A notion of the correctness of the Xle disambiguation would be very nice. A common way of doing this would be an FDR. This could be done in this situation by getting pseudorandom theoretical fragments and mapping them to the same input data. The pseudorandom data could be the predicted peptides with a small shift (1-10 Da). If this is done with many different shifts you can see how often fragments are found that are based on nothing. This could potentially be broken down further to only look into the w and d ions used to disambiguate the Xle position.
A notion of the correctness of the Xle disambiguation would be very nice. A common way of doing this would be an FDR. This could be done in this situation by getting pseudorandom theoretical fragments and mapping them to the same input data. The pseudorandom data could be the predicted peptides with a small shift (1-10 Da). If this is done with many different shifts you can see how often fragments are found that are based on nothing. This could potentially be broken down further to only look into the w and d ions used to disambiguate the Xle position.