A comprehensive solution for native top down mass spectrometry data analyses across structural biology and biopharma

跨结构生物学和生物制药的原生自上而下质谱数据分析的综合解决方案

• 批准号: 10621751
• 负责人: Kenneth Durbin
• 金额: $ 79.67万
• 依托单位: PROTEINACEOUS, INC.
• 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 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10621751
• 关键词: 3-Dimensional; Address; Adopted; Algorithms; Amino Acid Sequence; Antibodies; Binding; Bioinformatics; Biological Process; Clinical; Clip; Complex; Computer software; Cryoelectron Microscopy; Data; Data Analyses; Databases; Dedications; Development; Disease; Dissociation; Electron Microscopy; Elements; Ensure; Family; Grant; Heterogeneity; Individual; Industry; Informatics; Intuition; Ions; Learning; Ligand Binding; Ligands; Maps; Mass Spectrum Analysis; Modification; Molecular Weight; Names; Pathway Analysis; Peptides; Pharmaceutical Preparations; Phase; Protein Complex Subunit; Protein Databases; Proteins; Research; Scientist; Side; Software Tools; Structural Biologist; Techniques; Technology; Therapeutic Studies; Time; Validation; Visualization; Work; X-Ray Crystallography; algorithm development; commercialization; complex data; drug development; experience; experimental study; high throughput analysis; improved; industry partner; insight; mass spectrometer; novel; pre-clinical; protein complex; protein structure; screening; search engine; small molecule; stoichiometry; structural biology; success; therapeutic development; therapeutic protein; tool

PROJECT SUMMARY Native top down mass spectrometry is continuing to evolve into a powerhouse analytical technique that can generate transformative data on the native state of proteoforms and protein complexes. Technological advances in mass spectrometers have spurred the rapid rise of nTDMS over recent years, paving impressive avenues for structural biology research and protein therapeutics development. For instance, new insights into non-covalent ligand binding and localization can be revealed by nTDMS data that are complementary to traditional structural biology approaches such as electron microscopy and NMR. Drug developers can apply nTDMS to study therapeutic proteins in preclinical and clinical settings to learn more about modifications that are present and the complexes being formed. The number of novel protein and protein complex drug molecules is ever increasing, each with a host of difficult analytical and data analysis challenges. On the bioinformatics side of nTDMS, strides have been made in algorithmic development for mass determination of large molecules; however, no fully featured analysis platform for nTDMS currently exists that also integrates search. Here, Proteinaceous is developing and commercializing a new software named ProSight Native to fill this analysis void. In Phase I of the development, a first-of-its-kind platform was introduced for analyzing targeted protein complex data from the classic nTDMS complex-down experiment. The platform offers deconvolution for intact complexes and their dissociated subunits, as well as search for subunit identification and a stoichiometry calculation for complex composition determination. For the Phase II grant, a host of new research will be undertaken to enable a comprehensive platform to be commercialized that features an improved deconvolution algorithm for native proteoforms, the first-ever nTDMS-specific high-throughput search, and robust quantitation workflows for biopharma applications. Major development effort will be spent here on new techniques for nTDMS searches of both proteoforms and complexes, including a multi-pronged approach for scoring automated stoichiometry assignments. Additionally, structural biology elements will be integrated alongside proteoform fragmentation data to bring these important components together and facilitate connections between the two. Lastly, the results will be displayed in an intuitive, structural biology-centric viewer that will make analysis approachable for mass spectrometrists and non-mass spectrometrist alike. In total, ProSight Native will aim to significantly advance nTDMS with these novel features, while also increasing accessibility to the powerful data that can be generated using nTDMS techniques.

项目摘要 本地自上而下的质谱法正在继续发展为一项强大的分析技术，可以 生成有关蛋白质和蛋白质复合物的天然状态的变革性数据。技术进步 在质谱仪中，近年来NTDM的迅速上升，铺平了令人印象深刻的途径 结构生物学研究与蛋白质治疗学的开发。例如，对非共价的新见解 NTDMS数据可以揭示配体的结合和定位，这些数据与传统结构互补 生物学方法，例如电子显微镜和NMR。药物开发人员可以应用NTDM进行研究 临床前和临床环境中的治疗蛋白，以了解有关存在的修改和 形成复合物。新型蛋白质和蛋白质复合药物分子的数量越来越多， 每个都有许多困难的分析和数据分析挑战。在NTDM的生物信息学方面，大步前进 已经在算法开发中进行了大分子的批量测定；但是，没有完全 当前存在的NTDM的特色分析平台也存在于集成搜索。在这里，蛋白质是 开发和商业化一个名为Prosight Nation的新软件来填充此分析无效。在第一阶段 引入了该开发的第一平台，用于分析来自 经典的NTDM复合体实验。该平台为完整的复合物提供了反卷积及其 分离的亚基，以及为复合物寻找亚基识别和化学计量计算 组成确定。对于第二阶段赠款，将进行大量新研究，以实现 全面的平台要商业化，该平台具有改进的原生的反卷积算法 蛋白质机构，有史以来第一个特定于NTDMS的高通量搜索和可靠的定量工作流程 生物制药应用。重大的开发工作将在这里花在NTDMS搜索的新技术上 蛋白质成型和复合物，包括用于评分自动化学计量法的多管制方法 作业。此外，结构生物学元素将与蛋白质成型碎片数据一起集成 将这些重要组成部分汇集在一起​​，并促进两者之间的连接。最后，结果将 以直观的，结构生物学的观众为中 光谱师和非质量光谱师。总体而言，Prosight本地人将旨在显着促进 NTDM具有这些新颖的功能，同时还可以增加对可以生成的强大数据的可访问性 使用NTDMS技术。

项目成果

Advancing Intact Protein Quantitation with Updated Deconvolution Routines.

通过更新的解卷积程序推进完整蛋白质定量。

• DOI: 10.1021/acs.analchem.3c02345
• 发表时间: 2023
• 期刊: Analytical chemistry
• 影响因子: 7.4
• 作者: Robey,MatthewT;Utley,Daisha;Greer,JosephB;Fellers,RyanT;Kelleher,NeilL;Durbin,KennethR
• 通讯作者: Durbin,KennethR