What constitutes a good “hit” from a SEQUEST search?
(from http://www.enovatia.com/stories/storyReader$64) DelCn is the Delta Correlation value. When you are viewing the summary page, DelCn tells you how different the first hit is from the second hit in your search results. A general rule of thumb is that a DelCn of 0.1 or greater is good. If you are searching a large database (nr.fasta or owl.fasta) you may find that your DelCn values are smaller than those obtained by searching a small database. This is due to the fact that the chance of sequence similarity is higher in the larger databases. Sp is the preliminary score. SEQUEST performs two types of scoring. After finding all peptides that match within your mass tolerance, SEQUEST does a preliminary scoring of these candidates to weed the list down to 500 for the final correlation analysis. The scoring is based on the number of ions in the MS/MS spectrum that match with the experimental data. The higher the value of Sp the better. A good value is 200 and above. One thing to note is tha
