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 Epub Date: 2022-12-26 DOI:10.1080/14789450.2022.2160324

Yasset Perez-Riverol

{"title":"Proteomic repository data submission, dissemination, and reuse: key messages.","authors":"Yasset Perez-Riverol","doi":"10.1080/14789450.2022.2160324","DOIUrl":null,"url":null,"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.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":"19 7-12","pages":"297-310"},"PeriodicalIF":3.8000,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7614296/pdf/EMS159053.pdf","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Expert Review of Proteomics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1080/14789450.2022.2160324","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2022/12/26 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}

引用次数: 0

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.

Abstract Image

查看原文本刊更多论文

蛋白质组资源库数据的提交、传播和再利用：关键信息。

简介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，以及全球范围内公共质谱蛋白质组学数据的广泛再分析。ProteomeXchange 引发了蛋白质组学数据公开传播的趋势，促进了公共数据集的评估、再利用、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 整合而成：在此，我们回顾并讨论了当前用于蛋白质组学数据传播和再分析的资源、指南和文件格式生态系统。我们将特别关注以定量和翻译后修饰为导向的新资源。此外，还讨论了数据沉积所面临的挑战和未来发展方向，包括缺乏元数据和基于云的高性能软件解决方案，无法对现有数据进行快速、可重现的再分析：ProteomeXchange 的成功以及公共领域中可获得的大量蛋白质组学数据引发了其他蛋白质知识库资源的创建和/或增长。数据再利用是一个领先、活跃和不断发展的领域；它支持创建新的格式、工具和工作流程，以重新发现和重塑公共蛋白质组学数据。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

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.