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. DLRS*TWDK
and DLRST*WDK. 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