Y Biotin Phenol (APEX) spectral library


I have done some APEX proximity labeling experiments in which I enrich for Y-biotin phenol sites using anti biotin.  I would now like to build a spectral library to perform targeted quantification of these sites.  I have searched the data with MaxQuant and tried importing the peptide search as usually done, but it is not recognizing the Y-biotin phenol modified peptides in my msms.txt file and these are being excluded from the spectral library.  I have added the Y-biotin phenol modification to the list of modification in the peptides settings.  Is there some text from the msms.txt and skyline settings that needs to match in a certain way for these peptides to be imported properly?