How to develop a MRM Method from scratch for known proteins (protocol/tutorial)

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How to develop a MRM Method from scratch for known proteins (protocol/tutorial) AWY  2021-02-03
 

I am interested in developing MRM biomarkers for specific plant proteins (Arabidopsis and Maize)

May I know if anyone could share any practical tutorial on how to develop a QqQ method from interested proteins.

Doesn't have to bein plant example protocol from any organism is OK to understand the workflow.

From theoretical digestion, how to identify unique peptides, to develop QqQ method.

Thank you.

 
 
Nick Shulman responded:  2021-02-03
I think the Targeted Method Editing and Targeted Method Refinement tutorials are good places to start:

Targeted method editing:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_method_edit
Targeted method refinement:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_method_refine

If you want to insert proteins into your Skyline document, and have Skyline perform a digestion on them give you a list of peptides to target, I would recommend using the "Edit > Insert > FASTA" menu item.

-- Nick
 
AWY responded:  2021-02-03
Thanks a heap, Nick. Appreciate your kind help.