Modification ratios are calculated in the default Peptide workflow reports per peptide sequence. If the user would like to group different peptides spanning the same modification position and calculate relative intensities of all such peptides, the Blgc_Pivot_All_Peptide_PTM_Quant tab template is provided with the software to accomplish this task.
Please note that you may want to change the calculation from XIC AUC to XIC area summed isoX normalized for deamidated peptide. This is the best way to calculate deamidations as it will use to C12 isotope to correct for any overlap (it doesn't change how any other modifications are being calculated).
If you want to know which peptides are being used in the percentage calculation, you can bring in the sequence information.
Also, if you bring in the duplicate wildtypes in the filter, please check the WT DUPLICATE (which are automatically being filtered out in show hide window). These are added because some long peptides may span more than one modification site, hence would need to be included in different groups.