Characterization and diagnostic value of amino acid side chain neutral losses following electron-transfer dissociation.
Characterization and diagnostic value of amino acid side chain neutral losses following electron-transfer dissociation.
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DOI：
10.1007/s13361-010-0029-0
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发表时间：
2011-02
影响因子：
3.2
通讯作者：
Coon, Joshua J.
中科院分区：
文献类型：
--
作者：
Xia, Qiangwei;Lee, M. Violet;Rose, Christopher M.;Marsh, Alyce J.;Hubler, Shane L.;Wenger, Craig D.;Coon, Joshua J.
关键词：
使用大量高质量精度和分辨率的 ETD 串联质谱，我们表征了 ETD 引起的中性损失。根据这些数据，我们推导出其中 20 种损失的化学式。其中许多先前已在电子捕获解离（ECD）光谱中观察到，例如精氨酸、天冬氨酸、谷氨酸、谷氨酰胺、天冬酰胺、亮氨酸、组氨酸和脲甲基化半胱氨酸残基侧链的丢失。有了这些信息，我们检查了这些氨基酸特异性损失的诊断价值。在 1285 个肽谱匹配中，92.5% 的中性丢失衍生肽氨基酸组成与肽序列一致。此外，我们表明，仅使用基于中性损失的准确前体质量和氨基酸组成就可以唯一地识别肽；通过添加侧链丢失信息，精确质量查询中候选序列的中位数从 21 减少到 8。除了增加肽鉴定的信心外，我们的研究结果表明，ETD 谱中的这些诊断损失可能会用于改善错误发现率估计并增强数据库搜索算法中评分函数的性能。
Using a large set of high mass accuracy and resolution ETD tandem mass spectra, we characterized ETD-induced neutral losses. From these data we deduced the chemical formula for 20 of these losses. Many of them have been previously observed in electron-capture dissociation (ECD) spectra, such as losses of the side chains of arginine, aspartic acid, glutamic acid, glutamine, asparagine, leucine, histidine, and carbamidomethylated cysteine residues. With this information, we examined the diagnostic value of these amino acid-specific losses. Among 1285 peptide–spectrum matches, 92.5% have agreement between neutral loss-derived peptide amino acid composition and the peptide sequences. Moreover, we show that peptides can be uniquely identified by using only the accurate precursor mass and amino acid composition based on neutral losses; the median number of sequence candidates from an accurate mass query is reduced from 21 to 8 by adding side chain loss information. Besides increasing confidence in peptide identification, our findings suggest the potential use of these diagnostic losses in ETD spectra to improve false discovery rate estimation and to enhance the performance of scoring functions in database search algorithms.
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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.
DOI：
10.1073/pnas.0607084104
发表时间：
2007-02-13
影响因子：
11.1
作者：
Chi, An;Huttenhower, Curtis;Hunt, Donald F.
通讯作者：
Hunt, Donald F.
影响因子：
7.4
作者：
Kjeldsen, F;Haselmann, KF;Zubarev, RA
通讯作者：
Zubarev, RA
影响因子：
8
作者：
Cournoyer, JJ;Pittman, JL;O'Connor, PB
通讯作者：
O'Connor, PB
DOI：
10.1073/pnas.83.17.6233
发表时间：
1986-09-01
影响因子：
11.1
作者：
HUNT, DF;YATES, JR;HAUER, CR
通讯作者：
HAUER, CR