When I create a library from a maxquant search skyline seems to fail to recognize the fixed modification. Once my library is built I find several peptides that do not have the fixed modification. When I create a library from mascot everything is fine.

Matt, can you have a look?

I think this is a quasi-duplicate of https://skyline.ms/issues/home/issues/details.view?issueId=645

The missing fixed mod (Propionyl N-term) is a variant specificity of one of the variable mods (Propionyl K). But I will confirm that's what's going on.

The problem wasn't what I thought. Fixed peptide terminal mods for MaxQuant simply weren't supported by BiblioSpec before. I've committed a fix which should be in the next Skyline-daily. Fixed protein terminal mods for MaxQuant will still not be supported, so make sure to put the protein terminal mods in the variable mods section (that should have a negligible effect on search space and time).