How can I select endogenous peptides not spiked-in iRT peptides for RT nomalization in Skyline?

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How can I select endogenous peptides not spiked-in iRT peptides for RT nomalization in Skyline? andyzcq  2020-07-23
 

I have acquired diaPASEF data, but I forgot to spike iRT peptide into the samples.

So how can I select endogenous peptides for RT normalization?

CiRT peptides in the CiRT calculator are not applicable.

 
 
Kaipo responded:  2020-08-21

Sorry for the delay in response on this. You can have Skyline select iRT peptides for you automatically.
First open the Edit iRT Calculator dialog: Settings > Peptide Settings > Prediction > Calculator > Add. Then, click the "Calibrate" button to bring up the Calibrate iRT Calculator dialog. From there, you can click the "Use Results" button to have Skyline pick the iRT peptides.
It attempts to pick peptides based on their retention time and score.

Thanks,
Kaipo