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 蛋白质成型是生物过程的驱动力。准确的识别，表征和 因此，蛋白质的定量对于理解人类疾病中的蛋白质作用至关重要。自顶向下 蛋白质组学侧重于直接分析蛋白质成型，提供了揭示精度所需的特异性 生物学现象中的分子参与者。蛋白质组学的景观一直从消化中发生变化 - 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中获得立足点 和药物研究。现在需要专门针对有针对性的自上而下蛋白质组学的软件解决方案 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。在此提议中 研究，蛋白质将进一步开发一种名为Proteoform Finder的新生物信息学工具，以提供 质谱社区具有针对靶向自上而下蛋白质组学的蛋白基础软件解决方案。 蛋白质相结合器将通过蛋白质成型型家族网络图呈现蛋白质成型数据。一个蛋白质型漏斗 将在发现自上而下的搜索中以蛋白质生成型搜索来实施用于进口蛋白质成型的家族 结果或通过直观的图形用户界面创建它们。蛋白质成型家族网络的节点 将代表单个蛋白质成型，每种蛋白质成型型都与基础表征库相连 和定量数据。以这种方式处理数据将允许在定量研究中进行无缝比较 以及碎片图和光谱的合并，以产生最佳的表征覆盖范围 蛋白质成型。蛋白质相结合器将具有可靠的定量管道，用于量化利益蛋白质成型。在 此外，表征研究将可以使用任何可用的碎片数据进行。这 蛋白质相构造中的定量发动机已完成与理论匹配的同位素拟合算法 基于蛋白质成型化学公式的同位素分布到实验数据。而不是 基于“平均”基于同位素拟合方法，使用蛋白质成型的确切公式减少了出发 在理论和观察到的分布之间，同时也消除了经常在 蛋白质分析具有非靶向质量测定算法。我们的特征算法将存在 将片段离子与蛋白质成型相匹配的高端用户体验，以及许多片段 验证功能。总体而言，蛋白质生化合型将是一个全面的针对性软件，用于分析顶部 质谱定量和表征数据下降，这些数据将有助于跨药物的研究人员 学术界和临床环境在做出重要的蛋白质形成型中。