Prosit Spectral Library Error

Prosit Spectral Library Error cbm11  2023-09-11 07:04

Good afternoon,
I have been trying to implement a Prosit Spectral Library in Skyline which I have done lots before with no trouble, but this morning a new error appeared. Any ideas what this could be caused by?

Best wishes,

Nick Shulman responded:  2023-09-11 07:29
My understanding is that Prosit can only handle a couple of different types of post translational modifications on the peptide sequence: specifically, oxidized methionine ("M[+16]") and carbamidomethyl cysteine ("C[+57]").

It looks like the peptide in your document has some other sort of modifications on its amino acids, so I would not expect that Prosit would be able to predict anything about that modified peptide.
Nevertheless, I would have expected the error to be a little different (or, actually, Skyline would just skip over any peptides whose modifications Prosit would not understand).

Could you send us your Skyline document? We will try to reproduce your errors and figure out what is going wrong.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
If that .zip file is less than 50MB you can attach it to this support request.
You can upload larger files here:

It's also possible that this was only a temporary problem with the Prosit server and if you tried everything again it would work for you now.
-- Nick