A proteoform-centric informatics platform for targeted top-down characterization and quantitation

以蛋白质组为中心的信息学平台，用于有针对性的自上而下的表征和定量

• 批准号: 10325492
• 负责人: Kenneth Durbin
• 金额: $ 25.2万
• 依托单位: PROTEINACEOUS, INC.
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-25 至 2022-10-24
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10325492
• 关键词: Academia; Adoption; Algorithmic Analysis; Algorithms; Biological Phenomena; Biological Process; Biology; Chemicals; Clinical; Color; Communities; Computer software; Consumption; Custom; Data; Data Analyses; Databases; Digestion; Disease; Environment; Family; Foundations; Generations; Individual; Informatics; Infrastructure; Intuition; Ions; Isotopes; Leg; Libraries; Link; Location; Manuals; Maps; Mass Spectrum Analysis; Measurement; Methods; Modification; Molecular; Names; Participant; Pharmaceutical Preparations; Pharmacologic Substance; Process; Protein Analysis; Protein Isoforms; Proteins; Proteomics; Reproducibility; Research; Research Personnel; Role; Shapes; Side; Software Tools; Specificity; Structure; Technology; Text; Therapeutic; Time; Validation; Vision; Visual; Visualization; Work; base; bioinformatics tool; biological systems; clinical biomarkers; cluster computing; design; disulfide bond; driving force; experience; experimental study; follow-up; graphical user interface; human disease; innovation; insight; instrument; interest; protein function; repository; search engine; tool

ABSTRACT Proteoforms are the driving force of biological processes. Accurate identification, characterization, and quantitation of proteoforms is therefore essential for understanding protein roles in human disease. Top-down proteomics focuses on the direct analysis of proteoforms, providing the specificity needed to uncover the precise molecular participants in biological phenomena. The landscape of proteomics has been changing from digestion- based methods to intact protein analyses, with top-down proteomics gaining a foothold in important biomedical and pharmaceutical studies. Software solutions dedicated to targeted top-down proteomics are needed now more than ever to propel the next wave of innovation and top-down technology adoption. In this proposed research, Proteinaceous will develop further a new bioinformatic tool named Proteoform Finder to provide the mass spectrometry community with a proteoform-centric software solution for targeted top-down proteomics. Proteoform Finder will present proteoform data through proteoform family network diagrams. A proteoform funnel will be implemented in Proteoform Finder for importing proteoform families from discovery top-down search results or creating them through an intuitive graphical user interface. The nodes of the proteoform family network will represent individual proteoforms, with each proteoform linked to an underlying repository of characterization and quantitative data. Handling the data in this way will allow seamless comparisons across quantitative studies as well as merging of fragmentation maps and spectra to produce optimal characterization coverage of proteoforms. Proteoform Finder will have a robust quantitation pipeline for quantifying proteoforms-of-interest. In addition, characterization studies will be able to be carried out with any fragmentation data available. The quantitative engine in Proteoform Finder is comprised of an isotopic fitting algorithm that matches theoretical isotopic distributions based on proteoform chemical formulas to the experimental data. As opposed to “averagine”-based isotopic fitting methods, using the exact formula for the proteoform reduces deviations between theoretical and observed distributions, while also eliminating off-by-one errors often observed during protein analysis with non-targeted mass determination algorithms. Our characterization algorithms will present a high-end user experience for matching fragment ions to proteoforms, along with a host of fragmentation validation features. Altogether, Proteoform Finder will be a comprehensive targeted software for analyzing top- down mass spectrometry quantitation and characterization data that will assist researchers across pharma, academia, and clinical settings in making important proteoform discoveries.

抽象的 蛋白质形式是生物过程的准确识别、表征和分析的驱动力。 因此，蛋白质形式的定量对于自上而下了解蛋白质在人类疾病中的作用至关重要。 蛋白质组学侧重于蛋白质形式的直接分析，提供揭示精确蛋白质所需的特异性 生物现象中的分子参与者。蛋白质组学的格局已经从消化- 基于完整蛋白质分析的方法，自上而下的蛋白质组学在重要的生物医学领域获得立足点 现在需要专用于目标自上而下蛋白质组学的软件解决方案。 在此提议中，比以往任何时候都更能推动下一波创新和自上而下的技术采用。 Proteinaceous 将进一步开发一种名为 Proteoform Finder 的新生物信息学工具，以提供 质谱社区，提供以蛋白质形式为中心的软件解决方案，用于目标自上而下的蛋白质组学。 Proteoform Finder 将通过 proteoform 家族网络图呈现 proteoform 数据。 将在 Proteoform Finder 中实现，用于从自上而下的发现搜索中导入 proteoform 家族 结果或通过直观的图形用户界面创建它们 proteoform 家族网络的节点。 将代表单个蛋白质形式，每个蛋白质形式都与底层表征存储库相关联 以这种方式处理数据将允许定量研究之间的无缝比较。 以及合并碎片图和光谱以产生最佳的表征覆盖范围 Proteoforms.Proteoform Finder 将有一个强大的定量管道来量化感兴趣的蛋白质。 此外，可以利用任何可用的碎片数据进行表征研究。 Proteoform Finder 中的引擎由同位素拟合算法组成，该算法与理论值相匹配 基于蛋白质化学式与实验数据的同位素分布。 基于“averagine”的同位素拟合方法，使用蛋白质形式的精确公式减少偏差 理论分布和观察到的分布之间的差异，同时还消除了在过程中经常观察到的相差一误差 我们将介绍采用非目标质量测定算法的蛋白质分析。 将碎片离子与蛋白质形式相匹配以及大量碎片的高端用户体验 总而言之，Proteoform Finder 将是一个用于分析顶级的综合性目标软件。 质谱定量和表征数据将帮助制药行业的研究人员， 学术界和临床环境中做出重要的蛋白质组发现。