Comprehensive Database System for Modern MALDI- TOF and TOF-TOF MS and MS-MS

描述（由申请人提供）：我们的研究重点是开发集成系统，为真正的全球生物系统分析提供所需的分析工具。该方法通过使用准直孔结构（CHS）和单片支撑的新型三维样品板，将多维分离耦合到高性能MALDI TOF质谱仪上，作为采用电喷雾电离的LC-MS-MS系统的替代方案。近年来，采用电喷雾电离和纳米流液相色谱的高性能离子阱质谱仪的发展显著提高了分析生物样品的能力，但这种技术在动态范围和速度上存在严重的固有局限性。MALDI的早期应用受到现有TOF仪器相对较低的分辨率和质量精度的限制，并且缺乏与液相色谱的通用接口。我们最近的工作已经克服了这些限制，现在可以使用具有高容量分离接口的高性能MALDI-TOF和TOF-TOF仪器。这些仪器提供的速度、分辨率、动态范围和灵敏度数量级优于市售仪器的性能。这些仪器和接口提供了生物样本全局分析所需的性能，但该项目中提出的数据库和生物信息学工具对于将大量数据转换为有用信息至关重要。虽然全球蛋白质组学显然比人类基因组测序更具挑战性，但在这个项目和相关项目中开发的技术将为蛋白质组学类似于人类基因组计划的重大进展提供所需的工具。剩下的主要挑战是如何将这些仪器无法产生的大量数据转化为可随时用于解决生物学问题的信息。这是拟议项目的重点。

DESCRIPTION (provided by applicant): Our research is focused on developing integrated systems that provide analytical tools needed for truly global analyses of biological systems. The approach employs multi-dimensional separations coupled to high- performance MALDI TOF mass spectrometers via new three-dimensional sample plates using collimated hole structures (CHS) and monolithic supports as an alternative to established LC-MS-MS systems employing electrospray ionization. Recent advances in high performance ion trap mass spectrometers employing electrospray ionization and nanoflow liquid chromatography have significantly improved capabilities for analyzing biological samples, but this technology has serious inherent limitations on dynamic range and speed. Early applications of MALDI were limited by relatively low resolving power and mass accuracy of available TOF instruments, and the lack of a commonly available interface with liquid chromatography. Our recent work has overcome these limitations and high performance MALDI-TOF and TOF-TOF instruments interfaced with high capacity separations are now available. These instruments provide speed, resolution, dynamic range, and sensitivity orders of magnitude superior to the performance of commercially available instruments. These instruments and interfaces provide the performance required for global analysis of biological samples, but the database and bioinformatics tools proposed for development in this project are essential for converting this massive volume of data to useful information. Although global proteomics is clearly much more challenging than sequencing the human genome, the technology developed in this and related projects will provide the tools required for significant progress in the proteomics analog to the human genome project. The major remaining challenge involves converting the massive volume of data than can be produced by these instruments into information that can be readily used to address biological problems. This is the focus of the proposed project. PUBLIC HEALTH RELEVANCE: Major initiatives by The Human Proteome Organization are focused on plasma, liver, and brain proteomics. The premise of these initiatives is that "A comprehensive, systematic characterization of circulating proteins in health and disease will greatly facilitate development of biomarkers for prevention, diagnosis, and therapy of cancer and other diseases." This project will demonstrate that the technology described in this proposal provides a feasible route to achieving the goals of these initiatives.