Do you have a "modifications.xml" file anywhere on your computer that you could send us?

When BiblioSpec is building a library from MaxQuant search results, BiblioSpec tries to find a file called "modifications.xml" or "modification.xml" in the same directory as your msms.txt.
If BiblioSpec does not find "modifications.xml" there, then BiblioSpec uses our own default one, which we last updated in 2015 (I have attached it).

Our default modifications.xml does not know what the modification "Propionyl (N-term)" is supposed to be (chemical formula, etc).

My guess is that you have your own "modifications.xml" that does have a definition for that modification in it, and if you copied it into the same directory as your msms.txt, everything would work. (I don't know much about MaxQuant-- is there maybe a "modifications.xml" file in MaxQuant's installation directory?)

Also, if you send us that file, we could update the default modifications.xml that BiblioSpec uses.

Hope this helps,
-- Nick

MaxQuant creates a modifications.local.xml file with my new modification but even when I place it in my folder skyline still does not create a library with a fixed modification. My modification is Propionate labeling reagent light form (N-term).

It sounds like we should change BiblioSpec to look for a "modifications.local.xml" file, and then effectively merge it with whatever other modifications.xml BiblioSpec was planning on using. I will try to fix this in an upcoming release of Skyline-Daily.

Thanks!
-- Nick