A fast SEQUEST cross correlation algorithm
A fast SEQUEST cross correlation algorithm
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DOI：
10.1021/pr800420s
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发表时间：
2008-10-01
影响因子：
4.4
通讯作者：
MacCoss, Michael J.
中科院分区：
文献类型：
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作者：
Eng, Jimmy K.;Fischer, Bernd;MacCoss, Michael J.
SEQUEST程序是第一个，并且仍然是最广泛使用的工具之一，用于将数据库中的肽序列分配给串联质谱图。交叉相关分数是在SEQUEST中实现的主要分数函数，正是该分数使该工具特别敏感。不幸的是，这个分数的计算成本很高，因此，为了使分数易于管理，SEQUEST使用不太敏感但速度较快的初始分数，并将交叉关联限制为仅由初步分数返回的前500个多肽。传统上，互相关分数是使用快速傅立叶变换(FFT)来计算的，以生成全相关函数。我们描述了一种计算互相关分数的替代方法，该方法不需要FFT，并且可以在一小部分时间内高效地计算。该快速计算允许通过互相关函数对所有候选肽进行评分，潜在地减轻了对初始分数的需要，并且使得能够基于对从序列数据库获得的所有候选肽序列计算的互相关分数分布来进行E值显著性计算。
The SEQUEST program was the first and remains one of the most widely used tools for assigning a peptide sequence within a database to a tandem mass spectrum. The cross correlation score is the primary score function implemented within SEQUEST and it is this score that makes the tool particularly sensitive. Unfortunately, this score is computationally expensive to calculate, and thus, to make the score manageable, SEQUEST uses a less sensitive but fast preliminary score and restricts the cross correlation to just the top 500 peptides returned by the preliminary score. Classically, the cross correlation score has been calculated using Fast Fourier Transforms (FFT) to generate the full correlation function. We describe an alternate method of calculating the cross correlation score that does not require FFTs and can be computed efficiently in a fraction of the time. The fast calculation allows all candidate peptides to be scored by the cross correlation function, potentially mitigating the need for the preliminary score, and enables an E-value significance calculation based on the cross correlation score distribution calculated on all candidate peptide sequences obtained from a sequence database.