Dear Skyline team,
I am currently measuring 3 transitions per peptide of interest in my MRM on a LC-TQ. Firstly, is the community preference to use all transitions or the most intense (peak rank =1) transition for quantitative proteomics? Secondly, if the answer is to use the peak rank=1 transitions I am finding that different samples from the same experiment and MS run have different peak rank=1 fragment ions for a given peptide, as I don't want to compare different transitions as this is surely unfair can I define which transition is the quantifier ion to be used for all calculations? And/or define 2 or more other transitions as just qualifier ions for helping peak picking etc.
Thanks,
Orla