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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.
Eng et al. (Sat,) studied this question.