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How to develop MRM method for interested proteins

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How to develop MRM method for interested proteins VJ  2018-04-11 18:00
 
I'm new to MRM and going to develop a method for organelle markers.

I would be so much grateful if you could send me tutorials for;

-How to develop MRM method for interested proteins; with spectral libraries and without libraries (with theoretical digestions)

- Normalization and scaling the data.

Thanks for considering my request. I’m looking forward to your reply.
 
 
Nick Shulman responded:  2018-04-11 19:46
The Targeted Method Editing and Targeted Method Refinement tutorials are what we have for SRM method development:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_method_edit
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_method_refine

If you want to compare quantities between samples then you should look at the Grouped Studies tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_grouped

Or if you want to know the absolute amount of the protein in the samples, then check out the Absolute Quantification tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_absolute_quant
 
VJ responded:  2018-04-11 20:09
Thnks Nick.

Do you have a tutorial for developing MRM without a library match? These proteins have not identified by qTOF earlier!
Just by theoretical digestion, what is the procedure?
Thank you!
 
Brendan MacLean responded:  2018-04-11 20:57
Both the Grouped Studies tutorial and the Absolute Quantification tutorial in Nick's list deal with peptides without library spectra. Hopefully, they will help.
 
VJ responded:  2018-04-11 21:00
Thanks, Brendon and Nick.
Thanks for the email as well Brendon.