Drift time predictor training from SkylineRunner

Drift time predictor training from SkylineRunner Aivett Bilbao  2019-08-30

Dear Skyline team,

I'm using the SkylineRunner to extract data from Agilent (.d) ion mobility files, importing a transition list (small molecules format, with RT). Please I have 2 questions:

  1. Is it possible to execute the "Drift time predictor" (using results) from the SkylineRunner?
    I would like to import the ms files, train the Drift train predictor, then re-import the ms files (to have better signal by filtering with the drift time).
  2. Could you provide some details about what the "Drift train predictor" is doing? is it taking the drift time from the most intense ion mobility peak it finds?

Thank you in advance for your help and thank you so much for the great software!

Brendan MacLean responded:  2019-08-30

Hi Aivett,
The drift time predictor training is not yet available from the command-line, but I added a TODO issue for this, which you can track (https://skyline.ms/issues/home/issues/details.view?issueId=679).

The predictor training takes the spectrum for the apex time of the selected peak and slides the extraction window (defined by resolving power on Agilent) and slides it across the precursor m/z window calculating the signal it would extract at each IMS value. It then takes the IMS value with the maximum extracted signal. This avoids having to do peak detection and dealing with multiple conformers, etc.

Hope this is helpful. Sorry, we haven't exposed training at the command line yet.


Aivett Bilbao responded:  2019-08-30

Hi Brendan,

Great! Thanks a lot for the prompt reply!