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.

摘要 蛋白形式是生物过程的驱动力。准确识别、表征和 因此，蛋白质型的定量对于理解蛋白质在人类疾病中的作用至关重要。顶向下 蛋白质组学侧重于蛋白质的直接分析，提供所需的特异性，以揭示精确的蛋白质组学。 参与生物现象的分子。蛋白质组学的前景已经从消化- 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站稳脚跟。 和药物研究。现在需要专门针对自上而下的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。在此提出的 Proteinaceous将进一步开发一种名为Proteoform的新生物信息学工具， 质谱社区与proteoform为中心的软件解决方案，有针对性的自上而下的蛋白质组学。 Proteoform将通过Proteoform家族网络图呈现Proteoform数据。一种蛋白质漏斗 将在Proteoform中实施，用于从发现自顶向下搜索导入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 将代表单独的蛋白质组，每个蛋白质组都与一个基本的特征库相关联 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 蛋白质型Proteoform将拥有一个强大的定量管道，用于定量感兴趣的蛋白质。在 此外，将能够利用任何现有的碎裂数据进行表征研究。的 Proteoform中的定量引擎由同位素拟合算法组成，该算法与理论上的 同位素分布的基础上proteoform化学公式的实验数据。而不是 “averagine”为基础的同位素拟合方法，使用精确的公式为proteoform减少偏差 理论分布和观测分布之间的差异，同时还消除了 使用非靶向质量测定算法进行蛋白质分析。我们的表征算法将呈现 高端用户体验，可将碎片离子与蛋白质形态匹配，沿着大量碎片化 验证功能。总而言之，Proteoform将是一个全面的有针对性的软件，用于分析顶部， 下质谱定量和表征数据，这将有助于研究人员在制药， 在学术界和临床环境中进行重要的蛋白质型发现。