Dear Skyline team,
I currently use PRM in the identification of several peptides. My reference peptides are, however, not labeled and hence I measure them in separate runs. I know it is possible to get dotp values for each measurement in comparison to the corresponding library spectrum but I would prefer the dot product of the selected transitions in comparison to my control run (similar to the rdotp value for labeled and unlabeled peaks within one run). Is it possible to get this value?
I would like to use this value instead of the dotp against the library spectrum because I guess that than all the MS2 spectra below the peak would count for the calculation, while in the library only those spectra are retained that are nicely identified.
Best regards,
Juergen