Real time optimization of electron-based fragmentation for middle and top-down proteomics in mass spectrometry

质谱中中自上而下蛋白质组学基于电子的碎片实时优化

• 批准号: 10081127
• 负责人: Valery G. Voinov
• 金额: $ 21.28万
• 依托单位: E-MSION, INC.
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-07-01 至 2021-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10081127
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The identification and quantification of biological macromolecules remains challenging despite major advances in the speed, resolution and mass accuracy of modern mass spectrometers. A key weakness with current instrumentation lies in the methods used to induce fragmentation. The reliance in particular on collision-induced dissociation (CID) has limited such analyses to bottom-up workflows of trypsin-digested peptides of 10-30 residues. At e-MSion, we have developed an efficient electron-fragmentation technology called ExD for large proteins and are now co-marketed our ExD Option with Agilent, and soon will be with Thermo and Waters instruments. What has really captured the interest of the biopharma and top-down communities in the past year is the exceptional sequence coverage of native proteins we obtain with the same ExD cell. The resulting spectra are less congested than those obtained with currently available ETD/UVPD/CID fragmentation methodologies. We have shown that our technology works faster and gives cleaner spectra with more complete dissociation with larger macromolecular protein complexes than has ever been possible before, while still preserving labile post translational modifications. In addition, fragmentation with higher energy electrons can be used to provide complementary data to improve protein and glycan identification. The challenge now has become how to optimally collect and process these data to maximize the utility of ExD fragmentation. Last summer, Xilinx released its Versal Adaptive Compute Acceleration Platform (ACAP), a massively parallel processor with 50 billion transistors targeted to transform digital signal processing, handling of big data and artificial intelligence. This ACAP technology has already accelerated Illumina DNA sequence assembly by 90-fold. Our feasibility question asks how to effectively harness this new highly parallelized technology to preprocess complex top-down mass spectra on- the-fly. This will allow us to actively optimize data acquisition by enabling adaptive operation of the ExD cell and mass spectrometer. The objective is to maximize both fragmentation and dissociation of native proteins, enabling faster and comprehensive characterization of challenging proteoforms important to the biopharmaceutical industry and biomedical researchers. Success will offer an extremely fast, cost-effective solution to characterize complexes of macromolecules under native conditions with increased accuracy, speed, and fewer misidentifications. Our ExD technology with the Versal ACAP can be both retrofitted into existing mass spectrometers as well as being available in new generations of mass spectrometers at a price below other less-effective alternative fragmentation technologies like ETD and UVPD. Thus, it will provide new abilities for many NIH investigators to advance basic research, probe disease mechanisms and permit more sophisticated searches for both diagnostic and therapeutic biomarkers.

尽管很重要，但生物大分子的识别和量化仍然具有挑 现代质谱仪的速度，分辨率和质量准确性的进步。一个关键的弱点 当前的仪器在于用于诱导碎片化的方法。特别依赖 碰撞引起的解离（CID）的这种分析限制在胰蛋白酶消化的自下而上的工作流程 10-30种残基的肽。在E-MSION，我们开发了一种有效的电子碎片技术 称为大蛋白的EXD，现在已与Agilent共同营销我们的EXD选项，很快就会与 温暖和沃特仪器。真正吸引了生物制药和自上而下的兴趣 过去一年中的社区是我们以相同的方式获得的本机蛋白质的特殊顺序覆盖范围 EXD细胞。所得的光谱比当前可用的光谱不那么拥挤 ETD/UVPD/CID碎片方法。我们已经表明，我们的技术工作速度更快，并提供 更清洁的光谱与更大的大分子蛋白复合物更完整地分离 以前有可能，同时仍保留不稳定的翻译后修改。此外， 用较高能量电子的碎片可用于提供互补数据以改善蛋白质 和聚糖识别。现在的挑战已成为如何最佳地收集和处理这些数据到 最大化EXD碎片的实用性。去年夏天，Xilinx发布了其广泛的自适应计算 加速平台（ACAP），这是一个大规模并行处理器，针对500亿个晶体管 改变数字信号处理，处理大数据和人工智能。这种ACAP技术有 已经加速了Illumina DNA序列组装90倍。我们的可行性问题询问如何 有效利用这项新的高度平行技术来预处理复杂的自上而下的质谱 - 飞翔。这将使我们能够通过启用EXD单元格的自适应操作来积极优化数据获取 和质谱仪。目的是最大化天然蛋白的破碎和解离， 使具有挑战性的蛋白质类型对重要的蛋白质形成率提高和全面表征 生物制药行业和生物医学研究人员。 成功将提供一个非常快速，具有成本效益的解决方案，以表征 在天然条件下的大分子的准确性，速度和较少的错误识别。我们的 具有VERSAL ACAP的EXD技术既可以改装为现有的质谱仪，又可以进行 以新一代的质谱仪以低于其他效率低的替代方案的价格购买 ETD和UVPD等破碎技术。因此，它将为许多NIH提供新的能力 调查人员进步基础研究，探测疾病机制并允许更复杂的搜索 用于诊断和治疗生物标志物。