Abstract：
: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.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Eng JK,Fischer B,Grossmann J,Maccoss MJdoi
10.1021/pr800420ssubject
Has Abstractpub_date
2008-10-01 00:00:00pages
4598-602issue
10eissn
1535-3893issn
1535-3907journal_volume
7pub_type
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