Storage location for custom PTMs

Storage location for custom PTMs dkueltz  2020-10-07

Hi Nick, Brendan,
I have generated quite a few custom PTMS for one of my skyline documents (peptide settings/ modifications/ add) and would like to have them available for future documents. Where are these added PTMs stored? With only the Skyline document I entered them for or somewhere central?

Nick Shulman responded:  2020-10-07
Skyline uses the Microsoft .Net feature "User settings". These settings get stored in an XML file somewhere under "AppData\Local\Apps\2.0\..." in your home directory on your Windows computer.

There is a description about how to find that file in this help page:

If you want to share your settings with someone else, you should use the Skyline menu item:
Settings > Save Current
in order to give your current settings a name, and then:
Settings > Share
in order to export the settings to an XML file that you can send to someone else.
and then they can use the menu item:
Settings > Import
in order to read in that XML file.

-- Nick
Brendan MacLean responded:  2020-10-19
There is an easier way, however, which I have helped other groups to realize. Just create a Skyline document (.sky file) where you have all the modifications you would like to share with others checked in the Peptide Settings - Modifications tab. Don't worry about how they apply to targets. You don't even need to add any targets to this PTM sharing document. Save it without any targets.

Then share it with whomever you like and ask them to open this document in a running instance of Skyline. This will load all of the PTMs into the settings for that instance, and once you exit Skyline, those PTMs will get saved where Nick has described.

That's it. Just create a PTM sharing document and share it.

Hope you find this as helpful as others have.