Influence of Peptide Structure on Dissociation

蛋白质在生物体中起着核心作用，例如作为酶。 催化代谢反应，作为结构或机械单位，以及作为细胞信号 分子。蛋白质组学领域，这需要大规模的鉴定和结构 蛋白质的表征在很大程度上依赖于串联质谱仪(MS/MS) 以及利用MS/MS光谱进行数据库搜索。这件事的首要目标是 建议通过串联质谱法改进多肽和蛋白质的自动化鉴定 光谱分析。拟议的研究将确定和全面描述 两种主要互补激活的多肽的碎裂行为簇 MS/MS活化方法、电子转移解离(ETD)和碰撞- 激活解离(CAD)，当两者都应用于两个突出的仪器时 用于蛋白质组学实验的平台(线性离子陷阱和四极飞行时间， QTOF)。指导这项研究的基本假设是，计算机算法 用于多肽和蛋白质的测序、鉴定和定量，以及 嵌入式数据采集软件，可以通过统计分析如何改进 多肽在分子水平上发生片断。对差异行为的先验知识 氨基酸为观察到的可能碎片模式提供了重要的洞察力 MS/MS谱图和这些数据将用于改进数据采集和数据 分析。这项研究汇集了三个研究小组，Wysocki小组和 在多肽裂解机制和数据挖掘方面的专业知识，曾小组与 生物统计/生物信息学方面的专业知识(执行分类和分类 大型光谱数据集的回归树分析)，以及Coon小组， 线性离子陷阱/轨道捕捉质谱仪中的电子转移解离(ETD)

Proteins play a central role in living organisms, serving, for example, as enzymes that catalyze metabolic reactions, as structural or mechanical units, and as cell signaling molecules. The field of proteomics, which entails large scale identification and structural characterization of proteins, depends strongly on tandem mass spectrometry (MS/MS) and database searches that make use of MS/MS spectra. The overarching goal of this proposal is to improve automated peptide and protein identification by tandem mass spectrometry. The proposed research will identify and comprehensively characterize clusters of fragmentation behavior for peptides activated by two major complementary MS/MS activation methods, electron transfer dissociation (ETD) and collisionally- activated dissociation (CAD), when both are applied in two prominent instrument platforms used for proteomics experiments (linear ion trap and quadrupole time-of-flight, QTOF). The underlying hypothesis guiding this research is that the computer algorithms that are used for peptide and protein sequencing, identification, and quantitation, and the embedded data acquisition software, can be improved by statistically analyzing how peptides fragment at a molecular level. A priori knowledge of the behavior of differenct amino acids provides significant insight into the possible fragmentation patterns observed and the MS/MS spectra and these data will be used to improve data acquisition and data analysis. This research brings together three research groups, the Wysocki group with expertise in peptide fragmentation mechanisms and data mining, the Tseng group with expertise in biostatistics/ bioinformatics( to perform clustering plus classification and regression tree analysis of large spectral datasets), and the Coon group, developers of electron transfer dissociation (ETD) in the linear ion trap/Orbitrap mass spectrometer.