Each identified peptide has a delta score (DScore), which is a measure of the difference between the top two scores for the peptides identified by that spectrum. The application calculates this score as follows:
The application displays the delta score only for rank 1 peptides. For peptides with ranks greater than 1, the Delta Score column is blank.
The application always calculates the delta score from the score specified as the “main score” of a search engine. The following table shows how the application defines the main score for the different search engines. The application compares the scores according to the precision with which it displays them. This means that it considers two Ions Score values displayed for a Mascot search to be equal to two XCorr values displayed for a Sequest HT search when the displayed score value is the same.
Search engine | Main score | Precision (digits) |
|---|---|---|
Mascot | Ions Score | 0 (integer) |
Sequest HT | XCorr | 2 |
The application handles two special cases:
- The peptide that is ranked 1 has the same score as the peptide that is ranked 2, and both have the same sequence. In this case, the two peptides differ by their modification state. The search engine used cannot score them differently, so the ordering of these two peptides as rank 1 and rank 2 is only by chance. You can apply the calculation described in the first paragraph of this topic to situations where the peptides with ranks 1 to n have the same score and the same sequence. The peptides with ranks 1 to n all display the same delta score, which is the normalized difference of the score of the rank n + 1 peptide.
- If no peptide is ranked 2, the peptide with rank 1 displays a delta score of 1.0. The same is true when the peptides with ranks 1 to n have the same score and the same sequence, but there is no peptide with rank n + 1. In this case, all peptides with rank 1 to n display a delta score of 1.0.