Capacity: BBSRC-NSF/BIO: Globally harmonized re-analysis of Data Independent Acquisition (DIA) proteomics datasets enables the creation of new resources (DIA-eXchange)

能力:BBSRC-NSF/BIO:数据独立采集(DIA)蛋白质组数据集的全球统一重新分析能够创建新资源(DIA-eXchange)

基本信息

  • 批准号:
    2324882
  • 负责人:
  • 金额:
    $ 120.07万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Continuing Grant
  • 财政年份:
    2023
  • 资助国家:
    美国
  • 起止时间:
    2023-09-01 至 2026-08-31
  • 项目状态:
    未结题

项目摘要

The research community has generated millions of datasets that were used to answer scientific questions of interest, and deposited those datasets into public data repositories as part of the mandated data sharing policies of funding agencies worldwide. Especially for datasets generated to measure the protein content of biological samples, substantial additional information can be extracted from these public datasets using newer techniques, newer versions of software, and newer reference information during re-analysis. This project will develop a software infrastructure for globally harmonized re-analysis of an emerging type of proteomics dataset to extract new information from older data. The infrastructure will improve our ability to turn proteomics data into knowledge about global relative protein abundances and about interactions between proteins inferred from how protein abundances are correlated. The project will also provide opportunities for students to learn skills in scientific data analysis. This project is an international collaboration with the Proteomics Team at EMBL-EBI (Hinxton, UK) and the Institute of Systems, Molecular and Integrative Biology (ISMIB) at the University of Liverpool (UoL; UK).This project will make the datasets generated by the method known as data-independent acquisition (DIA) mass spectrometry proteomics more findable, accessible, interoperable, and reusable (FAIR). This will be accomplished by developing an indexing system for the libraries of mass spectra that are used to analyze the data from DIA experiments. The project will further develop benchmarks and guidelines to advance the field, and then develop data analysis pipelines to process thousands of public experiments at scale and make the results available to the research community. The resulting protein abundance maps across thousands of experiments will enable the development of protein interaction maps via inference from protein co-expression patterns extracted from these datasets, something that can only be accomplished by thousands of datasets analyzed in unison. Students will be given opportunities to participate in the work in order to build their skills, and all software and data products will be made publicly available to further advance the field.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
研究界已经生成了数百万个用于回答感兴趣的科学问题的数据集,并将这些数据集存入公共数据库,作为全球资助机构强制数据共享政策的一部分。 特别是对于为测量生物样品的蛋白质含量而生成的数据集,可以在再分析期间使用更新的技术、更新版本的软件和更新的参考信息从这些公共数据集中提取大量附加信息。该项目将开发一个软件基础设施,用于对一种新出现的蛋白质组学数据集进行全球统一的重新分析,以便从旧数据中提取新信息。该基础设施将提高我们将蛋白质组学数据转化为关于全球相对蛋白质丰度以及从蛋白质丰度如何相关推断的蛋白质之间相互作用的知识的能力。该项目还将为学生提供学习科学数据分析技能的机会。 该项目是EMBL-EBI(Hinxton,UK)的蛋白质组学团队和利物浦大学(UoL; UK)的系统、分子和整合生物学研究所(ISMIB)的国际合作项目。该项目将使由称为数据独立采集(DIA)质谱蛋白质组学的方法生成的数据集更加可发现、可访问、可互操作和可重用(FAIR)。这将通过开发用于分析DIA实验数据的质谱库的索引系统来实现。该项目将进一步制定基准和指导方针,以推动该领域的发展,然后开发数据分析管道,以处理数千个大规模的公共实验,并将结果提供给研究界。在数千个实验中得到的蛋白质丰度图将通过从这些数据集中提取的蛋白质共表达模式进行推断来开发蛋白质相互作用图,这只能通过一致分析数千个数据集来完成。学生将有机会参与这项工作,以培养他们的技能,所有的软件和数据产品将公开提供,以进一步推动该领域的发展。该奖项反映了NSF的法定使命,并已被认为是值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估的支持。

