成立以来制定的有效方法制定。 成立于2002年。这意味着我们将聚集来自世界各地的重要利益攸关方， 共同开发标准，创建规范文档和示例。这些规范文件 然后进行正式的PSI文件流程，每个提议的标准都要经过三轮 反复的审查和改进。然后，我们将开发开源软件，使这些使用 标准在多种编程语言，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在三个最大的ProteomeXchange蛋白组学数据 这将确保高可见性。这三个相互关联的标准的制定将 在蛋白质组学MS领域取得实质性进展，并很可能扩展到基于MS的代谢组学 也

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.