Protein Identification Using Top-Down
Protein Identification Using Top-Down
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DOI：
10.1074/mcp.m111.008524
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发表时间：
2012-06-01
影响因子：
7
通讯作者：
Pevzner, Pavel A.
中科院分区：
文献类型：
--
作者：
Liu, Xiaowen;Sirotkin, Yakov;Pevzner, Pavel A.
在过去的两年中，由于蛋白质分离和质谱的进步，自上而下的质谱从分析单一蛋白质转向分析复杂样品，并识别数百甚至数千种蛋白质。然而，自上而下的光谱对蛋白质数据库的数据库搜索的计算工具仍处于起步阶段。我们描述了MS-Align+，一种基于光谱比对的自上而下蛋白质鉴定的快速算法，可以搜索意想不到的翻译后修饰。我们还提出了一种自上而下的蛋白质鉴定的统计学意义的评估方法，并进一步基准各种软件工具上的两个自上而下的数据集从酿酒酵母和鼠伤寒沙门氏菌。我们证明，MS-Align+显着增加了识别光谱的数量相比，MASCOT和OMSSA的两个数据集。尽管MS-Align+和ProSightPC在鼠伤寒沙门氏菌数据集上具有相似的性能，但MS-Align+在（更复杂的）酿酒酵母数据集上的性能优于ProSightPC。Molecular & Cellular Proteomics 11：10.1074/mcp. M111.008524，1-13，2012.
In the last two years, because of advances in protein separation and mass spectrometry, top-down mass spectrometry moved from analyzing single proteins to analyzing complex samples and identifying hundreds and even thousands of proteins. However, computational tools for database search of top-down spectra against protein databases are still in their infancy. We describe MS-Align+, a fast algorithm for top-down protein identification based on spectral alignment that enables searches for unexpected post-translational modifications. We also propose a method for evaluating statistical significance of top-down protein identifications and further benchmark various software tools on two top-down data sets from Saccharomyces cerevisiae and Salmonella typhimurium. We demonstrate that MS-Align+ significantly increases the number of identified spectra as compared with MASCOT and OMSSA on both data sets. Although MS-Align+ and ProSightPC have similar performance on the Salmonella typhimurium data set, MS-Align+ outperforms ProSightPC on the (more complex) Saccharomyces cerevisiae data set. Molecular & Cellular Proteomics 11: 10.1074/mcp.M111.008524, 1-13, 2012.