Spectral library problem from MaxQuant search (no isotopic labels) Steve S  2019-09-13 09:56
 

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
 
 
Matt Chambers responded:  2019-09-13 13:30

Hi Steve,

I think this problem has been fixed in Skyline-daily (which will be included in an upcoming 19.1.1 patch). Can you try the latest Skyline-daily and see if that fixes the problem.?

Thanks,
-Matt
 
Steve S responded:  2019-09-19 11:22

Hi Matt,

Thanks for your help. Repeating the library creation with the latest Skyline Daily solved the problem.

All the best,

Steve
 
Matt Chambers responded:  2019-09-19 11:35

Glad to hear it!