Valens: A Mass Spectrometry-Based Antibody Sequencing Tool by Digital Proteomics

Valens：数字蛋白质组学基于质谱的抗体测序工具

• 批准号: 8474794
• 负责人: Natalie Castellana
• 金额: $ 23.87万
• 依托单位: DIGITAL PROTEOMICS LLC
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-06-01 至 2014-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8474794
• 关键词: Algorithms; Amino Acid Sequence; Amino Acid Sequence Databases; Antibodies; Antibody Therapy; Attention; B-Lymphocytes; Base Sequence; Binding; California; Cell Line; Cells; Client; Clinic; Clinical; Collaborations; Complementary DNA; Computer software; Computers; Computing Methodologies; DNA Sequence; DNA Sequence Rearrangement; Data; Databases; Development; Diagnostic; Diagnostic Procedure; Digestion; Engineering; Enzymes; Equipment; Exhibits; Future; Genes; Genomics; Hour; Housing; Immunogenetics; Ions; Laboratories; Licensing; Marketing; Mass Spectrum Analysis; Methods; Monoclonal Antibodies; Peptide Fragments; Peptide Sequence Determination; Peptides; Pharmacologic Substance; Process; Protein Chemistry; Protein Databases; Proteins; Proteome; Proteomics; Quality Control; Reading; Research; Resources; Running; Sampling; Services; Shotguns; Side; Source; Specificity; Structure; Techniques; Therapeutic; Therapeutic Agents; Therapeutic antibodies; Time; Translations; Universities; antibody engineering; base; comparative; computing resources; digital; drug market; flexibility; genome sequencing; graphical user interface; improved; innovation; next generation; novel; preference; protein expression; research study; tool; tool development

DESCRIPTION (provided by applicant): Monoclonal antibodies exhibit high specificity for target molecules and for that reason have been successfully utilized as therapeutic and diagnostic agents. The sequence of amino acids comprising the primary structure of an antibody is largely responsible for its binding preference and efficacy. Therefore, antibody sequencing is a central requirement for the development of novel antibody therapies. We propose a method of performing antibody sequencing directly from the protein sequence, without requiring the source cell, which makes it practical for many lab and clinical settings. In addition, our proposed computational method is fully automated, and will increase throughput by dramatically reducing the time required for sequencing from weeks to hours. We plan to implement our method in both a stand-alone tool that may be run on a single desktop computer, or make use of the vast resources available in cloud computing. We will also provide an in-house sequencing service for users without access to the mass spectrometry equipment or computing resources.

描述（由申请人提供）：单克隆抗体对靶分子具有高度特异性，因此已成功用作治疗和诊断试剂。构成抗体一级结构的氨基酸序列在很大程度上决定了其结合偏好和效力。因此，抗体测序是开发新型抗体疗法的核心要求。我们提出了一种直接从蛋白质序列进行抗体测序的方法，而不需要源细胞，这使得它适用于许多实验室和临床环境。此外，我们提出的计算方法是完全自动化的，并且将通过将测序所需的时间从数周减少到数小时来增加通量。 我们计划在一个可以在单个桌面计算机上运行的独立工具中实现我们的方法，或者利用云计算中可用的大量资源。我们还将为无法访问质谱设备或计算资源的用户提供内部测序服务。