Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets.
Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets.
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DOI：
10.1002/pmic.200900567
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发表时间：
2010-03
期刊：
影响因子：
3.4
通讯作者：
Aebersold, Ruedi
中科院分区：
文献类型：
--
作者：
Deutsch, Eric W.;Shteynberg, David;Lam, Henry;Sun, Zhi;Eng, Jimmy K.;Carapito, Christine;von Haller, Priska D.;Tasman, Natalie;Mendoza, Luis;Farrah, Terry;Aebersold, Ruedi
电子转移解离 (ETD) 是碰撞诱导解离 (CID) 的替代碎裂技术，最近已商业化。 ETD 与 CID 相比有几个优点。它不太容易断裂氨基酸侧链，尤其是那些经过修饰的氨基酸侧链，从而产生具有更均匀峰强度的碎片离子光谱。此外，可以裂解和鉴定较长肽和较高电荷态的前体离子。然而，ETD 光谱分析有一些重要的差异，需要优化用于 CID 数据分析的软件包，或开发专用工具。我们采用了跨蛋白质组管道 (TPP) 来处理 ETD 数据。具体来说，我们增加了对来自高电荷前体的碎片离子光谱的支持、与电荷状态估计算法的兼容性、使用 Lys-C 蛋白酶的规定、ETD 光谱库构建功能以及更新数据格式以区分 CID 和 ETD 光谱。我们展示了处理来自几种不同类型的 ETD 仪器的数据集的结果，并证明了 ETD 增强型 TPP 的应用可以将固定错误发现率下的频谱识别数量比单个序列搜索引擎的本机输出提高多达 100%。
Electron transfer dissociation (ETD) is an alternative fragmentation technique to collision induced dissociation (CID) that has recently become commercially available. ETD has several advantages over CID. It is less prone to fragmenting amino acid side chains, especially those that are modified, thus yielding fragment ion spectra with more uniform peak intensities. Further, precursor ions of longer peptides and higher charge states can be fragmented and identified. However, analysis of ETD spectra has a few important differences that require the optimization of the software packages used for the analysis of CID data, or the development of specialized tools. We have adapted the Trans-Proteomic Pipeline (TPP) to process ETD data. Specifically, we have added support for fragment ion spectra from high charge precursors, compatibility with charge-state estimation algorithms, provisions for the use of the Lys-C protease, capabilities for ETD spectrum library building, and updates to the data formats to differentiate CID and ETD spectra. We show the results of processing datasets from several different types of ETD instruments and demonstrate that application of the ETD-enhanced TPP can increase the number of spectrum identifications at a fixed false discovery rate by as much as 100% over native output from a single sequence search engine.
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影响因子：
3.4
作者：
Deutsch, Eric W.;Mendoza, Luis;Shteynberg, David;Farrah, Terry;Lam, Henry;Tasman, Natalie;Sun, Zhi;Nilsson, Erik;Pratt, Brian;Prazen, Bryan;Eng, Jimmy K.;Martin, Daniel B.;Nesvizhskii, Alexey I.;Aebersold, Ruedi
通讯作者：
Aebersold, Ruedi
影响因子：
4.4
作者：
McAlister, Graeme C.;Berggren, W. Travis;Griep-Raming, Jens;Horning, Stevan;Makarov, Alexander;Phanstiel, Doug;Stafford, George;Swaney, Danielle L.;Syka, John E. P.;Zabrouskov, Vlad;Coon, Joshua J.
通讯作者：
Coon, Joshua J.
影响因子：
4.4
作者：
Domon, Bruno;Bodenmiller, Bernd;Aebersold, Ruedi
通讯作者：
Aebersold, Ruedi
影响因子：
3.4
作者：
Deutsch, Eric
通讯作者：
Deutsch, Eric
影响因子：
7.4
作者：
Nesvizhskii, AI;Keller, A;Aebersold, R
通讯作者：
Aebersold, R