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ion mobility issue in Bruker prm-PASEF method setup

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ion mobility issue in Bruker prm-PASEF method setup ruoyu wu  2022-02-10 23:35
 

Dear Support team,

I have two problems when I establish a prm-PASEF method in Skyline.
When I finish targeted peptides selection and export the method, it would show that some targets our of my DDA-PASEF method's ion mobility range.
However, the corresponding target's ion mobility is suitable in the method's ion mobility range. The error seems to be occurred from resolving power's setting would give the target a mobility range (defined ion mobility± the specified number) (for example, a target's ion mobility is 0.9223 and my DDA-PASEF template ion mobility range is 0.75-1.3 with ion mobility resolving power is 60 in Skyline; when I export the method, it would show an error that ion mobility range is not within the limit). All I could do is delete the correlative target in my list but I'm wondering that do you have other suggested solution for this problem because the target (ion mobility 0.9223) I've deleted is in the range (0.75-1.3) actually.

Another question is Skyline would request to add the retention time predictor when export method (the Skyline version I've used is 21.0.9.118) but I don't have the retention time predictor. Could you please provide the retention time predictor or other suggestion that I can avoid this problem?

Thanks a lot!

Best Regards,
Ruoyu
 
 
Kaipo Tamura responded:  2022-02-11 11:16

Hi Ruoyu,
Would you mind sharing your Skyline document and the template file here so I can take a look?

Thanks,
Kaipo
 
ruoyu wu responded:  2022-02-17 19:16

Dear Kaipo,

Thanks for your timely reply. The attachments are the .sky data all setting done and the corresponding .prmsqlite.
The problems I found are as following:

  1. When I'd like to export method, I chose scheduled as method type, it shows that needs the retention time predictor. (as pic scheduled method as attached)
  2. As point1, is practical editing retention time predictor by use result directly?
  3. I've tried to edit retention time predictor by use result directly, then backed to export method with selecting scheduled as method type and import corresponding .prmsqlite. However, it showed some error occur about ion mobility.

Many thanks for your kindly support again.

Best Regards,
Ruoyu
 
Kaipo Tamura responded:  2022-02-22 12:30

Hi Ruoyu,
Would you mind attaching the ion mobility (.imsdb) library? Also, have you tried changing the ion mobility range in the template file?

Thanks,
Kaipo
 
ruoyu wu responded:  2022-03-03 20:59

Dear Kaipo,

Sorry for late reply. Here is ion mobility (.imsdb) library.
We haven't tried changing the ion mobility range in the template file cause we were concerned if we use different ion mobility range between prmsqlite (template file) and its referred DDA method would lead to ion mobility shift of same ion.

Best Regards,
Ruoyu
 
Kaipo Tamura responded:  2022-03-08 13:07

Hi Ruoyu,
You could edit the retention time predictor directly but there are better ways. The tutorial here might be helpful in setting up a retention time calculator: https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_irt

Regarding the ion mobility, the range would either have to be changed in the template method or through window settings (under Transition Settings > Ion Mobility). In this case, it looks like you are using resolving power 60, Skyline is using this formula to calculate window width: 2.0 * IonMobility / ResolvingPower. So for some targets, the window may lie outside the 0.75 - 1.3 range.

Thanks,
Kaipo
 
ruoyu wu responded:  2022-03-09 20:09

Dear Kaipo,

Good to know these information and many thanks for your kindly and timely reply : )

Best Regards,
Ruoyu