Custom iRT peptides

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Custom iRT peptides benoit fatou  2020-09-24
 

Dear Skyline Team,

I was wondering if it is possible to create custom iRT peptides for RT adjustment in MRM experiments. In fact, I am working on plasma samples and I would like to use some endogenous peptides from the serum albumin in my samples.
Thanks for your help,
Best,
Benoit

 
 
Kaipo responded:  2020-09-24

Hi Benoit,
You can choose your iRT peptides from the Edit iRT calculator dialog (Settings > Peptide Settings > Prediction > Calculator). From this dialog you can paste in the iRT peptides you want to use. Or, you can click "Calibrate" to bring up the calibration dialog which has a "Use Results" button where Skyline will automatically select peptides for you.

Also, for more understanding of how to set up iRT peptides in Skyline, you can refer to the tutorial here: https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_irt

Thanks,
Kaipo

 
benoit fatou responded:  2020-09-24

Hi Kaipo,

Thanks for your reply.
According to the tutorial, they used the iRT peptides from Biognosys. However, I was wondering if I can create my own iRT peptides (not the ones listed in Skyline).
Thanks for your help,
Benoit

 
Kaipo responded:  2020-09-28

Hi Benoit,
You can use your own iRT peptides - from the Edit iRT calculator dialog, click the "Calibrate" button where you can input your own iRT peptides (or click Use Results to have Skyline select them for you from your document).

Thanks,
Kaipo