export isolation list: multiple scheduled methods for prm fails

export isolation list: multiple scheduled methods for prm fails Markus  2019-07-11

Hi Skyline team,

we are having issues when trying to export isolation lists for PRMs as multiple scheduled methods. We tried it in Skyline daily (versions & as well as in Skyline 4.2 but with the same result.

Here is what we are doing and what happens:

  • we have a skyline document with DDA MS1 data (196 precursors with according MSMS library), including custom retention time standards, which we would like to use to build a PRM assay
  • we have set the time window for scheduling to 5 min resulting in a max of 29 concurrent precursors per window
  • we would now like export multiple isolation lists with a max. of 20 concurrent precursors
  • when selecting Export Isolation List with the settings "Lumos, multiple methods, ignore proteins, scheduled" I cannot select less than 35 max. concurrent peptides. If I do there is no number of methods calculated and if try to export an error occurs saying: "An error occurred attempting to export. The number of required transitions 35 exceeds the maximum 15.".

What are we doing wrong? Why are 35 transitions required? (BTW, it might be a coincidence but 35 is the value of max. concurrent transitions for a 10 min window.)

Suggestions for solutions would be greatly appreciated!

Many thanks and kind regards,