Database search algorithm for identification of intact cross-links in proteins and peptides using tandem mass spectrometry.
Database search algorithm for identification of intact cross-links in proteins and peptides using tandem mass spectrometry.
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DOI：
10.1021/pr100369y
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发表时间：
2010-07-02
影响因子：
4.4
通讯作者：
Freitas MA
中科院分区：
文献类型：
--
作者：
Xu H;Hsu PH;Zhang L;Tsai MD;Freitas MA
开发了一种新的数据库搜索算法，用于从串联质谱数据中识别蛋白质和肽中的完整交联。使用该算法，可以高置信度地识别和表征蛋白质和肽中的完整交联。该算法使用 BS3（双[磺基琥珀酰亚胺基]辛二酸酯）交联细胞色素 C 进行测试。通过在优化实验条件下与其三维结构进行比较，识别并验证了五个交联的空间合理性。真阳性和假阳性的统计分数分布以及接收者操作特征分析表明该算法能够区分真阳性交联肽谱匹配和假阳性交联肽谱匹配。还证明了 MassMatrix 数据库搜索引擎能够在 BS3 交联的复杂大肠杆菌蛋白质组样本中搜索完整的交联。 MassMatrix 中的新算法为从串联质谱数据中发现蛋白质和肽中的交联提供了另一种方法。
A new database search algorithm has been developed for identification of intact cross-links in proteins and peptides from tandem mass spectrometric data. Using this algorithm, intact cross-links can be identified and characterized in proteins and peptides with high confidence. The algorithm was tested using BS3 (bis[sulfosuccinimidyl] suberate) cross-linked Cytochrome C. Five cross-links were identified and verified for spatial plausibility by comparison with its three-dimensional structure at optimized experimental conditions. The distributions of statistical scores for true and false positives and receiver operating characteristic analysis indicate that the algorithm is capable of discriminating true positive cross-linked peptide-spectrum matches from false ones. It has also been demonstrated that the MassMatrix database search engine is capable of searching for intact cross-links in complex Escherichia coli proteome samples cross-linked by BS3. The new algorithm in MassMatrix offers an additional approach for the discovery of cross-links in proteins and peptides from tandem mass spectrometric data.
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影响因子：
48
作者：
Rinner, Oliver;Seebacher, Jan;Aebersold, Ruedi
通讯作者：
Aebersold, Ruedi
影响因子：
3.4
作者：
Xu, Hua;Wang, Liwen;Freitas, Michael A.
通讯作者：
Freitas, Michael A.
影响因子：
5.6
作者：
BUSHNELL, GW;LOUIE, GV;BRAYER, GD
通讯作者：
BRAYER, GD
影响因子：
4.4
作者：
Xu, Hua;Zhang, Liwen;Freitas, Michael A.
通讯作者：
Freitas, Michael A.
影响因子：
2.3
作者：
Sinz, A
通讯作者：
Sinz, A