Integrated tools for higher order structure determination by cross-link analysis

总结 质谱法（MS）用于定量蛋白质表征的使用已经增加 戏剧性地;识别和定量成千上万的蛋白质不再是一项英雄任务， 详细描述治疗性蛋白质。由于广泛使用的软件， 光谱测定法已成为常规并广泛用于解决基础生物学中的问题， 转化医学和药物开发。MS方法现在准备有类似的 对蛋白质相互作用和高级结构（HOS）研究的影响 保持战略定力 特别是交联质谱，它获得了距离和可及性 限制从两端的化学修饰，正在成为一个强大的工具，地图 蛋白质相互作用界面近年来，交联技术有了很大的改进， 质谱分析法来然而，尽管有这些进步，交联分析还不是一种技术， 由于一系列问题，如低丰度的 交联肽，专利试剂的不可用，需要不同的搜索 采用特定交联剂的算法，以及可靠表征的困难 交联肽谱。 为了缓解这些问题并使交联的使用大众化，我们建议开发 标准化和有效的交联方法， 搜索算法，整合到我们完善的Byonic搜索引擎中。我们的算法 将支持几乎所有市售的交联化学和大多数主要的肽 裂解方法（ETD，CAD/HCD，EthcD），以及可裂解和不可裂解 交联剂。该软件的普遍适用性和易用性将促进快速 在学术研究和生物制药中采用交联质谱 发展

Summary The use of mass spectrometry (MS) for quantitative protein characterization has increased dramatically; identifying and quantifying thousands of proteins is no longer a heroic task nor is characterizing therapeutic proteins in detail. Due to widely available software, quantitative mass spectrometry has become routine and widely used for addressing questions in basic biology, translational medicine and drug development. MS Methods are now poised to have similar impact on the study of protein-protein interaction and higher order structure (HOS) determination. In particular, crosslinking mass spectrometry, which obtains distance and accessibility constraints from two-ended chemical modifications, is emerging as a powerful tool to map protein-protein interaction interfaces. Recent years have seen large improvements in crosslink mass spectrometry. Yet despite these advances, crosslink analysis is not yet a technique that has found widespread use, due to a range of problems such as the low abundance of crosslinked peptides, unavailability of proprietary reagents, the need for different search algorithms adopted to specific cross-linkers, and the difficulty of reliably characterizing crosslinked peptide spectra. To alleviate these problems and democratize the use of crosslinking, we propose to develop standardized and effective methods for crosslinking in conjunction with sensitive and accurate search algorithms, incorporated into our well-established Byonic search engine. Our algorithms will support almost all commercially available crosslinking chemistries and most major peptide fragmentation methods (ETD, CAD/HCD, EthcD), as well as cleavable and non-cleavable crosslinkers. The near universal applicability and ease-of-use of the software will promote rapid adoption of crosslinking mass spectrometry in academic research and biopharmaceutical development.