MassIVE.quant: a curated and scalable community resource for quantitative proteomics

MassIVE.quant：定量蛋白质组学的精选且可扩展的社区资源

• 批准号: 10436166
• 负责人: Nuno Bandeira
• 金额: $ 32.39万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-01 至 2023-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10436166
• 关键词: Area; Benchmarking; Biological; Biological Process; Biomedical Research; Collection; Communities; Complex; Computer software; Computing Methodologies; Data; Data Analyses; Data Set; Evaluation; Experimental Designs; FAIR principles; Individual; Infrastructure; Investigation; Journals; Link; Manuals; Mass Spectrum Analysis; Metadata; Molecular; Peptides; Procedures; Proteins; Proteome; Proteomics; Protocols documentation; Reproducibility; Research; Research Methodology; Research Personnel; Research Support; Resources; Sampling; Scientist; Standardization; Statistical Methods; Structure; Training; base; computerized data processing; data acquisition; data resource; design; experimental study; improved; innovation; insight; interest; novel; open source; outreach; peer; preservation; public repository; repository; repository infrastructure; tool; virtual environment

PROJECT SUMMARY The project will contribute MassIVE.quant, a novel data resource for quantitative mass spectrometry-based proteomics. Quantitative mass spectrometry characterizes proteins in complex biological mixtures with the highest available accuracy, sensitivity and throughput. Analysis of most such experiments involves identification of peptides and proteins that generated the spectra, and relative quantification of changes in abundance between pre-defined conditions. While the identifications workflows are now mature and ready for reproducible research, the quantitative workflows lag very far behind. No repositories can now store the analyses results across all workflows, and it is often impossible for authors to provide their data in a form that allows independent evaluation and reuse. This undermines the reproducibility and the impact of these investigations. The project combines the prior expertise of the Banderia’s lab in developing Mass spectrometry Interactive Virtual Environment (MassIVE), a public repository for storing, documenting and re-analyzing mass spectra for identification, and the prior expertise of the Vitek lab in developing MSstats, a broad-scope collection of statistical methods and software for quantitative proteomic workflows. First, the project will fully document and annotate a medium scale “training set” of quantitative investigations (which often rely on manual procedures), to develop standards for documenting and annotating the experiments with respect to the biological origins of the samples, and the technological aspects of data acquisition and processing. Second, the project will design functionalities for repository-wide complete and automated re-analyses of the original investigations, using a limited number of “good practice” workflows. The re-analyses will fully preserve the provenance of the results, and will be used to further characterize potential pitfalls in the experimental designs and conclusions. Finally, the project will place these investigations into a broader scientific context. It will design a query infrastructure that links each experiment to its peer investigations, i.e. investigations with similar biological or technological aspects, to provide insights into consistency of the results. Continuing the extensive prior outreach efforts of the PIs, the results will be disseminated to a broad community of stakeholders, including proteomic scientists, tool developers, journal editors, trainees, and scientists interested in protein-level information. The project will shift the mass spectrometry-based research paradigm, by creating a public resource that currently does not exist in any form. It will expand the technical capabilities of the field, ultimately allowing us to make more accurate of statements about the biological function.

项目概要 该项目将贡献 MassIVE.quant，这是一种基于定量质谱的新型数据资源 蛋白质组学。 定量质谱分析复杂生物混合物中蛋白质的特征，具有最高可用的 准确性、灵敏度和吞吐量。大多数此类实验的分析涉及肽的鉴定和 生成光谱的蛋白质，以及预定义之间丰度变化的相对定量 状况。虽然鉴定工作流程现已成熟并准备好进行可重复的研究，但 定量工作流程远远落后。现在没有存储库可以存储所有分析结果 工作流程，作者通常不可能以允许独立评估的形式提供数据 并重复使用。这破坏了这些研究的可重复性和影响。 该项目结合了 Banderia 实验室之前开发质谱互动的专业知识 虚拟环境 (MassIVE)，用于存储、记录和重新分析质谱的公共存储库 识别，以及 Vitek 实验室在开发 MSstats 方面的先前专业知识，MSstats 是一个广泛的统计数据集合 定量蛋白质组工作流程的方法和软件。首先，该项目将完整记录和注释 中等规模的定量研究“训练集”（通常依赖于手动程序），以开发 记录和注释有关样品生物起源的实验的标准， 以及数据采集和处理的技术方面。二、项目将设计功能 使用有限数量的数据对原始调查进行全存储库的完整和自动重新分析 “良好实践”工作流程。重新分析将完全保留结果的出处，并将用于 进一步描述实验设计和结论中的潜在陷阱。最后，该项目将放置 这些调查涉及更广泛的科学背景。它将设计一个链接每个的查询基础设施 对其同行调查进行实验，即具有类似生物或技术方面的调查，以提供 深入了解结果的一致性。 继续 PI 之前广泛的宣传工作，结果将传播给更广泛的社区 利益相关者，包括蛋白质组科学家、工具开发人员、期刊编辑、学员和感兴趣的科学家 蛋白质水平的信息。 该项目将通过创建公共资源来改变基于质谱的研究范式 目前不以任何形式存在。它将扩展该领域的技术能力，最终使我们能够 使有关生物功能的陈述更加准确。

项目成果

Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: a case study of an urothelial cancer cohort analyzed in the Galaxy framework.

• DOI: 10.1186/s12014-022-09347-z
• 发表时间: 2022-04-19
• 期刊: Clinical proteomics
• 影响因子: 3.8

Cardinal v3 - a versatile open source software for mass spectrometry imaging analysis.

Cardinal v3 - 一款用于质谱成像分析的多功能开源软件。

• DOI: 10.1101/2023.02.20.529280
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 作者: Bemis,KylieAriel;Föll,MelanieChristine;Guo,Dan;Lakkimsetty,SaiSrikanth;Vitek,Olga
• 通讯作者: Vitek,Olga

A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images.

• DOI: 10.1093/bioinformatics/btad067
• 发表时间: 2023-02-03
• 期刊: Bioinformatics (Oxford, England)