Proteomic repository data submission, dissemination, and reuse: key messages.

IF 3.8 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Expert Review of Proteomics Pub Date : 2022-07-01 DOI:10.1080/14789450.2022.2160324

Yasset Perez-Riverol

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引用次数: 1

Abstract

Introduction: The creation of ProteomeXchange data workflows in 2012 transformed the field of proteomics, consisting of the standardization of data submission and dissemination and enabling the widespread reanalysis of public MS proteomics data worldwide. ProteomeXchange has triggered a growing trend toward public dissemination of proteomics data, facilitating the assessment, reuse, comparative analyses, and extraction of new findings from public datasets. By 2022, the consortium is integrated by PRIDE, PeptideAtlas, MassIVE, jPOST, iProX, and Panorama Public.

Areas covered: Here, we review and discuss the current ecosystem of resources, guidelines, and file formats for proteomics data dissemination and reanalysis. Special attention is drawn to new exciting quantitative and post-translational modification-oriented resources. The challenges and future directions on data depositions including the lack of metadata and cloud-based and high-performance software solutions for fast and reproducible reanalysis of the available data are discussed.

Expert opinion: The success of ProteomeXchange and the amount of proteomics data available in the public domain have triggered the creation and/or growth of other protein knowledgebase resources. Data reuse is a leading, active, and evolving field; supporting the creation of new formats, tools, and workflows to rediscover and reshape the public proteomics data.

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蛋白质组学存储库数据提交、传播和重用:关键信息。

2012年ProteomeXchange数据工作流的创建改变了蛋白质组学领域，包括数据提交和传播的标准化，以及全球范围内公开的MS蛋白质组学数据的广泛再分析。ProteomeXchange已经引发了蛋白质组学数据公开传播的增长趋势，促进了公共数据集的评估、重用、比较分析和新发现的提取。到2022年，该联盟将由PRIDE、PeptideAtlas、MassIVE、jPOST、iProX和Panorama Public整合。涵盖领域:在这里，我们回顾并讨论了蛋白质组学数据传播和再分析的当前资源生态系统、指南和文件格式。特别关注新的令人兴奋的定量和翻译后修饰导向的资源。讨论了数据沉积的挑战和未来方向，包括缺乏元数据和基于云的高性能软件解决方案，用于对可用数据进行快速和可重复的再分析。专家意见:ProteomeXchange的成功和公共领域中可用的蛋白质组学数据的数量已经触发了其他蛋白质知识库资源的创建和/或增长。数据重用是一个领先的、活跃的、不断发展的领域;支持创建新的格式、工具和工作流程，以重新发现和重塑公共蛋白质组学数据。

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来源期刊

Expert Review of Proteomics 生物-生化研究方法

CiteScore

7.60

自引率

0.00%

发文量

审稿时长

6-12 weeks

期刊介绍： Expert Review of Proteomics (ISSN 1478-9450) seeks to collect together technologies, methods and discoveries from the field of proteomics to advance scientific understanding of the many varied roles protein expression plays in human health and disease. The journal coverage includes, but is not limited to, overviews of specific technological advances in the development of protein arrays, interaction maps, data archives and biological assays, performance of new technologies and prospects for future drug discovery. The journal adopts the unique Expert Review article format, offering a complete overview of current thinking in a key technology area, research or clinical practice, augmented by the following sections: Expert Opinion - a personal view on the most effective or promising strategies and a clear perspective of future prospects within a realistic timescale Article highlights - an executive summary cutting to the author''s most critical points.

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