Problem with MS1 tutorial

Problem with MS1 tutorial comtewal  2018-11-19

In preparation for the Duke Skyline course I am going over the Skyline tutorials.
On the MS1 tutorial, when I import the xml files and the wiff files according with the instructions, the Phospho (S,T), Phospho (Y), and Ox (M) are not showing on the list (see screen shot attached).
If I try to add these modifications I get an error saying the mod already exist.
Please help

Brendan MacLean responded:  2018-11-19

Yeah. The tutorials are really written for a pristine system, and you seem to already have these modifications. Could you possibly already have them checked in the document you are starting with? (Have a look in Peptide Settings - Modifications.) I guess it would probably be better for Skyline to show all the modifications it sees that are already available and just show them already checked. But, since that can't happen in time for the course, you should try the following 2 things in this order to see which one you would need to get the tutorial working as expected.

  1. On the Settings menu, click Default (probably No about saving your current settings)
  2. On the Tools menu, click Options. Choose the Miscellaneous tab, click the Clear All Saved Settings button. Restart Skyline.

Hopefully, the first option will be enough, but the second really should be, since it will essentially set you back to a pristine installation.