Can I load ETD and/or CID searched DAT files into Scaffold?
Yes. When you combine CID and ETD data in the same DAT files, then Scaffold assumes that all the data is CID only and shows B/Y ions. However, this is just a display issue– since we don’t re-score the ion score from Mascot, the probabilities should be assigned correctly. We’ve made some progress towards addressing this display issue (it now works for Discoverer, the most common source of CID/ETD mixed data), but it hasn’t made it’s way to Mascot parsing yet.
