Hi,

we are using Skyline on HRMS / PRM data. We want to quantify based on MS1 area of the precursor. Then, we would like to use the ratio between fragment 1 and fragment 2 as a "Qualitative ion ratio".

Right now, I only see the option to set feature as either "Quantitative" or not "quantitative", i.e. it is either in the numerator or in the denominator of the "Qualitative ion ratio". The "Qualitative ion ratio" is then calculated as the sum of "not quant" divided by sum of "quant". Unfortunately, this includes the precursor ion count. I would like to exclude the precursor completely from the "qualitative ion ratio" calc and get only f1 / f2.

Is there any trick to do this with the current version of Skyline? E.g. exclude MS1 data from "qualitative ion ratio" calculation, so we could set one fragment to quantitative and use the other one as "qualifier"?