Global proteomics mass spectrometry data sharing infrastructure

全球蛋白质组质谱数据共享基础设施

• 批准号: 10556184
• 负责人: Nuno Bandeira
• 金额: $ 73.1万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-05-19 至 2028-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10556184
• 关键词: Acceleration; Address; Adopted; Affect; Aging; Authorization documentation; Biological; Certification; Clinical; Communities; Data; Data Files; Data Reporting; Data Science; Data Set; Deposition; Detection; Disease; Ensure; Experimental Designs; FAIR principles; Funding Agency; Generations; Goals; Health Insurance Portability and Accountability Act; Human; Infrastructure; Internet; Journals; Mass Spectrum Analysis; Measures; Metadata; Modernization; Paper; Peptides; Policies; Post-Translational Protein Processing; Procedures; Process; Protein Isoforms; Proteins; Proteome; Proteomics; Publishing; Reporting; Research Personnel; Resources; Risk; Sampling; Secure; Security; Staging; Standardization; Stress; Structure; System; Technology; Testing; Variant; authority; data access; data handling; data infrastructure; data portal; data repository; data sharing; data submission; design; differential expression; expectation; file format; human data; human subject; improved; indexing; instrumentation; member; open data; protein complex; repository; shared repository; technology development; therapeutic development; treatment response; web services

Global proteomics mass spectrometry data sharing infrastructure - Project Summary Technological developments and the increased pace of data generation in mass spectrometry (MS) now enable systematic probing of the human proteome, thus contributing to the characterization of biomolecular mechanisms required for the development of therapeutic responses to disease. Recognizing the scientific necessity of open data to enable new discoveries and to establish the reliability of published results, the proteomics community embraced data sharing as a common practice. The authors of thousands of papers have already publicly re- leased the underlying MS data using the resources that we propose to support and extend: the MassIVE repos- itory of mass spectrometry data and the ProteomeCentral data portal for the global ProteomeXchange consor- tium of MS data repositories. In this project, we propose to develop new proteomics MS data infrastructure, standards, workflows and data indexes to substantially advance FAIR (Findable, Accessible, Interoperable and Reusable) access to proteomics MS datasets. First, we will develop new community standards for representation of dataset metadata and for the detailed description of proteomics identifications and abundances detected in available datasets, including peptides, proteins, isoforms and post-translational modifications. We will also ex- tend workflows for dataset submission, processing and indexing to enable advanced queries by each dataset’s detected proteomics identifications. Second, we will create new infrastructure for researchers to share controlled access proteomics datasets from studies of human subjects where there may exist a significant risk of the data being identifiable. Third, we will extend the ProteomeCentral data portal to support the new dataset structures, metadata and indexes allowing for the global integration of the new levels of information across all Proteo- meXchange repositories.

全球蛋白质组质谱数据共享基础设施 - 项目摘要 技术的发展和质谱 (MS) 数据生成速度的加快现在使得 对人类蛋白质组的系统探测，从而有助于生物分子机制的表征 发展对疾病的治疗反应所必需的。认识开放的科学必要性 数据以实现新发现并确定已发表结果的可靠性，蛋白质组学界 将数据共享视为一种常见做法。数千篇论文的作者已经公开重新 使用我们建议支持和扩展的资源租赁底层 MS 数据：MassIVE 存储库 质谱数据的历史和全球 ProteomeXchange 联盟的 ProteomeCentral 数据门户 MS 数据存储库的tium。在这个项目中，我们建议开发新的蛋白质组学 MS 数据基础设施， 标准、工作流程和数据索引，以大幅推进 FAIR（可查找、可访问、可互操作和 可重复使用）访问蛋白质组学 MS 数据集。首先，我们将制定新的社区代表标准 数据集元数据以及蛋白质组学鉴定和检测到的丰度的详细描述 可用的数据集，包括肽、蛋白质、亚型和翻译后修饰。我们还将前 倾向于数据集提交、处理和索引的工作流程，以支持每个数据集的高级查询 检测到蛋白质组学鉴定。其次，我们将为研究人员创建新的基础设施来共享受控的 访问人类受试者研究中可能存在重大数据风险的蛋白质组学数据集 是可识别的。第三，我们将扩展 ProteomeCentral 数据门户以支持新的数据集结构， 元数据和索引允许跨所有 Proteo- 进行新级别信息的全球集成 meXchange 存储库。