Data Processing Algorithms for Analysis of High Resolution MSMS Spectra of Peptides with Complex Patterns of Posttranslational Modifications
Data Processing Algorithms for Analysis of High Resolution MSMS Spectra of Peptides with Complex Patterns of Posttranslational Modifications
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DOI：
10.1074/mcp.m900431-mcp200
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发表时间：
2010-05-01
影响因子：
7
通讯作者：
Burlingame, Alma L.
中科院分区：
文献类型：
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作者：
Guan, Shenheng;Burlingame, Alma L.
电子捕获解离（ECD）和电子转移解离（ETD）等高效片段化方法的出现为大量共价修饰的大肽和小蛋白（如完整组蛋白）的详细结构表征提供了机会。即使采用有效的气相离子分离，从而选择单个分子前体离子，重度修饰肽的MSMS光谱也可能揭示存在具有相同氨基酸序列和相同翻译后修饰（PTM）部分总数（相同PTM组成）但具有不同PTM构型或位点特异性占据异构体的肽的混合物。目前可用的数据分析方法依赖于分离同位素程序，当光谱（碎裂模式）包含许多重叠的同位素分布时，分离同位素程序变得不那么有效。肽数据库搜索引擎只能识别这种混合物中最丰富的PTM构型（不同残基上的PTM排列）。为了确定所有的PTM配置存在于这些混合物中，并估计其相对丰度，我们扩展了我们的碎片分配的视觉辅助程序搜索代表所有可能的配置的离子，受到总PTM组合物的约束。这导致在识别的PTM配置支持的独特的碎片离子，和他们的相对丰度估计通过使用非负最小二乘法程序。Molecular & Cellular Proteomics 9：804-810，2010.
The emergence of efficient fragmentation methods such as electron capture dissociation (ECD) and electron transfer dissociation (ETD) provides the opportunity for detailed structural characterization of heavily covalently modified large peptides and small proteins such as intact histones. Even with effective gas phase ion isolation so that a single molecular precursor ion is selected, the MSMS spectrum of a heavily modified peptide may reveal the presence of a mixture of peptides with the same amino acid sequence and the same total number of posttranslational modification (PTM) moieties (same PTM composition) but with different PTM configurations or site-specific occupancy isoforms. Currently available data analysis methods depend on a deisotoping procedure, which becomes less effective when spectra (fragmentation patterns) contain many overlapping isotopic distributions. Peptide database search engines can only identify the most abundant PTM configuration (PTM arrangement on different residues) in such mixtures. To identify all the PTM configurations present in these mixtures and to estimate their relative abundances, we extended our fragment assignment by visual assistance program to search for ions representing all possible configurations, subjected to the total PTM composition constraint. This resulted in the identification of PTM configurations supported by unique fragment ions, and their relative abundances were estimated by use of a non-negative least squares procedure. Molecular & Cellular Proteomics 9:804-810, 2010.