Comet parameter: explicit_deltacn

• This parameter controls whether or not Comet reports the deltaCn value calculated between the top two peptides (“explicit_deltacn = 1”) or between the top peptide and the first dissimilar peptide (default behavior, “explicit_deltacn = 0”).
• The deltaCn score is the normalized difference between two cross-correlation scores. So deltaCn between the top two peptides is calculated as “(xcorr1 - xcorr2) / xcorr1” where xcorr1 is the top scoring peptide and xcorr2 is the second best scoring peptide.
• However, there are cases were the top two (or top N) scoring peptides are very similar. They may be different modified forms of the same peptide e.g. DLRSTWDK and DLRSTWDK. In this case, the deltaCn score will be very small because the two peptides are very similar and will have very similar xcorr scores.
• To mitigate this issue of reporting the deltaCn score for similar peptides, Comet by default performs a crude sequence similarity analysis and reports the deltaCn score as the difference between the top scoring peptide and the first dissimilar peptide. This is the default behavior.
• This parameter was added to ignore the similarity analysis and always report deltaCn as the normalized difference between the top two xcorr scores.
• To keep the default behavior of using similarity analysis, set this parameter to “0”.
• To calculate deltaCn between the top two scoring peptides even if their sequences are similar, set this parameter to “1”.

Example:

explicit_deltacn = 0
explicit_deltacn = 1