Hi, Just a quick question - I have been using PeptideProphet (TPP 4.2.0) for Mascot data and have noticed that there is a * next to many of the ion scores (in both the viewer and the excel format). I have searched the documentation and this discussion board, but I can't find what the * means. The reason I ask this question is that many of these peptides have a reasonably large ion score (e.g., ion score of 40, with an identity score of 32), but the PeptideProphet probability score is small (e.g., 0.1). Inspection of the corresponding spectra show that the sequence is a good match and therefore I would expect the PeptideProphet probability to be much higher. Can you please help me understand what might be going on here.
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