项目成果

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Eric Deutsch其他文献

Implementation of flexible search for proteomics metadata
蛋白质组元数据灵活搜索的实现
  • DOI:
  • 发表时间:
    2016
  • 期刊:
  • 影响因子:
    0
  • 作者:
    Shin Kawano;Yuki Moriya;Tobias Ternent;Juan Antonio Vizcaino;Eric Deutsch
  • 通讯作者:
    Eric Deutsch
Evidence of Alveolar Macrophage Metabolic Shift Following Stereotactic Body Radiation Therapy -Induced Lung Fibrosis in Mice
立体定向体部放疗诱导小鼠肺纤维化后肺泡巨噬细胞代谢变化的证据
  • DOI:
    10.1016/j.ijrobp.2024.09.018
  • 发表时间:
    2025-02-01
  • 期刊:
  • 影响因子:
    6.500
  • 作者:
    Sarah Braga-Cohen;Jérémy Lavigne;Morgane Dos Santos;Georges Tarlet;Valérie Buard;Jan Baijer;Olivier Guipaud;Vincent Paget;Eric Deutsch;Mohamed Amine Benadjaoud;Michele Mondini;Fabien Milliat;Agnès François
  • 通讯作者:
    Agnès François
3836 In-vivo assessment of doses delivered to out-of-field lymphoid organs during head and neck radiotherapy using radiophotoluminescent glass dosimeters
3836 使用辐射光致发光玻璃剂量计对头颈部放射治疗期间场外淋巴器官所接受剂量的体内评估
  • DOI:
    10.1016/s0167-8140(25)01992-9
  • 发表时间:
    2025-05-01
  • 期刊:
  • 影响因子:
    5.300
  • 作者:
    Meïssane M'hamdi;Pauline Maury;Julie Colnot;Mesut Aydin;Marc André Boivin;Najma Douir;Eric Deutsch;Charlotte Robert;Ibrahima Diallo
  • 通讯作者:
    Ibrahima Diallo
3125: Cold liver metastases according to a CD8 radiomic-score : a new target for SBRT with immunotherapy?
3125:根据CD8放射线得分的冷肝转移:具有免疫疗法的SBRT的新靶标?
  • DOI:
    10.1016/s0167-8140(24)03186-4
  • 发表时间:
    2024-05-01
  • 期刊:
  • 影响因子:
    5.300
  • 作者:
    Roger Sun;Markus Hecht;Caroline Robert;Emilie Routier;Udo S. Gaipl;Benjamin Frey;Rastilav Bahleda;Charlotte Robert;Piet Ost;Eric Deutsch
  • 通讯作者:
    Eric Deutsch
Practice changing data and emerging concepts from recent radiation therapy randomised clinical trials
练习改变来自最近放疗随机临床试验的数据和新出现的概念
  • DOI:
    10.1016/j.ejca.2022.04.038
  • 发表时间:
    2022-08-01
  • 期刊:
  • 影响因子:
    7.100
  • 作者:
    Sophie Espenel;Cyrus Chargari;Pierre Blanchard;Sophie Bockel;Daphne Morel;Sofia Rivera;Antonin Levy;Eric Deutsch
  • 通讯作者:
    Eric Deutsch

Eric Deutsch的其他文献

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{{ truncateString('Eric Deutsch', 18)}}的其他基金

CIBR: PTMexchange: Globally harmonized re-analysis and sharing of data on post-translational modifications
CIBR:PTMexchange:全球统一的翻译后修饰数据重新分析和共享
  • 批准号:
    1933311
  • 财政年份:
    2019
  • 资助金额:
    $ 120.07万
  • 项目类别:
    Standard Grant
BD Spokes: PLANNING: WEST: Collaborative: Increasing collaborations in proteogenomics applications of genetic data
BD 发言人:规划:西方:合作:加强遗传数据蛋白质组学应用方面的合作
  • 批准号:
    1636903
  • 财政年份:
    2016
  • 资助金额:
    $ 120.07万
  • 项目类别:
    Standard Grant

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