I'm a new user of skyline, and trying to build a spectral library from MaxQuant results. I'm not sure whether this is a skyline problem or MaxQuant problem.
Mass Spectrometer: timsTOF Pro
MaxQuant version: 184.108.40.206
System running MaxQuant and skyline daily: Windows 10 enterprise
Problem: when using msms.txt file to build spectral library using skyline daily, an error message window popped up saying "ERROR: illegal character t found in sequence (Acetyl(protein N-term))AAA.... (line 3) ERROR: reading file msms.txt". I then delete this variable modification from the datafile and try to build the library again, however another similar error occurred "ERROR: illegal character d found in sequence AA...(Oxidation (M)) (line25) ERROR: reading file msms.txt". Error message screenshots are attached. It seems that the errors are due to modifications, unfortunately, I can't just delete them in my data file. Please let me know how to go forward.
Thank you very much.