Command line to set the peptide as a global standard jianqiaoshen  2022-10-08 01:02
 

Dear Skyline team, I am working on the automation for Skyline. I am wondering is there any command lines or ways to set one peptide as the global standard?

Regards,

Jianqiao Shen
 
 
Brian Pratt responded:  2022-10-10 11:03

There is no command line option for this, so you would have to set this in your template Skyline document.

Is this something that changes frequently in your workflow, such that the template approach isn't ideal?

Thanks for using the Skyline support board,

Brian PRatt
 
Nick Shulman responded:  2022-10-10 15:45
You can set a lot of properties on things using the "--import-annotations" commandline parameter.
Unfortunately, "Standard Type" is not one of the things that you can set that way.
(You can see all the things that you can set by going to "File > Export > Annotations")

I believe it would be very easy for us to add support for setting "Standard Type" that way. I hope to have this implemented in an update of Skyline-Daily soon.
-- Nick
 
jianqiaoshen responded:  2022-10-11 19:20
Thank you for your replies.

We have several normalizers and we want to pick three best normalizers as the global standards according to their dotp and peak area. Therefor th template approach may not be that helpful.

Currently I will directly edit the .sky file to set the normalizers as the global standards to solve this problem which is not a very elegant method. I think adding support for using the "--import-annotations" or even command lines will be very helpful. I am looking forward to the new features in Skyline-Daily!

Regards,
Jianqiao Shen