How to define your quantifier fragment ion

How to define your quantifier fragment ion Orla Coleman  2021-05-20

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.


Nick Shulman responded:  2021-05-20
You can tell Skyline that certain transitions should not be used for quantification. One way to do that is by right-clicking on the transition in the Targets tree and unchecking the menu item that says "Quantitative".

If a transition has been marked as non-quantitative then its peak area will not be included in the "Total Area" value in the Document Grid.

-- Nick