Error when importing MaxQuant

Error when importing MaxQuant r hardt  2016-07-04
Hi Skyline-Team,

i frequently generate spectral libraries from MaxQuant msms.txt files. For this to work, I know that I have to include the modifications.xml as well as the mqpar.xml into the same folder as the msms.txt file. Strangely, Skyline gives me the error that a unknown modification is supposed to be included in my msms.txt, which is not included in the modifications.xml table. I even checked at the respective row of the msms.txt file it could not handle, and it might be the case that Skyline cannot cope with a doubly modified peptide. Seems strange though, because it worked before for similar projects. One of the things causing this I could think of would be the used MaxQuant version, since I recently switched to the newest release

Hope you can help me figuring out this strange behaviour.


Brendan MacLean responded:  2016-07-04
Hi Robert,
It may be a little hard to read in the message form, because of the wrapping, the error message:

"Unknown modification 2 in sequence LIQ(De)RLQ(De)QET(2)ENVK..."

Is complaining about the modification denoted as "T(2)" and not either of the "Q(De)" modifications. Looking at your mqpar.xml this is probably the modification "2 Hex (ST)" (while Q(De) is "Deamidation (NQ)").

Looking at the library builder code, I think I have found the problem. The code makes assumptions that the abbreviation inside the parentheses is two letters long. Some effort is made to ensure this assumption does not run off the end of the sequence, but nothing beyond that. So, this code will end up looking for "2)" in your list of modifications, and of course it will not find any modification starting with those two characters. Hence the error message.

I will make sure this gets fixed and put out in a Skyline-daily release soon.

Thanks for taking the time to report this and making such a thorough report that it was easy to see the problem.