Dear Skyline Support,
I created a spectral library in Skyline from a large MaxQuant search. There were no errors. I can find the expected peptide IDs in the library.
However, when I choose "View Library Match", the wrong spectrum is shown. The raw-file name and scan time are correct, however I don't know where the spectrum is from- it is another MS2 spectrum, but it certainly is not the correct spectrum.
Do you have any suggestions for what could be causing this?
I read a few earlier problems related to heavy-labelled samples, however in this case the MaxQuant search is from an unlabelled sample (DDA data).
Thanks for your help.
All the best,
Steve